Starting phenix.real_space_refine on Tue Mar 19 10:39:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ynx_10859/03_2024/6ynx_10859_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ynx_10859/03_2024/6ynx_10859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ynx_10859/03_2024/6ynx_10859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ynx_10859/03_2024/6ynx_10859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ynx_10859/03_2024/6ynx_10859_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ynx_10859/03_2024/6ynx_10859_trim_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 82 5.49 5 Mg 2 5.21 5 S 273 5.16 5 C 45864 2.51 5 N 11221 2.21 5 O 12398 1.98 5 H 64331 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a GLU 137": "OE1" <-> "OE2" Residue "a PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 205": "OE1" <-> "OE2" Residue "a TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 309": "OD1" <-> "OD2" Residue "a ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 424": "OE1" <-> "OE2" Residue "a PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 90": "OE1" <-> "OE2" Residue "b PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 188": "OE1" <-> "OE2" Residue "d PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 154": "OE1" <-> "OE2" Residue "g TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "g TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ASP 209": "OD1" <-> "OD2" Residue "g ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g GLU 247": "OE1" <-> "OE2" Residue "g TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ASP 144": "OD1" <-> "OD2" Residue "h ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h GLU 151": "OE1" <-> "OE2" Residue "h TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h GLU 217": "OE1" <-> "OE2" Residue "h ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 194": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 241": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j GLU 268": "OE1" <-> "OE2" Residue "j TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ASP 22": "OD1" <-> "OD2" Residue "l PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l GLU 186": "OE1" <-> "OE2" Residue "l ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ASP 235": "OD1" <-> "OD2" Residue "l TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ASP 144": "OD1" <-> "OD2" Residue "e GLU 159": "OE1" <-> "OE2" Residue "e TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 112": not complete - not flipped Residue "B ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 209": "OD1" <-> "OD2" Residue "G ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 247": "OE1" <-> "OE2" Residue "G PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 194": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 241": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 268": "OE1" <-> "OE2" Residue "J TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 186": "OE1" <-> "OE2" Residue "L ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 235": "OD1" <-> "OD2" Residue "L PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i1 ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i1 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i2 ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i2 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i2 TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 134171 Number of models: 1 Model: "" Number of chains: 64 Chain: "a" Number of atoms: 7157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7157 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 9, 'TRANS': 423} Chain: "b" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 2678 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "d" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1764 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "f" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3373 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "i" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3461 Classifications: {'peptide': 209} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain: "k" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2903 Classifications: {'peptide': 179} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 175} Chain: "c" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1671 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "g" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4338 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 17, 'TRANS': 238} Chain: "h" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3836 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "j" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 4346 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 18, 'TRANS': 250} Chain: "l" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 4070 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 15, 'TRANS': 230} Chain: "m" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3696 Classifications: {'peptide': 221} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "n" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1960 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "o" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1599 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "p" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 2413 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "q" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1749 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "r" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2373 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "s" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1714 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "e" Number of atoms: 6681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6681 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 401} Chain: "A" Number of atoms: 7157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7157 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 9, 'TRANS': 423} Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 2675 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1764 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3374 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "I" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3461 Classifications: {'peptide': 209} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain: "K" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2903 Classifications: {'peptide': 179} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 175} Chain: "C" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1671 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "G" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4338 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 17, 'TRANS': 238} Chain: "H" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3836 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "J" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 4344 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 18, 'TRANS': 250} Chain: "L" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 4070 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 15, 'TRANS': 230} Chain: "M" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3696 Classifications: {'peptide': 221} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "N" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1960 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "O" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1599 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "P" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 2413 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "Q" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1749 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "R" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2288 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "S" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1728 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 6681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6681 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 401} Chain: "i1" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 474 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "i2" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 529 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "t" Number of atoms: 5889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5889 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 13, 'TRANS': 351} Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 200 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 305 Unusual residues: {'CDL': 3, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 207 Unusual residues: {'CDL': 1, 'PC1': 1, 'UQ8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 300 Unusual residues: {'CDL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {' MG': 1, 'ATP': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 200 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 299 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "p" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 500 Unusual residues: {'CDL': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 253 Unusual residues: {'CDL': 2, 'UQ8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 200 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {' MG': 1, 'ATP': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 299 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 39.69, per 1000 atoms: 0.30 Number of scatterers: 134171 At special positions: 0 Unit cell: (264.77, 135.29, 188.41, 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) S 273 16.00 P 82 15.00 Mg 2 11.99 O 12398 8.00 N 11221 7.00 C 45864 6.00 H 64331 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS j 125 " - pdb=" SG CYS j 155 " distance=2.03 Simple disulfide: pdb=" SG CYS n 109 " - pdb=" SG CYS n 144 " distance=2.03 Simple disulfide: pdb=" SG CYS o 120 " - pdb=" SG CYS o 132 " distance=2.03 Simple disulfide: pdb=" SG CYS J 125 " - pdb=" SG CYS J 155 " distance=2.03 Simple disulfide: pdb=" SG CYS N 109 " - pdb=" SG CYS N 144 " distance=2.03 Simple disulfide: pdb=" SG CYS O 120 " - pdb=" SG CYS O 132 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 85.74 Conformation dependent library (CDL) restraints added in 9.6 seconds 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15040 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 315 helices and 31 sheets defined 58.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 39.27 Creating SS restraints... Processing helix chain 'a' and resid 25 through 31 removed outlier: 4.701A pdb=" N THR a 29 " --> pdb=" O GLN a 25 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE a 30 " --> pdb=" O PRO a 26 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 25 through 31' Processing helix chain 'a' and resid 77 through 89 removed outlier: 3.936A pdb=" N SER a 89 " --> pdb=" O ALA a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 111 removed outlier: 3.858A pdb=" N GLN a 110 " --> pdb=" O SER a 106 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASN a 111 " --> pdb=" O VAL a 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 135 removed outlier: 3.713A pdb=" N ALA a 129 " --> pdb=" O SER a 125 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU a 130 " --> pdb=" O LYS a 126 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE a 131 " --> pdb=" O GLU a 127 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP a 132 " --> pdb=" O THR a 128 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU a 133 " --> pdb=" O ALA a 129 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR a 134 " --> pdb=" O LEU a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 137 through 153 removed outlier: 4.601A pdb=" N HIS a 141 " --> pdb=" O GLU a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 172 through 194 removed outlier: 5.105A pdb=" N LEU a 176 " --> pdb=" O LEU a 172 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP a 177 " --> pdb=" O VAL a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 224 removed outlier: 4.067A pdb=" N GLU a 220 " --> pdb=" O SER a 216 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA a 221 " --> pdb=" O GLY a 217 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU a 222 " --> pdb=" O THR a 218 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS a 223 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU a 224 " --> pdb=" O GLU a 220 " (cutoff:3.500A) Processing helix chain 'a' and resid 227 through 247 removed outlier: 5.374A pdb=" N GLY a 233 " --> pdb=" O ASP a 229 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU a 234 " --> pdb=" O ASP a 230 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR a 240 " --> pdb=" O PHE a 236 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL a 244 " --> pdb=" O TYR a 240 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE a 245 " --> pdb=" O VAL a 241 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE a 246 " --> pdb=" O PHE a 242 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 285 removed outlier: 3.807A pdb=" N ILE a 268 " --> pdb=" O CYS a 264 " (cutoff:3.500A) Proline residue: a 278 - end of helix Processing helix chain 'a' and resid 288 through 294 Processing helix chain 'a' and resid 301 through 344 removed outlier: 3.569A pdb=" N PHE a 308 " --> pdb=" O ALA a 304 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE a 320 " --> pdb=" O PHE a 316 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLN a 323 " --> pdb=" O ARG a 319 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TRP a 324 " --> pdb=" O ILE a 320 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE a 325 " --> pdb=" O LEU a 321 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG a 326 " --> pdb=" O ALA a 322 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL a 327 " --> pdb=" O GLN a 323 " (cutoff:3.500A) Processing helix chain 'a' and resid 347 through 352 removed outlier: 3.953A pdb=" N LEU a 351 " --> pdb=" O THR a 347 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE a 352 " --> pdb=" O ASN a 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 347 through 352' Processing helix chain 'a' and resid 376 through 416 removed outlier: 4.014A pdb=" N TRP a 409 " --> pdb=" O ALA a 405 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU a 410 " --> pdb=" O ILE a 406 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE a 411 " --> pdb=" O VAL a 407 " (cutoff:3.500A) Processing helix chain 'a' and resid 425 through 439 removed outlier: 4.201A pdb=" N LYS a 429 " --> pdb=" O ASP a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 440 through 445 removed outlier: 3.570A pdb=" N LYS a 445 " --> pdb=" O LEU a 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 4.681A pdb=" N THR A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 31' Processing helix chain 'A' and resid 77 through 89 removed outlier: 4.017A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.918A pdb=" N GLN A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.705A pdb=" N ALA A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 153 removed outlier: 4.617A pdb=" N HIS A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 5.148A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 removed outlier: 4.121A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 247 removed outlier: 5.471A pdb=" N GLY A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 removed outlier: 3.873A pdb=" N ILE A 268 " --> pdb=" O CYS A 264 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 301 through 344 removed outlier: 4.394A pdb=" N ILE A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TRP A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.829A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 352' Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.509A pdb=" N PHE A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 439 removed outlier: 4.212A pdb=" N LYS A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.817A pdb=" N LYS A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 97 removed outlier: 3.662A pdb=" N ILE b 88 " --> pdb=" O SER b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 113 Processing helix chain 'b' and resid 114 through 132 removed outlier: 4.785A pdb=" N VAL b 132 " --> pdb=" O GLY b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 157 removed outlier: 4.675A pdb=" N ILE b 143 " --> pdb=" O LYS b 139 " (cutoff:3.500A) Proline residue: b 144 - end of helix removed outlier: 5.375A pdb=" N PHE b 154 " --> pdb=" O GLN b 150 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR b 155 " --> pdb=" O LEU b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 186 Processing helix chain 'b' and resid 189 through 221 removed outlier: 3.647A pdb=" N ASN b 196 " --> pdb=" O ASN b 192 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR b 207 " --> pdb=" O GLY b 203 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TRP b 208 " --> pdb=" O GLN b 204 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP b 209 " --> pdb=" O LEU b 205 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE b 210 " --> pdb=" O GLU b 206 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER b 213 " --> pdb=" O ASP b 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR b 214 " --> pdb=" O ILE b 210 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY b 215 " --> pdb=" O HIS b 211 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU b 216 " --> pdb=" O THR b 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.664A pdb=" N ILE B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 114 through 132 removed outlier: 4.902A pdb=" N VAL B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 157 removed outlier: 4.564A pdb=" N ILE B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix removed outlier: 3.531A pdb=" N PHE B 149 " --> pdb=" O TRP B 145 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 189 through 221 removed outlier: 3.631A pdb=" N ASN B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TRP B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY B 215 " --> pdb=" O HIS B 211 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLU B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 157 removed outlier: 3.712A pdb=" N GLU d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU d 155 " --> pdb=" O PHE d 151 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR d 156 " --> pdb=" O GLU d 152 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 172 removed outlier: 3.569A pdb=" N ARG d 172 " --> pdb=" O PHE d 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 185 Processing helix chain 'd' and resid 196 through 204 Processing helix chain 'D' and resid 125 through 157 removed outlier: 3.724A pdb=" N GLU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU D 155 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASN D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 173 through 185 Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'f' and resid 2 through 10 Processing helix chain 'f' and resid 19 through 24 removed outlier: 5.673A pdb=" N ALA f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 57 removed outlier: 3.576A pdb=" N THR f 56 " --> pdb=" O MET f 52 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 66 removed outlier: 4.275A pdb=" N PHE f 63 " --> pdb=" O GLU f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 89 Proline residue: f 89 - end of helix Processing helix chain 'f' and resid 90 through 102 removed outlier: 5.118A pdb=" N LYS f 99 " --> pdb=" O TRP f 95 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ALA f 100 " --> pdb=" O LYS f 96 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 141 Processing helix chain 'f' and resid 164 through 171 removed outlier: 3.569A pdb=" N MET f 170 " --> pdb=" O MET f 166 " (cutoff:3.500A) Processing helix chain 'f' and resid 175 through 180 removed outlier: 4.137A pdb=" N ILE f 179 " --> pdb=" O PRO f 175 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL f 180 " --> pdb=" O GLY f 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 175 through 180' Processing helix chain 'f' and resid 182 through 200 removed outlier: 4.823A pdb=" N ASN f 186 " --> pdb=" O ASN f 182 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN f 187 " --> pdb=" O PRO f 183 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN f 188 " --> pdb=" O CYS f 184 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR f 189 " --> pdb=" O ARG f 185 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG f 190 " --> pdb=" O ASN f 186 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU f 191 " --> pdb=" O GLN f 187 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR f 192 " --> pdb=" O ASN f 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 13 Processing helix chain 'F' and resid 40 through 57 removed outlier: 3.563A pdb=" N THR F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 66 removed outlier: 4.271A pdb=" N PHE F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 89 Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 90 through 102 removed outlier: 5.036A pdb=" N LYS F 99 " --> pdb=" O TRP F 95 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 141 Processing helix chain 'F' and resid 164 through 171 removed outlier: 3.551A pdb=" N MET F 170 " --> pdb=" O MET F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 4.109A pdb=" N ILE F 179 " --> pdb=" O PRO F 175 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 175 through 180' Processing helix chain 'F' and resid 183 through 200 removed outlier: 4.278A pdb=" N GLN F 187 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU F 191 " --> pdb=" O GLN F 187 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 removed outlier: 3.899A pdb=" N TRP F 23 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA F 24 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 13 Processing helix chain 'i' and resid 14 through 20 Processing helix chain 'i' and resid 21 through 26 removed outlier: 4.768A pdb=" N LYS i 25 " --> pdb=" O GLU i 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG i 26 " --> pdb=" O LYS i 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 21 through 26' Processing helix chain 'i' and resid 28 through 38 Processing helix chain 'i' and resid 47 through 69 Processing helix chain 'i' and resid 72 through 79 removed outlier: 3.629A pdb=" N SER i 76 " --> pdb=" O SER i 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU i 77 " --> pdb=" O PHE i 73 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR i 78 " --> pdb=" O VAL i 74 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS i 79 " --> pdb=" O LYS i 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 72 through 79' Processing helix chain 'i' and resid 88 through 109 removed outlier: 4.261A pdb=" N ALA i 92 " --> pdb=" O PHE i 88 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE i 93 " --> pdb=" O ARG i 89 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL i 94 " --> pdb=" O HIS i 90 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU i 95 " --> pdb=" O PHE i 91 " (cutoff:3.500A) Proline residue: i 96 - end of helix removed outlier: 3.800A pdb=" N LEU i 103 " --> pdb=" O VAL i 99 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY i 104 " --> pdb=" O LEU i 100 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU i 105 " --> pdb=" O ALA i 101 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE i 106 " --> pdb=" O GLY i 102 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL i 107 " --> pdb=" O LEU i 103 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP i 109 " --> pdb=" O LEU i 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 115 removed outlier: 4.080A pdb=" N LYS i 114 " --> pdb=" O GLY i 110 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS i 115 " --> pdb=" O ASP i 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 110 through 115' Processing helix chain 'i' and resid 116 through 121 removed outlier: 4.085A pdb=" N ARG i 120 " --> pdb=" O TYR i 116 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE i 121 " --> pdb=" O SER i 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 116 through 121' Processing helix chain 'i' and resid 122 through 129 removed outlier: 3.650A pdb=" N GLY i 129 " --> pdb=" O LYS i 125 " (cutoff:3.500A) Processing helix chain 'i' and resid 136 through 141 removed outlier: 3.542A pdb=" N GLN i 140 " --> pdb=" O ASN i 136 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG i 141 " --> pdb=" O SER i 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 136 through 141' Processing helix chain 'i' and resid 147 through 173 removed outlier: 3.566A pdb=" N ALA i 155 " --> pdb=" O ALA i 151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG i 160 " --> pdb=" O GLU i 156 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS i 163 " --> pdb=" O LYS i 159 " (cutoff:3.500A) Processing helix chain 'i' and resid 176 through 185 removed outlier: 6.560A pdb=" N TYR i 184 " --> pdb=" O LYS i 180 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA i 185 " --> pdb=" O LYS i 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 14 through 20 Processing helix chain 'I' and resid 21 through 26 removed outlier: 4.852A pdb=" N LYS I 25 " --> pdb=" O GLU I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 38 Processing helix chain 'I' and resid 47 through 69 Processing helix chain 'I' and resid 72 through 79 removed outlier: 3.678A pdb=" N SER I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU I 77 " --> pdb=" O PHE I 73 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N HIS I 79 " --> pdb=" O LYS I 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 79' Processing helix chain 'I' and resid 88 through 109 removed outlier: 4.283A pdb=" N ALA I 92 " --> pdb=" O PHE I 88 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL I 94 " --> pdb=" O HIS I 90 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU I 95 " --> pdb=" O PHE I 91 " (cutoff:3.500A) Proline residue: I 96 - end of helix removed outlier: 3.823A pdb=" N LEU I 103 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY I 104 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE I 106 " --> pdb=" O GLY I 102 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 115 removed outlier: 4.053A pdb=" N LYS I 114 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 110 through 115' Processing helix chain 'I' and resid 116 through 121 removed outlier: 4.090A pdb=" N ARG I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE I 121 " --> pdb=" O SER I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 116 through 121' Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 136 through 141 removed outlier: 5.073A pdb=" N ARG I 141 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 173 removed outlier: 3.721A pdb=" N ALA I 155 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG I 160 " --> pdb=" O GLU I 156 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS I 163 " --> pdb=" O LYS I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 185 removed outlier: 7.103A pdb=" N TYR I 184 " --> pdb=" O LYS I 180 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA I 185 " --> pdb=" O LYS I 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 1 through 7 removed outlier: 3.780A pdb=" N TYR k 5 " --> pdb=" O MET k 1 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER k 7 " --> pdb=" O TYR k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 48 Processing helix chain 'k' and resid 51 through 75 removed outlier: 4.015A pdb=" N PHE k 59 " --> pdb=" O GLY k 55 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE k 62 " --> pdb=" O PHE k 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 80 through 102 removed outlier: 3.698A pdb=" N ASP k 95 " --> pdb=" O LEU k 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE k 101 " --> pdb=" O ALA k 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU k 102 " --> pdb=" O ALA k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 116 through 126 Processing helix chain 'k' and resid 127 through 140 removed outlier: 4.356A pdb=" N ASP k 131 " --> pdb=" O SER k 127 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN k 140 " --> pdb=" O TYR k 136 " (cutoff:3.500A) Processing helix chain 'k' and resid 141 through 152 Processing helix chain 'k' and resid 158 through 173 removed outlier: 3.617A pdb=" N ASN k 163 " --> pdb=" O GLU k 159 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET k 164 " --> pdb=" O LYS k 160 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL k 165 " --> pdb=" O ASP k 161 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS k 166 " --> pdb=" O LYS k 162 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 13 removed outlier: 3.867A pdb=" N ASN k 12 " --> pdb=" O GLN k 9 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU k 13 " --> pdb=" O SER k 10 " (cutoff:3.500A) Processing helix chain 'k' and resid 29 through 34 Proline residue: k 33 - end of helix Processing helix chain 'K' and resid 1 through 7 removed outlier: 3.818A pdb=" N TYR K 5 " --> pdb=" O MET K 1 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER K 7 " --> pdb=" O TYR K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 48 Processing helix chain 'K' and resid 51 through 75 removed outlier: 3.928A pdb=" N PHE K 59 " --> pdb=" O GLY K 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE K 62 " --> pdb=" O PHE K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 102 removed outlier: 3.613A pdb=" N LEU K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS K 100 " --> pdb=" O MET K 96 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU K 102 " --> pdb=" O ALA K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 126 Processing helix chain 'K' and resid 127 through 140 removed outlier: 4.391A pdb=" N ASP K 131 " --> pdb=" O SER K 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASN K 140 " --> pdb=" O TYR K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 152 removed outlier: 3.504A pdb=" N ALA K 151 " --> pdb=" O GLN K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 173 removed outlier: 3.699A pdb=" N ASN K 163 " --> pdb=" O GLU K 159 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET K 164 " --> pdb=" O LYS K 160 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL K 165 " --> pdb=" O ASP K 161 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYS K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 13 removed outlier: 3.862A pdb=" N ASN K 12 " --> pdb=" O GLN K 9 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU K 13 " --> pdb=" O SER K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 34 Proline residue: K 33 - end of helix Processing helix chain 'c' and resid 5 through 10 removed outlier: 4.580A pdb=" N PHE c 9 " --> pdb=" O LEU c 5 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU c 10 " --> pdb=" O ASP c 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 5 through 10' Processing helix chain 'c' and resid 15 through 20 removed outlier: 4.112A pdb=" N ARG c 19 " --> pdb=" O ASP c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 58 removed outlier: 5.014A pdb=" N GLN c 25 " --> pdb=" O ALA c 21 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE c 28 " --> pdb=" O GLU c 24 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE c 29 " --> pdb=" O GLN c 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR c 43 " --> pdb=" O LEU c 39 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE c 48 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TRP c 49 " --> pdb=" O VAL c 45 " (cutoff:3.500A) Proline residue: c 50 - end of helix removed outlier: 3.811A pdb=" N ARG c 57 " --> pdb=" O PHE c 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 69 through 78 Processing helix chain 'c' and resid 81 through 95 Processing helix chain 'C' and resid 5 through 10 removed outlier: 4.649A pdb=" N PHE C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU C 10 " --> pdb=" O ASP C 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 10' Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.157A pdb=" N ARG C 19 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 58 removed outlier: 4.989A pdb=" N GLN C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 29 " --> pdb=" O GLN C 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TRP C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix removed outlier: 3.949A pdb=" N ARG C 57 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'g' and resid 41 through 46 removed outlier: 5.228A pdb=" N TYR g 46 " --> pdb=" O LYS g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 71 removed outlier: 3.922A pdb=" N SER g 70 " --> pdb=" O LYS g 66 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS g 71 " --> pdb=" O PRO g 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 66 through 71' Processing helix chain 'g' and resid 77 through 99 removed outlier: 4.945A pdb=" N LEU g 89 " --> pdb=" O VAL g 85 " (cutoff:3.500A) Proline residue: g 90 - end of helix Processing helix chain 'g' and resid 104 through 122 removed outlier: 3.562A pdb=" N PHE g 110 " --> pdb=" O PHE g 106 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU g 111 " --> pdb=" O ASN g 107 " (cutoff:3.500A) Proline residue: g 112 - end of helix removed outlier: 4.436A pdb=" N PHE g 121 " --> pdb=" O PHE g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 148 removed outlier: 4.061A pdb=" N LYS g 129 " --> pdb=" O ALA g 125 " (cutoff:3.500A) Proline residue: g 135 - end of helix removed outlier: 3.765A pdb=" N LEU g 148 " --> pdb=" O ARG g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 153 through 165 removed outlier: 3.700A pdb=" N GLN g 163 " --> pdb=" O ASP g 159 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN g 164 " --> pdb=" O MET g 160 " (cutoff:3.500A) Proline residue: g 165 - end of helix Processing helix chain 'g' and resid 166 through 171 removed outlier: 4.495A pdb=" N TYR g 170 " --> pdb=" O GLU g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 191 through 196 Proline residue: g 196 - end of helix Processing helix chain 'g' and resid 200 through 207 removed outlier: 4.001A pdb=" N PHE g 206 " --> pdb=" O THR g 202 " (cutoff:3.500A) Processing helix chain 'g' and resid 271 through 279 removed outlier: 4.253A pdb=" N LYS g 277 " --> pdb=" O LYS g 273 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS g 278 " --> pdb=" O GLU g 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 5.105A pdb=" N TYR G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 71 removed outlier: 3.926A pdb=" N SER G 70 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 66 through 71' Processing helix chain 'G' and resid 77 through 99 removed outlier: 5.077A pdb=" N LEU G 89 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Proline residue: G 90 - end of helix removed outlier: 3.500A pdb=" N TRP G 95 " --> pdb=" O GLY G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 122 removed outlier: 4.754A pdb=" N LEU G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.585A pdb=" N GLN G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 148 removed outlier: 4.033A pdb=" N LYS G 129 " --> pdb=" O ALA G 125 " (cutoff:3.500A) Proline residue: G 135 - end of helix removed outlier: 3.807A pdb=" N LEU G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 165 removed outlier: 3.752A pdb=" N GLN G 163 " --> pdb=" O ASP G 159 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN G 164 " --> pdb=" O MET G 160 " (cutoff:3.500A) Proline residue: G 165 - end of helix Processing helix chain 'G' and resid 166 through 171 removed outlier: 4.705A pdb=" N TYR G 170 " --> pdb=" O GLU G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 Proline residue: G 196 - end of helix Processing helix chain 'G' and resid 200 through 207 removed outlier: 3.876A pdb=" N PHE G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 279 removed outlier: 4.449A pdb=" N LYS G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 104 removed outlier: 3.529A pdb=" N GLN h 101 " --> pdb=" O ARG h 97 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR h 102 " --> pdb=" O HIS h 98 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE h 103 " --> pdb=" O CYS h 99 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU h 104 " --> pdb=" O LYS h 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 127 removed outlier: 3.853A pdb=" N VAL h 123 " --> pdb=" O SER h 119 " (cutoff:3.500A) Proline residue: h 124 - end of helix Processing helix chain 'h' and resid 137 through 156 removed outlier: 3.561A pdb=" N LEU h 152 " --> pdb=" O ARG h 148 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR h 155 " --> pdb=" O GLU h 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 185 removed outlier: 3.555A pdb=" N GLY h 185 " --> pdb=" O LYS h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 188 through 209 removed outlier: 3.732A pdb=" N LYS h 207 " --> pdb=" O ALA h 203 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ARG h 209 " --> pdb=" O LYS h 205 " (cutoff:3.500A) Processing helix chain 'h' and resid 215 through 237 removed outlier: 4.176A pdb=" N VAL h 235 " --> pdb=" O ARG h 231 " (cutoff:3.500A) Proline residue: h 237 - end of helix Processing helix chain 'h' and resid 247 through 253 removed outlier: 4.697A pdb=" N PHE h 251 " --> pdb=" O ASN h 247 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU h 252 " --> pdb=" O VAL h 248 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU h 253 " --> pdb=" O ASN h 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 247 through 253' Processing helix chain 'H' and resid 83 through 104 removed outlier: 3.522A pdb=" N GLN H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR H 102 " --> pdb=" O HIS H 98 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE H 103 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 127 removed outlier: 4.027A pdb=" N VAL H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 137 through 156 removed outlier: 3.577A pdb=" N ASP H 149 " --> pdb=" O GLN H 145 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU H 152 " --> pdb=" O ARG H 148 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR H 155 " --> pdb=" O GLU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 185 removed outlier: 3.517A pdb=" N TRP H 174 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY H 185 " --> pdb=" O LYS H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 209 removed outlier: 4.886A pdb=" N ARG H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 235 removed outlier: 5.602A pdb=" N VAL H 235 " --> pdb=" O ARG H 231 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 17 removed outlier: 4.034A pdb=" N ASP j 14 " --> pdb=" O ILE j 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE j 15 " --> pdb=" O TYR j 11 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 42 Processing helix chain 'j' and resid 122 through 139 Processing helix chain 'j' and resid 140 through 155 removed outlier: 4.155A pdb=" N CYS j 144 " --> pdb=" O GLY j 140 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN j 145 " --> pdb=" O THR j 141 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER j 146 " --> pdb=" O GLU j 142 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU j 147 " --> pdb=" O LYS j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 156 through 186 removed outlier: 3.654A pdb=" N VAL j 167 " --> pdb=" O MET j 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG j 168 " --> pdb=" O LYS j 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 195 through 200 removed outlier: 3.881A pdb=" N VAL j 199 " --> pdb=" O THR j 195 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA j 200 " --> pdb=" O VAL j 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 195 through 200' Processing helix chain 'j' and resid 203 through 209 removed outlier: 4.028A pdb=" N GLY j 207 " --> pdb=" O THR j 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR j 208 " --> pdb=" O TRP j 204 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ARG j 209 " --> pdb=" O ILE j 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 203 through 209' Processing helix chain 'j' and resid 227 through 245 removed outlier: 3.516A pdb=" N ALA j 243 " --> pdb=" O GLU j 239 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG j 244 " --> pdb=" O ALA j 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 17 removed outlier: 4.032A pdb=" N ASP J 14 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE J 15 " --> pdb=" O TYR J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 42 Processing helix chain 'J' and resid 122 through 139 Processing helix chain 'J' and resid 140 through 155 removed outlier: 4.135A pdb=" N CYS J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN J 145 " --> pdb=" O THR J 141 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU J 147 " --> pdb=" O LYS J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 186 removed outlier: 3.574A pdb=" N VAL J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG J 168 " --> pdb=" O LYS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 200 removed outlier: 3.964A pdb=" N VAL J 199 " --> pdb=" O THR J 195 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 195 through 200' Processing helix chain 'J' and resid 203 through 209 removed outlier: 4.013A pdb=" N GLY J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR J 208 " --> pdb=" O TRP J 204 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG J 209 " --> pdb=" O ILE J 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 203 through 209' Processing helix chain 'J' and resid 227 through 245 removed outlier: 3.575A pdb=" N ALA J 243 " --> pdb=" O GLU J 239 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG J 244 " --> pdb=" O ALA J 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU J 245 " --> pdb=" O ARG J 241 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 30 removed outlier: 3.923A pdb=" N ASN l 28 " --> pdb=" O LYS l 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE l 29 " --> pdb=" O MET l 25 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU l 30 " --> pdb=" O ILE l 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 75 removed outlier: 3.597A pdb=" N ASP l 63 " --> pdb=" O LYS l 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU l 68 " --> pdb=" O PHE l 64 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Proline residue: l 70 - end of helix removed outlier: 4.152A pdb=" N SER l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU l 74 " --> pdb=" O PRO l 70 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER l 75 " --> pdb=" O LEU l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 83 Processing helix chain 'l' and resid 95 through 115 removed outlier: 3.922A pdb=" N PHE l 105 " --> pdb=" O PHE l 101 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY l 106 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU l 114 " --> pdb=" O LEU l 110 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU l 115 " --> pdb=" O ILE l 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 119 through 136 Processing helix chain 'l' and resid 165 through 173 removed outlier: 3.841A pdb=" N MET l 169 " --> pdb=" O TYR l 165 " (cutoff:3.500A) Processing helix chain 'l' and resid 185 through 194 removed outlier: 3.689A pdb=" N GLN l 194 " --> pdb=" O TRP l 190 " (cutoff:3.500A) Processing helix chain 'l' and resid 205 through 216 removed outlier: 4.518A pdb=" N ARG l 213 " --> pdb=" O LEU l 209 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE l 214 " --> pdb=" O VAL l 210 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA l 215 " --> pdb=" O SER l 211 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS l 216 " --> pdb=" O GLN l 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 30 removed outlier: 3.709A pdb=" N ASN L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 75 removed outlier: 4.006A pdb=" N LEU L 68 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) Proline residue: L 70 - end of helix removed outlier: 4.042A pdb=" N SER L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU L 74 " --> pdb=" O PRO L 70 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 95 through 115 removed outlier: 3.857A pdb=" N PHE L 105 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU L 114 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 136 removed outlier: 3.524A pdb=" N ARG L 123 " --> pdb=" O ASN L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 173 removed outlier: 3.783A pdb=" N MET L 169 " --> pdb=" O TYR L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 194 removed outlier: 3.794A pdb=" N GLN L 194 " --> pdb=" O TRP L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 216 removed outlier: 4.580A pdb=" N ARG L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE L 214 " --> pdb=" O VAL L 210 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS L 216 " --> pdb=" O GLN L 212 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 12 Processing helix chain 'm' and resid 21 through 46 removed outlier: 4.054A pdb=" N ILE m 32 " --> pdb=" O ARG m 28 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS m 33 " --> pdb=" O TYR m 29 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS m 34 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N MET m 35 " --> pdb=" O SER m 31 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP m 37 " --> pdb=" O LYS m 33 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS m 44 " --> pdb=" O GLU m 40 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU m 45 " --> pdb=" O THR m 41 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA m 46 " --> pdb=" O THR m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 65 removed outlier: 4.298A pdb=" N ASP m 64 " --> pdb=" O ASP m 60 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP m 65 " --> pdb=" O PRO m 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 60 through 65' Processing helix chain 'm' and resid 73 through 95 Processing helix chain 'm' and resid 101 through 157 removed outlier: 3.962A pdb=" N ARG m 105 " --> pdb=" O ASN m 101 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THR m 106 " --> pdb=" O ILE m 102 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N MET m 107 " --> pdb=" O ARG m 103 " (cutoff:3.500A) Proline residue: m 112 - end of helix removed outlier: 5.462A pdb=" N TYR m 153 " --> pdb=" O LYS m 149 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU m 154 " --> pdb=" O GLN m 150 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU m 155 " --> pdb=" O ASN m 151 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU m 156 " --> pdb=" O GLU m 152 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS m 157 " --> pdb=" O TYR m 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 158 through 178 removed outlier: 5.713A pdb=" N HIS m 178 " --> pdb=" O LEU m 174 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 204 removed outlier: 4.890A pdb=" N PHE m 189 " --> pdb=" O LYS m 185 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS m 190 " --> pdb=" O ALA m 186 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP m 191 " --> pdb=" O CYS m 187 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER m 192 " --> pdb=" O ASP m 188 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE m 194 " --> pdb=" O LYS m 190 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR m 203 " --> pdb=" O PHE m 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 12 Processing helix chain 'M' and resid 21 through 46 removed outlier: 3.510A pdb=" N LYS M 30 " --> pdb=" O LEU M 26 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE M 32 " --> pdb=" O ARG M 28 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS M 33 " --> pdb=" O TYR M 29 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS M 34 " --> pdb=" O LYS M 30 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET M 35 " --> pdb=" O SER M 31 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS M 44 " --> pdb=" O GLU M 40 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU M 45 " --> pdb=" O THR M 41 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 65 removed outlier: 4.218A pdb=" N ASP M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP M 65 " --> pdb=" O PRO M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 60 through 65' Processing helix chain 'M' and resid 73 through 95 Processing helix chain 'M' and resid 101 through 157 removed outlier: 3.947A pdb=" N ARG M 105 " --> pdb=" O ASN M 101 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET M 107 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Proline residue: M 112 - end of helix removed outlier: 5.417A pdb=" N TYR M 153 " --> pdb=" O LYS M 149 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU M 154 " --> pdb=" O GLN M 150 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU M 155 " --> pdb=" O ASN M 151 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS M 157 " --> pdb=" O TYR M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 178 removed outlier: 5.744A pdb=" N HIS M 178 " --> pdb=" O LEU M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 204 removed outlier: 4.952A pdb=" N PHE M 189 " --> pdb=" O LYS M 185 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS M 190 " --> pdb=" O ALA M 186 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP M 191 " --> pdb=" O CYS M 187 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE M 194 " --> pdb=" O LYS M 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR M 203 " --> pdb=" O PHE M 199 " (cutoff:3.500A) Processing helix chain 'n' and resid 68 through 74 removed outlier: 3.904A pdb=" N TYR n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN n 73 " --> pdb=" O ALA n 69 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR n 74 " --> pdb=" O SER n 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 68 through 74' Processing helix chain 'n' and resid 87 through 94 removed outlier: 4.278A pdb=" N LEU n 91 " --> pdb=" O HIS n 87 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA n 92 " --> pdb=" O LEU n 88 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU n 93 " --> pdb=" O GLY n 89 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU n 94 " --> pdb=" O LYS n 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 87 through 94' Processing helix chain 'n' and resid 101 through 106 removed outlier: 4.165A pdb=" N GLN n 105 " --> pdb=" O TYR n 101 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU n 106 " --> pdb=" O LYS n 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 101 through 106' Processing helix chain 'n' and resid 109 through 123 Processing helix chain 'n' and resid 126 through 131 removed outlier: 6.132A pdb=" N TYR n 130 " --> pdb=" O PHE n 126 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG n 131 " --> pdb=" O LYS n 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 126 through 131' Processing helix chain 'n' and resid 132 through 158 removed outlier: 3.705A pdb=" N ALA n 137 " --> pdb=" O GLU n 133 " (cutoff:3.500A) Processing helix chain 'n' and resid 165 through 170 removed outlier: 4.374A pdb=" N ARG n 169 " --> pdb=" O SER n 165 " (cutoff:3.500A) Proline residue: n 170 - end of helix No H-bonds generated for 'chain 'n' and resid 165 through 170' Processing helix chain 'n' and resid 173 through 178 removed outlier: 3.983A pdb=" N LEU n 177 " --> pdb=" O GLN n 173 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY n 178 " --> pdb=" O PHE n 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 173 through 178' Processing helix chain 'N' and resid 68 through 74 removed outlier: 3.962A pdb=" N TYR N 72 " --> pdb=" O GLU N 68 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN N 73 " --> pdb=" O ALA N 69 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 68 through 74' Processing helix chain 'N' and resid 87 through 94 removed outlier: 4.226A pdb=" N LEU N 91 " --> pdb=" O HIS N 87 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA N 92 " --> pdb=" O LEU N 88 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU N 93 " --> pdb=" O GLY N 89 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU N 94 " --> pdb=" O LYS N 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 94' Processing helix chain 'N' and resid 101 through 106 removed outlier: 4.184A pdb=" N GLN N 105 " --> pdb=" O TYR N 101 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU N 106 " --> pdb=" O LYS N 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 106' Processing helix chain 'N' and resid 109 through 123 Processing helix chain 'N' and resid 126 through 131 removed outlier: 6.162A pdb=" N TYR N 130 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 126 through 131' Processing helix chain 'N' and resid 132 through 158 removed outlier: 3.612A pdb=" N ALA N 137 " --> pdb=" O GLU N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 170 removed outlier: 4.514A pdb=" N ARG N 169 " --> pdb=" O SER N 165 " (cutoff:3.500A) Proline residue: N 170 - end of helix No H-bonds generated for 'chain 'N' and resid 165 through 170' Processing helix chain 'N' and resid 173 through 178 removed outlier: 4.081A pdb=" N LEU N 177 " --> pdb=" O GLN N 173 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY N 178 " --> pdb=" O PHE N 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 173 through 178' Processing helix chain 'o' and resid 88 through 106 Processing helix chain 'o' and resid 110 through 123 removed outlier: 3.797A pdb=" N ASN o 114 " --> pdb=" O GLY o 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS o 122 " --> pdb=" O ARG o 118 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU o 123 " --> pdb=" O ASN o 119 " (cutoff:3.500A) Processing helix chain 'o' and resid 125 through 136 Processing helix chain 'o' and resid 141 through 150 Processing helix chain 'O' and resid 88 through 106 Processing helix chain 'O' and resid 110 through 123 removed outlier: 3.968A pdb=" N ASN O 114 " --> pdb=" O GLY O 110 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS O 122 " --> pdb=" O ARG O 118 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU O 123 " --> pdb=" O ASN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 136 Processing helix chain 'O' and resid 141 through 150 Processing helix chain 'p' and resid 18 through 23 removed outlier: 4.175A pdb=" N ILE p 22 " --> pdb=" O HIS p 18 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU p 23 " --> pdb=" O THR p 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 18 through 23' Processing helix chain 'p' and resid 24 through 58 removed outlier: 4.187A pdb=" N GLN p 29 " --> pdb=" O SER p 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL p 37 " --> pdb=" O ILE p 33 " (cutoff:3.500A) Proline residue: p 38 - end of helix removed outlier: 3.533A pdb=" N ASN p 57 " --> pdb=" O MET p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 66 removed outlier: 5.347A pdb=" N LYS p 64 " --> pdb=" O GLN p 60 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU p 65 " --> pdb=" O SER p 61 " (cutoff:3.500A) Proline residue: p 66 - end of helix Processing helix chain 'p' and resid 67 through 103 removed outlier: 3.564A pdb=" N LEU p 79 " --> pdb=" O ALA p 75 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY p 93 " --> pdb=" O PHE p 89 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU p 95 " --> pdb=" O LYS p 91 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN p 96 " --> pdb=" O SER p 92 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA p 99 " --> pdb=" O GLU p 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN p 103 " --> pdb=" O ALA p 99 " (cutoff:3.500A) Processing helix chain 'p' and resid 110 through 115 removed outlier: 3.871A pdb=" N VAL p 114 " --> pdb=" O LYS p 110 " (cutoff:3.500A) Proline residue: p 115 - end of helix No H-bonds generated for 'chain 'p' and resid 110 through 115' Processing helix chain 'p' and resid 116 through 121 removed outlier: 6.126A pdb=" N TYR p 121 " --> pdb=" O LEU p 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 23 removed outlier: 4.216A pdb=" N ILE P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 18 through 23' Processing helix chain 'P' and resid 24 through 58 removed outlier: 4.150A pdb=" N GLN P 29 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL P 37 " --> pdb=" O ILE P 33 " (cutoff:3.500A) Proline residue: P 38 - end of helix removed outlier: 3.596A pdb=" N ASN P 57 " --> pdb=" O MET P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 66 removed outlier: 5.307A pdb=" N LYS P 64 " --> pdb=" O GLN P 60 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) Proline residue: P 66 - end of helix Processing helix chain 'P' and resid 67 through 103 removed outlier: 3.618A pdb=" N LEU P 79 " --> pdb=" O ALA P 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY P 82 " --> pdb=" O THR P 78 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY P 93 " --> pdb=" O PHE P 89 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU P 95 " --> pdb=" O LYS P 91 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN P 103 " --> pdb=" O ALA P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 115 removed outlier: 3.907A pdb=" N VAL P 114 " --> pdb=" O LYS P 110 " (cutoff:3.500A) Proline residue: P 115 - end of helix No H-bonds generated for 'chain 'P' and resid 110 through 115' Processing helix chain 'P' and resid 116 through 121 removed outlier: 6.138A pdb=" N TYR P 121 " --> pdb=" O LEU P 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 63 through 79 removed outlier: 5.767A pdb=" N PHE q 79 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 88 removed outlier: 5.959A pdb=" N ASN q 88 " --> pdb=" O LYS q 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 92 through 97 removed outlier: 3.804A pdb=" N HIS q 96 " --> pdb=" O VAL q 92 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY q 97 " --> pdb=" O LEU q 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 92 through 97' Processing helix chain 'q' and resid 99 through 114 Processing helix chain 'q' and resid 119 through 127 removed outlier: 3.606A pdb=" N ILE q 123 " --> pdb=" O SER q 119 " (cutoff:3.500A) Proline residue: q 124 - end of helix removed outlier: 5.475A pdb=" N ASN q 127 " --> pdb=" O ILE q 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 119 through 127' Processing helix chain 'q' and resid 128 through 146 Processing helix chain 'Q' and resid 63 through 79 removed outlier: 5.680A pdb=" N PHE Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 88 removed outlier: 6.041A pdb=" N ASN Q 88 " --> pdb=" O LYS Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 97 removed outlier: 3.701A pdb=" N HIS Q 96 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY Q 97 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 92 through 97' Processing helix chain 'Q' and resid 99 through 114 Processing helix chain 'Q' and resid 119 through 127 removed outlier: 3.613A pdb=" N ILE Q 123 " --> pdb=" O SER Q 119 " (cutoff:3.500A) Proline residue: Q 124 - end of helix removed outlier: 5.461A pdb=" N ASN Q 127 " --> pdb=" O ILE Q 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 119 through 127' Processing helix chain 'Q' and resid 128 through 146 Processing helix chain 'r' and resid 17 through 22 Processing helix chain 'r' and resid 23 through 67 removed outlier: 4.783A pdb=" N TYR r 27 " --> pdb=" O ASP r 23 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN r 28 " --> pdb=" O LEU r 24 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY r 29 " --> pdb=" O TYR r 25 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS r 46 " --> pdb=" O TYR r 42 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE r 47 " --> pdb=" O LYS r 43 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR r 48 " --> pdb=" O ALA r 44 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE r 61 " --> pdb=" O LEU r 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE r 62 " --> pdb=" O VAL r 58 " (cutoff:3.500A) Processing helix chain 'r' and resid 79 through 84 removed outlier: 4.392A pdb=" N GLU r 83 " --> pdb=" O GLY r 79 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET r 84 " --> pdb=" O LYS r 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 79 through 84' Processing helix chain 'r' and resid 89 through 107 removed outlier: 5.538A pdb=" N GLU r 107 " --> pdb=" O ARG r 103 " (cutoff:3.500A) Processing helix chain 'r' and resid 113 through 118 removed outlier: 4.278A pdb=" N LYS r 117 " --> pdb=" O ASP r 113 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR r 118 " --> pdb=" O PRO r 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 113 through 118' Processing helix chain 'r' and resid 119 through 127 removed outlier: 3.611A pdb=" N ASP r 125 " --> pdb=" O GLU r 121 " (cutoff:3.500A) Processing helix chain 'r' and resid 68 through 73 removed outlier: 3.572A pdb=" N GLY r 73 " --> pdb=" O ASP r 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 68 through 73' Processing helix chain 's' and resid 31 through 37 removed outlier: 3.707A pdb=" N ARG s 35 " --> pdb=" O PRO s 31 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N MET s 37 " --> pdb=" O VAL s 33 " (cutoff:3.500A) Processing helix chain 's' and resid 73 through 88 removed outlier: 4.102A pdb=" N TRP s 77 " --> pdb=" O ASP s 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY s 86 " --> pdb=" O ASP s 82 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER s 87 " --> pdb=" O PHE s 83 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE s 88 " --> pdb=" O LEU s 84 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 100 removed outlier: 3.519A pdb=" N ASN s 99 " --> pdb=" O ASP s 95 " (cutoff:3.500A) Processing helix chain 's' and resid 113 through 125 removed outlier: 3.865A pdb=" N ASP s 123 " --> pdb=" O ALA s 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS s 125 " --> pdb=" O VAL s 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 60 removed outlier: 4.018A pdb=" N ILE e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS e 57 " --> pdb=" O ASN e 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP e 58 " --> pdb=" O HIS e 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 76 through 81 removed outlier: 3.778A pdb=" N ARG e 80 " --> pdb=" O ILE e 76 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE e 81 " --> pdb=" O TYR e 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 76 through 81' Processing helix chain 'e' and resid 89 through 95 removed outlier: 5.270A pdb=" N HIS e 95 " --> pdb=" O SER e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 96 through 102 removed outlier: 4.185A pdb=" N SER e 100 " --> pdb=" O PHE e 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE e 101 " --> pdb=" O SER e 97 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN e 102 " --> pdb=" O LYS e 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 96 through 102' Processing helix chain 'e' and resid 144 through 149 removed outlier: 4.999A pdb=" N ILE e 148 " --> pdb=" O ASP e 144 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYS e 149 " --> pdb=" O PHE e 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 144 through 149' Processing helix chain 'e' and resid 150 through 158 Proline residue: e 158 - end of helix Processing helix chain 'e' and resid 176 through 184 removed outlier: 4.042A pdb=" N LYS e 180 " --> pdb=" O HIS e 176 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR e 181 " --> pdb=" O LYS e 177 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE e 182 " --> pdb=" O TYR e 178 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 202 through 222 removed outlier: 4.400A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN e 207 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N PHE e 208 " --> pdb=" O GLU e 204 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE e 209 " --> pdb=" O CYS e 205 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL e 210 " --> pdb=" O PHE e 206 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP e 212 " --> pdb=" O PHE e 208 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU e 213 " --> pdb=" O PHE e 209 " (cutoff:3.500A) Processing helix chain 'e' and resid 243 through 258 Processing helix chain 'e' and resid 304 through 311 removed outlier: 3.841A pdb=" N ASP e 308 " --> pdb=" O GLN e 304 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY e 311 " --> pdb=" O LEU e 307 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 369 removed outlier: 3.602A pdb=" N TYR e 354 " --> pdb=" O TRP e 350 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA e 357 " --> pdb=" O TRP e 353 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL e 358 " --> pdb=" O TYR e 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS e 364 " --> pdb=" O ARG e 360 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN e 368 " --> pdb=" O LYS e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 413 through 437 removed outlier: 3.810A pdb=" N MET e 427 " --> pdb=" O TRP e 423 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA e 428 " --> pdb=" O ALA e 424 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS e 429 " --> pdb=" O LYS e 425 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS e 430 " --> pdb=" O GLY e 426 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE e 431 " --> pdb=" O MET e 427 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN e 432 " --> pdb=" O ALA e 428 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP e 433 " --> pdb=" O LYS e 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 60 removed outlier: 4.026A pdb=" N ILE E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.857A pdb=" N ARG E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 81' Processing helix chain 'E' and resid 89 through 95 removed outlier: 5.488A pdb=" N HIS E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 4.203A pdb=" N SER E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 102' Processing helix chain 'E' and resid 144 through 149 removed outlier: 5.028A pdb=" N ILE E 148 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS E 149 " --> pdb=" O PHE E 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 149' Processing helix chain 'E' and resid 150 through 158 Proline residue: E 158 - end of helix Processing helix chain 'E' and resid 176 through 184 removed outlier: 4.001A pdb=" N LYS E 180 " --> pdb=" O HIS E 176 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 222 removed outlier: 4.715A pdb=" N PHE E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N PHE E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE E 209 " --> pdb=" O CYS E 205 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL E 210 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 213 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 258 Processing helix chain 'E' and resid 304 through 311 removed outlier: 3.979A pdb=" N ASP E 308 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 369 removed outlier: 3.645A pdb=" N TYR E 354 " --> pdb=" O TRP E 350 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 357 " --> pdb=" O TRP E 353 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL E 358 " --> pdb=" O TYR E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 437 removed outlier: 3.734A pdb=" N GLY E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET E 427 " --> pdb=" O TRP E 423 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS E 430 " --> pdb=" O GLY E 426 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP E 433 " --> pdb=" O LYS E 429 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 27 Processing helix chain 'R' and resid 29 through 55 removed outlier: 3.967A pdb=" N LYS R 46 " --> pdb=" O TYR R 42 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE R 47 " --> pdb=" O LYS R 43 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 71 removed outlier: 4.033A pdb=" N PHE R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 84 removed outlier: 4.505A pdb=" N GLU R 83 " --> pdb=" O GLY R 79 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N MET R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 79 through 84' Processing helix chain 'R' and resid 89 through 106 Processing helix chain 'R' and resid 113 through 118 removed outlier: 4.272A pdb=" N LYS R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR R 118 " --> pdb=" O PRO R 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 113 through 118' Processing helix chain 'R' and resid 119 through 127 removed outlier: 3.509A pdb=" N ASP R 125 " --> pdb=" O GLU R 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 35 Proline residue: S 31 - end of helix removed outlier: 4.810A pdb=" N ASP S 34 " --> pdb=" O ARG S 30 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG S 35 " --> pdb=" O PRO S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 88 removed outlier: 4.117A pdb=" N TRP S 77 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY S 86 " --> pdb=" O ASP S 82 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER S 87 " --> pdb=" O PHE S 83 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE S 88 " --> pdb=" O LEU S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 100 Processing helix chain 'S' and resid 113 through 125 removed outlier: 3.622A pdb=" N ALA S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP S 123 " --> pdb=" O ALA S 119 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS S 125 " --> pdb=" O VAL S 121 " (cutoff:3.500A) Processing helix chain 'i1' and resid 79 through 89 Processing helix chain 'i1' and resid 93 through 106 Processing helix chain 'i2' and resid 75 through 89 removed outlier: 3.572A pdb=" N LEUi2 79 " --> pdb=" O ALAi2 75 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYRi2 88 " --> pdb=" O ILEi2 84 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HISi2 89 " --> pdb=" O LEUi2 85 " (cutoff:3.500A) Processing helix chain 'i2' and resid 93 through 106 Processing helix chain 't' and resid 139 through 149 removed outlier: 4.573A pdb=" N TRP t 143 " --> pdb=" O LEU t 139 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE t 144 " --> pdb=" O THR t 140 " (cutoff:3.500A) Proline residue: t 145 - end of helix Processing helix chain 't' and resid 153 through 158 removed outlier: 4.390A pdb=" N HIS t 157 " --> pdb=" O ASP t 153 " (cutoff:3.500A) Processing helix chain 't' and resid 178 through 194 removed outlier: 3.595A pdb=" N VAL t 186 " --> pdb=" O MET t 182 " (cutoff:3.500A) Processing helix chain 't' and resid 204 through 217 Processing helix chain 't' and resid 237 through 253 removed outlier: 3.509A pdb=" N THR t 251 " --> pdb=" O VAL t 247 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU t 252 " --> pdb=" O ASN t 248 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE t 253 " --> pdb=" O ALA t 249 " (cutoff:3.500A) Processing helix chain 't' and resid 259 through 271 Processing helix chain 't' and resid 273 through 285 removed outlier: 3.521A pdb=" N ILE t 284 " --> pdb=" O PHE t 280 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N SER t 285 " --> pdb=" O THR t 281 " (cutoff:3.500A) Processing helix chain 't' and resid 298 through 309 removed outlier: 3.727A pdb=" N ASN t 309 " --> pdb=" O ASN t 305 " (cutoff:3.500A) Processing helix chain 't' and resid 343 through 352 Proline residue: t 347 - end of helix Processing helix chain 't' and resid 375 through 380 removed outlier: 4.121A pdb=" N PHE t 379 " --> pdb=" O TRP t 375 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU t 380 " --> pdb=" O VAL t 376 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 375 through 380' Processing helix chain 't' and resid 381 through 396 removed outlier: 3.632A pdb=" N VAL t 385 " --> pdb=" O ASN t 381 " (cutoff:3.500A) Processing helix chain 't' and resid 445 through 458 removed outlier: 3.735A pdb=" N LEU t 457 " --> pdb=" O LEU t 453 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'a' and resid 60 through 64 removed outlier: 5.294A pdb=" N TYR a 60 " --> pdb=" O CYS a 170 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN a 166 " --> pdb=" O TYR a 64 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 60 through 64 removed outlier: 5.269A pdb=" N TYR A 60 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 166 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'g' and resid 175 through 179 removed outlier: 8.182A pdb=" N THR g 175 " --> pdb=" O VAL g 222 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS g 218 " --> pdb=" O LEU g 179 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLN g 212 " --> pdb=" O LEU g 186 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'g' and resid 248 through 251 removed outlier: 6.307A pdb=" N LEU g 254 " --> pdb=" O LEU g 269 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'g' and resid 212 through 222 removed outlier: 3.715A pdb=" N ALA g 226 " --> pdb=" O ASP g 221 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'G' and resid 175 through 179 removed outlier: 8.199A pdb=" N THR G 175 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS G 218 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLN G 212 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP G 180 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 248 through 251 removed outlier: 6.203A pdb=" N LEU G 254 " --> pdb=" O LEU G 269 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 212 through 222 removed outlier: 3.673A pdb=" N ALA G 226 " --> pdb=" O ASP G 221 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'j' and resid 78 through 81 removed outlier: 7.940A pdb=" N ILE j 78 " --> pdb=" O ALA j 107 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'J' and resid 78 through 81 removed outlier: 7.885A pdb=" N ILE J 78 " --> pdb=" O ALA J 107 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'l' and resid 196 through 199 removed outlier: 4.437A pdb=" N GLY l 196 " --> pdb=" O ALA l 234 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'L' and resid 196 through 199 removed outlier: 4.597A pdb=" N GLY L 196 " --> pdb=" O ALA L 234 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'p' and resid 6 through 9 Processing sheet with id= 14, first strand: chain 'p' and resid 122 through 125 removed outlier: 3.751A pdb=" N LYS p 131 " --> pdb=" O ASP p 125 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'P' and resid 6 through 9 Processing sheet with id= 16, first strand: chain 'P' and resid 122 through 125 removed outlier: 3.674A pdb=" N LYS P 131 " --> pdb=" O ASP P 125 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'q' and resid 45 through 49 removed outlier: 6.463A pdb=" N LEU q 45 " --> pdb=" O ARG q 56 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'Q' and resid 45 through 49 removed outlier: 6.789A pdb=" N LEU Q 45 " --> pdb=" O ARG Q 56 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'e' and resid 36 through 39 removed outlier: 5.995A pdb=" N ASP e 36 " --> pdb=" O ARG e 129 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG e 128 " --> pdb=" O LEU e 124 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN e 120 " --> pdb=" O TYR e 132 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'e' and resid 106 through 110 Processing sheet with id= 21, first strand: chain 'e' and resid 161 through 165 removed outlier: 4.146A pdb=" N ARG e 260 " --> pdb=" O PHE e 230 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'e' and resid 264 through 268 removed outlier: 8.087A pdb=" N ASN e 264 " --> pdb=" O THR e 282 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR e 278 " --> pdb=" O LEU e 268 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'e' and resid 379 through 386 removed outlier: 6.355A pdb=" N THR e 390 " --> pdb=" O THR e 386 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'e' and resid 275 through 282 removed outlier: 5.717A pdb=" N GLN e 275 " --> pdb=" O TYR e 292 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'E' and resid 36 through 39 removed outlier: 5.880A pdb=" N ASP E 36 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG E 128 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 124 " --> pdb=" O ARG E 128 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN E 120 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 106 through 110 Processing sheet with id= 27, first strand: chain 'E' and resid 161 through 165 removed outlier: 4.305A pdb=" N ARG E 260 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 264 through 268 removed outlier: 8.098A pdb=" N ASN E 264 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR E 278 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 379 through 386 removed outlier: 6.344A pdb=" N THR E 390 " --> pdb=" O THR E 386 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 275 through 282 removed outlier: 5.825A pdb=" N GLN E 275 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 286 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 't' and resid 96 through 99 removed outlier: 5.892A pdb=" N ILE t 96 " --> pdb=" O ARG t 121 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG t 116 " --> pdb=" O ASN t 164 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR t 134 " --> pdb=" O LEU t 163 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY t 223 " --> pdb=" O ALA t 198 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG t 327 " --> pdb=" O THR t 222 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP t 361 " --> pdb=" O ALA t 328 " (cutoff:3.500A) 2899 hydrogen bonds defined for protein. 8649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 47.23 Time building geometry restraints manager: 90.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 64268 1.03 - 1.23: 248 1.23 - 1.42: 30862 1.42 - 1.62: 40060 1.62 - 1.82: 629 Bond restraints: 136067 Sorted by residual: bond pdb=" C3' ATP G 301 " pdb=" C4' ATP G 301 " ideal model delta sigma weight residual 1.526 1.282 0.244 1.10e-02 8.26e+03 4.93e+02 bond pdb=" C3' ATP g 301 " pdb=" C4' ATP g 301 " ideal model delta sigma weight residual 1.526 1.282 0.244 1.10e-02 8.26e+03 4.91e+02 bond pdb=" C1' ATP g 301 " pdb=" C2' ATP g 301 " ideal model delta sigma weight residual 1.531 1.272 0.259 1.20e-02 6.94e+03 4.66e+02 bond pdb=" C1' ATP G 301 " pdb=" C2' ATP G 301 " ideal model delta sigma weight residual 1.531 1.274 0.257 1.20e-02 6.94e+03 4.57e+02 bond pdb=" C3B NAD E 900 " pdb=" C4B NAD E 900 " ideal model delta sigma weight residual 1.523 1.288 0.235 2.00e-02 2.50e+03 1.38e+02 ... (remaining 136062 not shown) Histogram of bond angle deviations from ideal: 95.95 - 104.38: 974 104.38 - 112.82: 149943 112.82 - 121.25: 64947 121.25 - 129.69: 25750 129.69 - 138.12: 609 Bond angle restraints: 242223 Sorted by residual: angle pdb=" PB ATP G 301 " pdb=" O3B ATP G 301 " pdb=" PG ATP G 301 " ideal model delta sigma weight residual 139.87 121.81 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PB ATP g 301 " pdb=" O3B ATP g 301 " pdb=" PG ATP g 301 " ideal model delta sigma weight residual 139.87 122.04 17.83 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA ATP G 301 " pdb=" O3A ATP G 301 " pdb=" PB ATP G 301 " ideal model delta sigma weight residual 136.83 124.23 12.60 1.00e+00 1.00e+00 1.59e+02 angle pdb=" PA ATP g 301 " pdb=" O3A ATP g 301 " pdb=" PB ATP g 301 " ideal model delta sigma weight residual 136.83 124.80 12.03 1.00e+00 1.00e+00 1.45e+02 angle pdb=" N1 ATP G 301 " pdb=" C2 ATP G 301 " pdb=" N3 ATP G 301 " ideal model delta sigma weight residual 128.69 120.26 8.43 1.00e+00 1.00e+00 7.11e+01 ... (remaining 242218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 63696 35.94 - 71.89: 2413 71.89 - 107.83: 83 107.83 - 143.77: 14 143.77 - 179.72: 15 Dihedral angle restraints: 66221 sinusoidal: 36272 harmonic: 29949 Sorted by residual: dihedral pdb=" CD ARG B 112 " pdb=" NE ARG B 112 " pdb=" CZ ARG B 112 " pdb=" NH1 ARG B 112 " ideal model delta sinusoidal sigma weight residual 0.00 179.72 -179.72 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" O2 PEE J 304 " pdb=" C1 PEE J 304 " pdb=" C2 PEE J 304 " pdb=" O3P PEE J 304 " ideal model delta sinusoidal sigma weight residual -59.96 109.28 -169.24 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PEE J 304 " pdb=" C1 PEE J 304 " pdb=" C2 PEE J 304 " pdb=" O3P PEE J 304 " ideal model delta sinusoidal sigma weight residual 62.73 -129.19 -168.08 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 66218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 8424 0.067 - 0.133: 1112 0.133 - 0.200: 24 0.200 - 0.267: 3 0.267 - 0.334: 5 Chirality restraints: 9568 Sorted by residual: chirality pdb=" C3D NAD e 900 " pdb=" C2D NAD e 900 " pdb=" C4D NAD e 900 " pdb=" O3D NAD e 900 " both_signs ideal model delta sigma weight residual False -2.73 -2.39 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C3D NAD E 900 " pdb=" C2D NAD E 900 " pdb=" C4D NAD E 900 " pdb=" O3D NAD E 900 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C3B NAD e 900 " pdb=" C2B NAD e 900 " pdb=" C4B NAD e 900 " pdb=" O3B NAD e 900 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 9565 not shown) Planarity restraints: 19495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASNi1 83 " 0.023 2.00e-02 2.50e+03 2.40e-02 8.66e+00 pdb=" CG ASNi1 83 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASNi1 83 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASNi1 83 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASNi1 83 " 0.036 2.00e-02 2.50e+03 pdb="HD22 ASNi1 83 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU l 115 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO l 116 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO l 116 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO l 116 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 73 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO G 74 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " -0.020 5.00e-02 4.00e+02 ... (remaining 19492 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.82: 469 1.82 - 2.51: 101770 2.51 - 3.21: 405874 3.21 - 3.90: 549916 3.90 - 4.60: 889282 Nonbonded interactions: 1947311 Sorted by model distance: nonbonded pdb="HG23 THR f 37 " pdb=" OB4 CDL f 304 " model vdw 1.119 2.620 nonbonded pdb="HG21 THR f 37 " pdb=" OB4 CDL f 304 " model vdw 1.269 2.620 nonbonded pdb=" CG2 THR f 37 " pdb=" OB4 CDL f 304 " model vdw 1.374 3.100 nonbonded pdb=" O SER J 54 " pdb="HH12 ARG L 94 " model vdw 1.456 1.850 nonbonded pdb=" HE ARG L 123 " pdb=" OA4 CDL L 301 " model vdw 1.489 1.850 ... (remaining 1947306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 62 through 222 or resid 401 through 402)) selection = (chain 'b' and (resid 62 through 111 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 113 th \ rough 171 or (resid 172 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE or name HH11 or name HH12 or name HH21)) or resid 173 through 222 or r \ esid 401 through 402)) } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = (chain 'F' and (resid 2 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3 or name HZ1 or name HZ3)) or resid 105 through 201 or r \ esid 900)) selection = (chain 'f' and (resid 2 through 201 or resid 301)) } ncs_group { reference = (chain 'G' and (resid 31 through 286 or resid 301 through 303)) selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = (chain 'I' and (resid 1 through 161 or (resid 162 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 163 through 209 or resid 302 through 303)) selection = (chain 'i' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD21)) or resid 51 through 209 or resid 302 throug \ h 303)) } ncs_group { reference = (chain 'J' and (resid 5 through 273 or resid 301 through 302)) selection = (chain 'j' and (resid 5 through 97 or (resid 98 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE2 or name HE3 or name HZ2)) or resid 99 through 273 or resid 301 throug \ h 302)) } ncs_group { reference = chain 'K' selection = (chain 'k' and (resid 1 through 179 or resid 201 through 202)) } ncs_group { reference = chain 'L' selection = (chain 'l' and (resid 2 through 247 or resid 301)) } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = (chain 'r' and resid 10 through 149) } ncs_group { reference = (chain 'S' and ((resid 22 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 23 through 126)) selection = chain 's' } ncs_group { reference = chain 'i1' selection = (chain 'i2' and ((resid 79 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 80 through 106)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.470 Extract box with map and model: 43.460 Check model and map are aligned: 1.460 Set scattering table: 0.990 Process input model: 349.440 Find NCS groups from input model: 4.960 Set up NCS constraints: 1.760 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 424.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.259 71736 Z= 0.610 Angle : 1.003 18.064 96303 Z= 0.512 Chirality : 0.044 0.334 9568 Planarity : 0.003 0.041 11938 Dihedral : 16.887 179.718 28378 Min Nonbonded Distance : 1.374 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.30 % Allowed : 3.28 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -2.86 (0.08), residues: 7847 helix: -2.30 (0.06), residues: 3827 sheet: -1.31 (0.25), residues: 358 loop : -1.33 (0.09), residues: 3662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP j 68 HIS 0.006 0.001 HIS d 165 PHE 0.021 0.002 PHE A 426 TYR 0.021 0.002 TYR t 364 ARG 0.018 0.001 ARG t 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 1270 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1249 time to evaluate : 7.982 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: b 163 PHE cc_start: 0.7652 (t80) cc_final: 0.7106 (m-80) REVERT: f 19 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: f 161 MET cc_start: 0.8819 (ttm) cc_final: 0.8541 (ttm) REVERT: i 124 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8845 (tp) REVERT: k 90 ASP cc_start: 0.8643 (t70) cc_final: 0.8074 (t0) REVERT: k 140 ASN cc_start: 0.8270 (m-40) cc_final: 0.8048 (m110) REVERT: j 146 SER cc_start: 0.8944 (t) cc_final: 0.8710 (p) REVERT: j 221 ASP cc_start: 0.7798 (p0) cc_final: 0.7581 (p0) REVERT: l 14 THR cc_start: 0.9175 (p) cc_final: 0.8974 (p) REVERT: l 17 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7968 (mt-10) REVERT: o 68 MET cc_start: 0.8287 (mmt) cc_final: 0.7539 (mmt) REVERT: p 10 ASP cc_start: 0.7907 (t0) cc_final: 0.7636 (t0) REVERT: p 97 GLN cc_start: 0.8678 (tp40) cc_final: 0.8310 (tp40) REVERT: p 144 GLN cc_start: 0.6987 (tm-30) cc_final: 0.6704 (tm-30) REVERT: q 57 ASN cc_start: 0.8202 (p0) cc_final: 0.7867 (p0) REVERT: r 64 ASP cc_start: 0.8320 (m-30) cc_final: 0.7980 (m-30) REVERT: A 359 ASP cc_start: 0.8162 (m-30) cc_final: 0.7770 (m-30) REVERT: A 387 TYR cc_start: 0.8511 (t80) cc_final: 0.8290 (t80) REVERT: B 177 ASN cc_start: 0.8354 (t0) cc_final: 0.8118 (t0) REVERT: F 21 ASP cc_start: 0.7948 (m-30) cc_final: 0.7497 (m-30) REVERT: I 177 ASP cc_start: 0.7638 (t70) cc_final: 0.7274 (t70) REVERT: K 90 ASP cc_start: 0.8881 (t70) cc_final: 0.8504 (t0) REVERT: K 96 MET cc_start: 0.8101 (tpt) cc_final: 0.7800 (mmm) REVERT: K 101 ILE cc_start: 0.8883 (tt) cc_final: 0.8676 (pp) REVERT: C 63 GLU cc_start: 0.8415 (pm20) cc_final: 0.8205 (pm20) REVERT: H 191 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8435 (tp-100) REVERT: M 67 MET cc_start: 0.9228 (tpt) cc_final: 0.8844 (tpt) REVERT: M 107 MET cc_start: 0.8597 (tpp) cc_final: 0.8318 (tpp) REVERT: O 102 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7526 (tm-30) REVERT: O 126 LYS cc_start: 0.9135 (tttt) cc_final: 0.8910 (tttm) REVERT: P 3 ASN cc_start: 0.8130 (t0) cc_final: 0.7918 (t0) REVERT: P 65 LEU cc_start: 0.8782 (mt) cc_final: 0.8574 (mt) REVERT: P 141 GLN cc_start: 0.7888 (pt0) cc_final: 0.7609 (pt0) REVERT: Q 54 VAL cc_start: 0.8812 (t) cc_final: 0.8592 (m) REVERT: Q 128 LYS cc_start: 0.8478 (mttt) cc_final: 0.8234 (mtpt) REVERT: S 21 THR cc_start: 0.7856 (t) cc_final: 0.7613 (p) REVERT: E 439 ARG cc_start: 0.7006 (mmt90) cc_final: 0.6583 (tpt170) outliers start: 21 outliers final: 8 residues processed: 1266 average time/residue: 3.4913 time to fit residues: 5669.7604 Evaluate side-chains 838 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 828 time to evaluate : 7.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 19 GLN Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain l residue 205 TRP Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain e residue 398 TYR Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 652 optimal weight: 3.9990 chunk 585 optimal weight: 0.9990 chunk 325 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 395 optimal weight: 0.7980 chunk 313 optimal weight: 1.9990 chunk 605 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 368 optimal weight: 3.9990 chunk 450 optimal weight: 0.0570 chunk 701 optimal weight: 10.0000 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 146 ASN a 443 ASN f 4 HIS f 8 GLN i 167 ASN k 147 GLN g 97 GLN j 192 GLN l 7 GLN l 50 GLN n 73 GLN p 9 GLN q 47 GLN q 58 GLN r 11 GLN r 15 ASN s 48 GLN s 110 GLN ** e 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 219 GLN B 196 ASN K 146 ASN K 149 GLN G 97 GLN H 133 GLN H 178 GLN L 50 GLN O 72 HIS O 113 GLN P 137 HIS Q 141 GLN S 23 GLN E 147 GLN E 361 ASN t 151 GLN t 170 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 71736 Z= 0.170 Angle : 0.524 8.265 96303 Z= 0.280 Chirality : 0.038 0.150 9568 Planarity : 0.004 0.059 11938 Dihedral : 18.734 178.207 12342 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.04 % Allowed : 9.18 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.37 (0.09), residues: 7847 helix: 0.41 (0.08), residues: 3810 sheet: -0.67 (0.28), residues: 302 loop : -0.84 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 174 HIS 0.007 0.001 HIS e 221 PHE 0.021 0.001 PHE l 60 TYR 0.017 0.001 TYR A 231 ARG 0.010 0.001 ARG b 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 972 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 899 time to evaluate : 8.064 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: a 329 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8788 (mp) REVERT: b 94 ASP cc_start: 0.7963 (m-30) cc_final: 0.7717 (m-30) REVERT: b 163 PHE cc_start: 0.7667 (t80) cc_final: 0.7039 (m-80) REVERT: f 25 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8052 (mtpp) REVERT: f 161 MET cc_start: 0.8881 (ttm) cc_final: 0.8589 (ttm) REVERT: o 68 MET cc_start: 0.8340 (mmt) cc_final: 0.7623 (mmt) REVERT: p 10 ASP cc_start: 0.7928 (t0) cc_final: 0.7721 (t0) REVERT: p 54 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8437 (mm-30) REVERT: p 97 GLN cc_start: 0.8807 (tp40) cc_final: 0.8565 (tp40) REVERT: p 144 GLN cc_start: 0.7012 (tm-30) cc_final: 0.6739 (tm-30) REVERT: p 147 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: q 58 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8012 (mp-120) REVERT: r 28 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7892 (mt0) REVERT: A 359 ASP cc_start: 0.8075 (m-30) cc_final: 0.7851 (m-30) REVERT: A 387 TYR cc_start: 0.8816 (t80) cc_final: 0.8586 (t80) REVERT: B 110 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8480 (ppp) REVERT: B 177 ASN cc_start: 0.8096 (t0) cc_final: 0.7832 (m-40) REVERT: B 191 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: B 216 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6981 (tm-30) REVERT: F 5 GLU cc_start: 0.7971 (tt0) cc_final: 0.7765 (tp30) REVERT: I 177 ASP cc_start: 0.7413 (t70) cc_final: 0.7041 (t70) REVERT: K 69 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8378 (t0) REVERT: C 63 GLU cc_start: 0.8402 (pm20) cc_final: 0.8155 (pm20) REVERT: H 191 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8345 (tp-100) REVERT: J 233 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: M 107 MET cc_start: 0.8840 (tpp) cc_final: 0.8543 (tpp) REVERT: P 39 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: P 80 LEU cc_start: 0.8869 (tp) cc_final: 0.8669 (mm) REVERT: S 21 THR cc_start: 0.7934 (t) cc_final: 0.7688 (p) REVERT: E 439 ARG cc_start: 0.6999 (mmt90) cc_final: 0.6645 (tpt170) REVERT: t 182 MET cc_start: 0.8530 (mtp) cc_final: 0.8179 (mtp) REVERT: t 187 MET cc_start: 0.8887 (mmp) cc_final: 0.8329 (mmp) outliers start: 73 outliers final: 21 residues processed: 936 average time/residue: 3.2706 time to fit residues: 4010.4239 Evaluate side-chains 821 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 791 time to evaluate : 7.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain l residue 205 TRP Chi-restraints excluded: chain p residue 47 LEU Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 126 ASP Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain i1 residue 97 ILE Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 390 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 584 optimal weight: 2.9990 chunk 477 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 703 optimal weight: 5.9990 chunk 759 optimal weight: 0.9990 chunk 626 optimal weight: 1.9990 chunk 697 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 564 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN g 97 GLN h 133 GLN q 58 GLN r 11 GLN e 165 ASN H 133 GLN O 72 HIS Q 64 GLN Q 141 GLN t 151 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 71736 Z= 0.202 Angle : 0.491 10.004 96303 Z= 0.259 Chirality : 0.038 0.150 9568 Planarity : 0.004 0.153 11938 Dihedral : 17.291 177.368 12333 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.06 % Allowed : 9.54 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.43 (0.09), residues: 7847 helix: 1.26 (0.08), residues: 3817 sheet: -0.73 (0.26), residues: 352 loop : -0.60 (0.10), residues: 3678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 139 HIS 0.006 0.001 HIS E 221 PHE 0.018 0.001 PHE l 60 TYR 0.017 0.001 TYR m 79 ARG 0.020 0.000 ARG b 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 900 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 825 time to evaluate : 7.961 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: a 329 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8793 (mp) REVERT: b 163 PHE cc_start: 0.7689 (t80) cc_final: 0.7054 (m-80) REVERT: f 25 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8100 (mtpp) REVERT: f 161 MET cc_start: 0.8900 (ttm) cc_final: 0.8616 (ttm) REVERT: i 84 MET cc_start: 0.7803 (ttm) cc_final: 0.7313 (ttm) REVERT: h 221 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: o 68 MET cc_start: 0.8382 (mmt) cc_final: 0.7613 (mmt) REVERT: p 10 ASP cc_start: 0.7993 (t0) cc_final: 0.7747 (t0) REVERT: p 97 GLN cc_start: 0.8869 (tp40) cc_final: 0.8594 (tp40) REVERT: p 144 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6785 (tm-30) REVERT: p 147 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8369 (ptmm) REVERT: r 11 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7926 (mm-40) REVERT: r 28 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7867 (mt0) REVERT: A 25 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: A 359 ASP cc_start: 0.8160 (m-30) cc_final: 0.7944 (m-30) REVERT: A 387 TYR cc_start: 0.8857 (t80) cc_final: 0.8632 (t80) REVERT: B 177 ASN cc_start: 0.8313 (t0) cc_final: 0.7976 (m-40) REVERT: B 191 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: I 177 ASP cc_start: 0.7566 (t70) cc_final: 0.7175 (t70) REVERT: K 50 GLU cc_start: 0.8227 (pt0) cc_final: 0.7804 (pt0) REVERT: K 57 MET cc_start: 0.8754 (tpp) cc_final: 0.8381 (tpp) REVERT: C 63 GLU cc_start: 0.8364 (pm20) cc_final: 0.8140 (pm20) REVERT: L 34 GLN cc_start: 0.8444 (mm110) cc_final: 0.8160 (mm-40) REVERT: M 67 MET cc_start: 0.9256 (tpt) cc_final: 0.8908 (tpt) REVERT: P 39 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8490 (mt0) REVERT: P 80 LEU cc_start: 0.8922 (tp) cc_final: 0.8704 (mm) REVERT: S 21 THR cc_start: 0.7994 (t) cc_final: 0.7741 (p) REVERT: E 439 ARG cc_start: 0.7028 (mmt90) cc_final: 0.6662 (tpt170) REVERT: t 187 MET cc_start: 0.8906 (mmp) cc_final: 0.8229 (mmp) outliers start: 75 outliers final: 34 residues processed: 863 average time/residue: 3.3310 time to fit residues: 3786.0144 Evaluate side-chains 807 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 766 time to evaluate : 7.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain b residue 133 ASP Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain j residue 137 MET Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 205 TRP Chi-restraints excluded: chain m residue 161 LYS Chi-restraints excluded: chain o residue 106 SER Chi-restraints excluded: chain o residue 134 ASP Chi-restraints excluded: chain p residue 47 LEU Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 118 SER Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 694 optimal weight: 9.9990 chunk 528 optimal weight: 2.9990 chunk 364 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 335 optimal weight: 10.0000 chunk 472 optimal weight: 2.9990 chunk 705 optimal weight: 1.9990 chunk 747 optimal weight: 0.3980 chunk 368 optimal weight: 2.9990 chunk 668 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN k 140 ASN k 147 GLN g 97 GLN g 120 GLN h 133 GLN p 9 GLN p 128 ASN ** e 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN M 16 GLN O 72 HIS Q 141 GLN t 151 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 71736 Z= 0.265 Angle : 0.513 7.161 96303 Z= 0.272 Chirality : 0.040 0.169 9568 Planarity : 0.004 0.134 11938 Dihedral : 16.621 176.058 12331 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.22 % Allowed : 9.65 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.72 (0.09), residues: 7847 helix: 1.51 (0.08), residues: 3840 sheet: -0.77 (0.26), residues: 366 loop : -0.48 (0.10), residues: 3641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 139 HIS 0.007 0.001 HIS E 221 PHE 0.020 0.001 PHE i 82 TYR 0.020 0.001 TYR m 79 ARG 0.011 0.001 ARG t 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 875 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 789 time to evaluate : 8.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 329 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8815 (mp) REVERT: b 163 PHE cc_start: 0.7740 (t80) cc_final: 0.7036 (m-80) REVERT: f 25 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: f 161 MET cc_start: 0.8944 (ttm) cc_final: 0.8692 (ttm) REVERT: i 84 MET cc_start: 0.7949 (ttm) cc_final: 0.7592 (ttm) REVERT: k 90 ASP cc_start: 0.8491 (t70) cc_final: 0.8023 (t0) REVERT: l 69 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7904 (ttp-170) REVERT: o 68 MET cc_start: 0.8463 (mmt) cc_final: 0.7671 (mmt) REVERT: p 10 ASP cc_start: 0.8000 (t0) cc_final: 0.7785 (t0) REVERT: p 54 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8342 (mm-30) REVERT: p 97 GLN cc_start: 0.8897 (tp40) cc_final: 0.8575 (tp40) REVERT: p 144 GLN cc_start: 0.7222 (tm-30) cc_final: 0.6859 (tm-30) REVERT: p 147 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8338 (ptmm) REVERT: q 145 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: r 28 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7873 (mt0) REVERT: A 23 TYR cc_start: 0.7913 (t80) cc_final: 0.7698 (t80) REVERT: A 25 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: A 78 MET cc_start: 0.9049 (tpp) cc_final: 0.8782 (tpp) REVERT: A 359 ASP cc_start: 0.8283 (m-30) cc_final: 0.8043 (m-30) REVERT: B 177 ASN cc_start: 0.8492 (t0) cc_final: 0.8251 (t0) REVERT: B 191 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: B 216 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7163 (tm-30) REVERT: I 177 ASP cc_start: 0.7685 (t70) cc_final: 0.7288 (t70) REVERT: C 63 GLU cc_start: 0.8352 (pm20) cc_final: 0.7958 (pm20) REVERT: G 255 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7393 (mtt90) REVERT: L 34 GLN cc_start: 0.8521 (mm110) cc_final: 0.8204 (mm-40) REVERT: M 67 MET cc_start: 0.9315 (tpt) cc_final: 0.8956 (tpt) REVERT: P 39 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: P 80 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8737 (mm) REVERT: S 21 THR cc_start: 0.8062 (t) cc_final: 0.7817 (p) REVERT: E 439 ARG cc_start: 0.7079 (mmt90) cc_final: 0.6642 (tpt170) REVERT: i2 82 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8530 (mm-30) REVERT: t 187 MET cc_start: 0.8920 (mmp) cc_final: 0.8190 (mmp) REVERT: t 252 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7140 (mp0) outliers start: 86 outliers final: 33 residues processed: 837 average time/residue: 3.2842 time to fit residues: 3595.7566 Evaluate side-chains 799 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 756 time to evaluate : 7.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain b residue 133 ASP Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain j residue 137 MET Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain o residue 106 SER Chi-restraints excluded: chain o residue 134 ASP Chi-restraints excluded: chain p residue 47 LEU Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 145 GLU Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 118 SER Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain i2 residue 82 GLU Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Chi-restraints excluded: chain t residue 252 GLU Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 415 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 622 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 556 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 637 optimal weight: 2.9990 chunk 516 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 381 optimal weight: 2.9990 chunk 670 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN i 178 GLN k 140 ASN k 147 GLN g 97 GLN g 120 GLN h 133 GLN p 129 ASN r 11 GLN e 165 ASN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN M 16 GLN O 72 HIS P 141 GLN Q 141 GLN E 165 ASN t 151 GLN t 170 ASN t 439 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 71736 Z= 0.349 Angle : 0.541 8.518 96303 Z= 0.288 Chirality : 0.041 0.151 9568 Planarity : 0.004 0.162 11938 Dihedral : 16.575 176.527 12329 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.19 % Allowed : 10.11 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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 (0.09), residues: 7847 helix: 1.55 (0.08), residues: 3847 sheet: -0.72 (0.26), residues: 366 loop : -0.50 (0.10), residues: 3634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP s 77 HIS 0.007 0.001 HIS d 165 PHE 0.022 0.002 PHE i 82 TYR 0.022 0.002 TYR m 79 ARG 0.021 0.001 ARG p 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 875 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 791 time to evaluate : 8.005 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: a 329 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8841 (mp) REVERT: b 163 PHE cc_start: 0.7818 (t80) cc_final: 0.7098 (m-80) REVERT: f 19 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: f 25 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8109 (mtpp) REVERT: f 161 MET cc_start: 0.8965 (ttm) cc_final: 0.8716 (ttm) REVERT: i 84 MET cc_start: 0.8099 (ttm) cc_final: 0.7827 (ttm) REVERT: k 90 ASP cc_start: 0.8492 (t70) cc_final: 0.8039 (t0) REVERT: l 69 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.8011 (tmm160) REVERT: o 68 MET cc_start: 0.8493 (mmt) cc_final: 0.7656 (mmt) REVERT: p 10 ASP cc_start: 0.8018 (t0) cc_final: 0.7782 (t0) REVERT: p 54 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8222 (mm-30) REVERT: p 97 GLN cc_start: 0.8926 (tp40) cc_final: 0.8600 (tp40) REVERT: p 144 GLN cc_start: 0.7320 (tm-30) cc_final: 0.6918 (tm-30) REVERT: p 147 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8348 (ptmm) REVERT: q 145 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: r 11 GLN cc_start: 0.8252 (mm-40) cc_final: 0.8029 (mm-40) REVERT: r 28 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7901 (mt0) REVERT: A 25 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: A 359 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: B 177 ASN cc_start: 0.8545 (t0) cc_final: 0.8321 (t0) REVERT: B 191 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: I 177 ASP cc_start: 0.7702 (t70) cc_final: 0.7315 (t70) REVERT: K 50 GLU cc_start: 0.8398 (pt0) cc_final: 0.7954 (pt0) REVERT: C 63 GLU cc_start: 0.8335 (pm20) cc_final: 0.7978 (pm20) REVERT: G 217 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: G 255 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7438 (mtt90) REVERT: L 34 GLN cc_start: 0.8512 (mm110) cc_final: 0.8221 (mm-40) REVERT: M 67 MET cc_start: 0.9345 (tpt) cc_final: 0.9001 (tpt) REVERT: P 39 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: P 80 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8738 (mm) REVERT: E 439 ARG cc_start: 0.7092 (mmt90) cc_final: 0.6664 (tpt170) REVERT: i2 82 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8536 (mm-30) REVERT: t 187 MET cc_start: 0.8910 (mmp) cc_final: 0.8126 (mmp) REVERT: t 252 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7163 (mp0) outliers start: 84 outliers final: 36 residues processed: 836 average time/residue: 3.2545 time to fit residues: 3565.6691 Evaluate side-chains 810 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 761 time to evaluate : 7.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain a residue 432 GLU Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 19 GLN Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain j residue 137 MET Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain o residue 106 SER Chi-restraints excluded: chain o residue 134 ASP Chi-restraints excluded: chain p residue 47 LEU Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain q residue 57 ASN Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 145 GLU Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain H residue 242 ARG Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 118 SER Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain i2 residue 82 GLU Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Chi-restraints excluded: chain t residue 252 GLU Chi-restraints excluded: chain t residue 292 SER Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 415 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 251 optimal weight: 2.9990 chunk 672 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 747 optimal weight: 3.9990 chunk 620 optimal weight: 2.9990 chunk 346 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN i 178 GLN k 140 ASN k 147 GLN g 97 GLN h 133 GLN j 192 GLN l 7 GLN p 141 GLN A 110 GLN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN M 16 GLN P 42 ASN Q 141 GLN t 151 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 71736 Z= 0.326 Angle : 0.536 17.004 96303 Z= 0.283 Chirality : 0.041 0.151 9568 Planarity : 0.005 0.281 11938 Dihedral : 16.352 177.202 12329 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.12 % Allowed : 10.49 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.81 (0.09), residues: 7847 helix: 1.61 (0.08), residues: 3846 sheet: -0.65 (0.26), residues: 366 loop : -0.46 (0.10), residues: 3635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP s 77 HIS 0.007 0.001 HIS E 221 PHE 0.022 0.002 PHE i 82 TYR 0.022 0.002 TYR m 79 ARG 0.024 0.001 ARG b 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 848 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 769 time to evaluate : 8.105 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: a 329 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8837 (mp) REVERT: b 163 PHE cc_start: 0.7835 (t80) cc_final: 0.7060 (m-80) REVERT: f 19 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: f 25 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8105 (mtpp) REVERT: f 161 MET cc_start: 0.8967 (ttm) cc_final: 0.8725 (ttm) REVERT: i 26 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7565 (mtp-110) REVERT: i 84 MET cc_start: 0.8074 (ttm) cc_final: 0.7807 (ttm) REVERT: k 90 ASP cc_start: 0.8476 (t70) cc_final: 0.8030 (t0) REVERT: l 69 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.8001 (tmm160) REVERT: o 68 MET cc_start: 0.8513 (mmt) cc_final: 0.7678 (mmt) REVERT: p 10 ASP cc_start: 0.7982 (t0) cc_final: 0.7754 (t0) REVERT: p 54 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8265 (mm-30) REVERT: p 97 GLN cc_start: 0.8932 (tp40) cc_final: 0.8602 (tp40) REVERT: p 147 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (ptmm) REVERT: q 145 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: A 25 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: A 359 ASP cc_start: 0.8245 (m-30) cc_final: 0.8041 (m-30) REVERT: B 191 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: B 216 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7058 (tm-30) REVERT: I 177 ASP cc_start: 0.7698 (t70) cc_final: 0.7303 (t70) REVERT: K 50 GLU cc_start: 0.8463 (pt0) cc_final: 0.8022 (pt0) REVERT: K 83 SER cc_start: 0.9215 (m) cc_final: 0.8949 (p) REVERT: C 63 GLU cc_start: 0.8307 (pm20) cc_final: 0.7932 (pm20) REVERT: G 217 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: G 235 MET cc_start: 0.9187 (ptt) cc_final: 0.8982 (ptt) REVERT: G 255 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7449 (mtt90) REVERT: L 34 GLN cc_start: 0.8487 (mm110) cc_final: 0.8199 (mm-40) REVERT: M 67 MET cc_start: 0.9350 (tpt) cc_final: 0.9006 (tpt) REVERT: P 39 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: P 80 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (mm) REVERT: E 439 ARG cc_start: 0.7121 (mmt90) cc_final: 0.6656 (tpt170) REVERT: i2 82 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8502 (mm-30) REVERT: t 187 MET cc_start: 0.8892 (mmp) cc_final: 0.8145 (mmp) REVERT: t 252 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7187 (mp0) outliers start: 79 outliers final: 38 residues processed: 813 average time/residue: 3.4251 time to fit residues: 3667.5212 Evaluate side-chains 806 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 755 time to evaluate : 7.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 19 GLN Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain i residue 26 ARG Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain g residue 266 GLU Chi-restraints excluded: chain j residue 137 MET Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain o residue 106 SER Chi-restraints excluded: chain o residue 109 GLN Chi-restraints excluded: chain o residue 134 ASP Chi-restraints excluded: chain p residue 47 LEU Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 145 GLU Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 118 SER Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain i2 residue 82 GLU Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Chi-restraints excluded: chain t residue 252 GLU Chi-restraints excluded: chain t residue 292 SER Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 415 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 721 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 426 optimal weight: 2.9990 chunk 546 optimal weight: 2.9990 chunk 423 optimal weight: 1.9990 chunk 629 optimal weight: 1.9990 chunk 417 optimal weight: 0.9990 chunk 745 optimal weight: 2.9990 chunk 466 optimal weight: 1.9990 chunk 454 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN k 140 ASN k 147 GLN g 97 GLN h 133 GLN l 7 GLN r 11 GLN I 190 GLN G 97 GLN L 50 GLN M 16 GLN S 23 GLN t 151 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 71736 Z= 0.271 Angle : 0.511 8.799 96303 Z= 0.271 Chirality : 0.040 0.151 9568 Planarity : 0.004 0.185 11938 Dihedral : 15.883 178.107 12329 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.18 % Allowed : 10.43 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.93 (0.09), residues: 7847 helix: 1.71 (0.08), residues: 3846 sheet: -0.58 (0.27), residues: 366 loop : -0.41 (0.10), residues: 3635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP s 77 HIS 0.006 0.001 HIS E 221 PHE 0.021 0.001 PHE A 426 TYR 0.020 0.001 TYR m 79 ARG 0.014 0.000 ARG p 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 861 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 778 time to evaluate : 8.178 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: a 329 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8824 (mp) REVERT: b 163 PHE cc_start: 0.7810 (t80) cc_final: 0.7038 (m-80) REVERT: f 19 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: f 25 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8061 (mtpt) REVERT: f 161 MET cc_start: 0.8960 (ttm) cc_final: 0.8731 (ttm) REVERT: i 26 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7539 (mtp-110) REVERT: i 84 MET cc_start: 0.8015 (ttm) cc_final: 0.7774 (ttm) REVERT: k 90 ASP cc_start: 0.8465 (t70) cc_final: 0.7998 (t0) REVERT: l 69 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.7989 (tmm160) REVERT: o 68 MET cc_start: 0.8530 (mmt) cc_final: 0.7698 (mmt) REVERT: p 10 ASP cc_start: 0.7981 (t0) cc_final: 0.7707 (t0) REVERT: p 54 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8238 (mm-30) REVERT: p 97 GLN cc_start: 0.8940 (tp40) cc_final: 0.8598 (tp40) REVERT: q 145 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: A 25 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: A 359 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: B 62 MET cc_start: 0.7411 (ttt) cc_final: 0.7187 (ttt) REVERT: B 191 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: B 216 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7053 (tm-30) REVERT: I 177 ASP cc_start: 0.7702 (t70) cc_final: 0.7299 (t70) REVERT: K 50 GLU cc_start: 0.8441 (pt0) cc_final: 0.8138 (pt0) REVERT: K 57 MET cc_start: 0.8729 (tpp) cc_final: 0.8451 (tpp) REVERT: K 83 SER cc_start: 0.9224 (m) cc_final: 0.8977 (p) REVERT: K 86 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7821 (tmm-80) REVERT: K 132 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8092 (mm-40) REVERT: C 63 GLU cc_start: 0.8284 (pm20) cc_final: 0.7931 (pm20) REVERT: G 217 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: G 235 MET cc_start: 0.9180 (ptt) cc_final: 0.8974 (ptt) REVERT: G 255 ARG cc_start: 0.7730 (ttm-80) cc_final: 0.7436 (mtt90) REVERT: L 9 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8238 (mtpp) REVERT: L 34 GLN cc_start: 0.8478 (mm110) cc_final: 0.8190 (mm-40) REVERT: M 67 MET cc_start: 0.9345 (tpt) cc_final: 0.8998 (tpt) REVERT: P 39 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8457 (mt0) REVERT: P 80 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8752 (mm) REVERT: E 169 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: E 439 ARG cc_start: 0.7126 (mmt90) cc_final: 0.6654 (tpt170) REVERT: t 252 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7193 (mp0) outliers start: 83 outliers final: 42 residues processed: 826 average time/residue: 3.2842 time to fit residues: 3547.2254 Evaluate side-chains 821 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 765 time to evaluate : 7.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 19 GLN Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain i residue 26 ARG Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 101 ILE Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain g residue 266 GLU Chi-restraints excluded: chain h residue 240 ASP Chi-restraints excluded: chain j residue 137 MET Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain n residue 107 ILE Chi-restraints excluded: chain o residue 109 GLN Chi-restraints excluded: chain o residue 134 ASP Chi-restraints excluded: chain p residue 47 LEU Chi-restraints excluded: chain q residue 57 ASN Chi-restraints excluded: chain q residue 145 GLU Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 242 ARG Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 118 SER Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Chi-restraints excluded: chain t residue 252 GLU Chi-restraints excluded: chain t residue 292 SER Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 415 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 460 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 444 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 473 optimal weight: 3.9990 chunk 507 optimal weight: 0.3980 chunk 368 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 585 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN k 140 ASN k 147 GLN g 97 GLN h 133 GLN j 192 GLN l 7 GLN r 11 GLN G 31 GLN L 50 GLN Q 141 GLN S 23 GLN E 165 ASN t 151 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 71736 Z= 0.155 Angle : 0.466 6.360 96303 Z= 0.245 Chirality : 0.037 0.155 9568 Planarity : 0.004 0.180 11938 Dihedral : 14.962 179.742 12329 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.72 % Allowed : 10.97 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.19 (0.10), residues: 7847 helix: 1.94 (0.09), residues: 3844 sheet: -0.53 (0.27), residues: 378 loop : -0.29 (0.10), residues: 3625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 139 HIS 0.004 0.001 HIS d 135 PHE 0.020 0.001 PHE A 426 TYR 0.016 0.001 TYR m 79 ARG 0.015 0.000 ARG P 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 865 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 814 time to evaluate : 8.143 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: a 329 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8812 (mp) REVERT: b 163 PHE cc_start: 0.7671 (t80) cc_final: 0.6881 (m-80) REVERT: f 25 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8126 (mtpp) REVERT: f 161 MET cc_start: 0.8941 (ttm) cc_final: 0.8670 (ttm) REVERT: i 26 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7527 (mtp-110) REVERT: i 84 MET cc_start: 0.7809 (ttm) cc_final: 0.7561 (ttm) REVERT: k 86 ARG cc_start: 0.8482 (ttm110) cc_final: 0.8253 (ttp-110) REVERT: k 90 ASP cc_start: 0.8457 (t70) cc_final: 0.8003 (t0) REVERT: l 25 MET cc_start: 0.9313 (tpp) cc_final: 0.8951 (tpp) REVERT: l 69 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7976 (tmm160) REVERT: o 68 MET cc_start: 0.8521 (mmt) cc_final: 0.7678 (mmt) REVERT: p 10 ASP cc_start: 0.7981 (t0) cc_final: 0.7727 (t0) REVERT: p 54 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8247 (mm-30) REVERT: p 97 GLN cc_start: 0.8923 (tp40) cc_final: 0.8584 (tp40) REVERT: p 147 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8311 (ptmm) REVERT: r 28 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7818 (mt0) REVERT: A 23 TYR cc_start: 0.7908 (t80) cc_final: 0.7698 (t80) REVERT: A 25 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: B 216 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 220 ASP cc_start: 0.7887 (m-30) cc_final: 0.7373 (m-30) REVERT: I 177 ASP cc_start: 0.7673 (t70) cc_final: 0.7284 (t70) REVERT: K 57 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8357 (tpp) REVERT: K 83 SER cc_start: 0.9247 (m) cc_final: 0.8966 (p) REVERT: K 132 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8087 (mm-40) REVERT: C 63 GLU cc_start: 0.8261 (pm20) cc_final: 0.7887 (pm20) REVERT: G 217 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: L 34 GLN cc_start: 0.8424 (mm110) cc_final: 0.8171 (mm-40) REVERT: M 67 MET cc_start: 0.9313 (tpt) cc_final: 0.8937 (tpt) REVERT: P 80 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8765 (mm) REVERT: E 439 ARG cc_start: 0.7127 (mmt90) cc_final: 0.6655 (tpt170) REVERT: t 99 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.6421 (p90) REVERT: t 252 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7195 (mp0) outliers start: 51 outliers final: 27 residues processed: 842 average time/residue: 3.2756 time to fit residues: 3607.7398 Evaluate side-chains 818 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 781 time to evaluate : 7.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain b residue 133 ASP Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain i residue 26 ARG Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain o residue 109 GLN Chi-restraints excluded: chain p residue 47 LEU Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain q residue 57 ASN Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain H residue 242 ARG Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Chi-restraints excluded: chain t residue 252 GLU Chi-restraints excluded: chain t residue 292 SER Chi-restraints excluded: chain t residue 415 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 677 optimal weight: 2.9990 chunk 713 optimal weight: 5.9990 chunk 651 optimal weight: 4.9990 chunk 694 optimal weight: 10.0000 chunk 417 optimal weight: 1.9990 chunk 302 optimal weight: 0.8980 chunk 545 optimal weight: 3.9990 chunk 213 optimal weight: 0.0970 chunk 627 optimal weight: 2.9990 chunk 656 optimal weight: 0.9990 chunk 691 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 8 GLN k 140 ASN k 147 GLN g 97 GLN h 133 GLN l 7 GLN p 9 GLN p 128 ASN p 141 GLN G 31 GLN L 50 GLN S 23 GLN E 165 ASN t 151 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 71736 Z= 0.230 Angle : 0.492 7.337 96303 Z= 0.260 Chirality : 0.039 0.153 9568 Planarity : 0.004 0.183 11938 Dihedral : 15.037 177.907 12329 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.77 % Allowed : 11.20 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.20 (0.10), residues: 7847 helix: 1.94 (0.08), residues: 3850 sheet: -0.50 (0.27), residues: 378 loop : -0.28 (0.10), residues: 3619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 139 HIS 0.006 0.001 HIS E 221 PHE 0.018 0.001 PHE i 82 TYR 0.019 0.001 TYR m 79 ARG 0.015 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 831 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 777 time to evaluate : 8.079 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: a 329 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8822 (mp) REVERT: b 163 PHE cc_start: 0.7792 (t80) cc_final: 0.7007 (m-80) REVERT: f 25 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8130 (mtpp) REVERT: f 161 MET cc_start: 0.8953 (ttm) cc_final: 0.8695 (ttm) REVERT: i 13 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6866 (tp30) REVERT: i 26 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7546 (mtp-110) REVERT: i 84 MET cc_start: 0.7964 (ttm) cc_final: 0.7741 (ttm) REVERT: k 86 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8255 (ttp-110) REVERT: k 90 ASP cc_start: 0.8472 (t70) cc_final: 0.8052 (t0) REVERT: l 25 MET cc_start: 0.9329 (tpp) cc_final: 0.8953 (tpp) REVERT: l 69 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7993 (tmm160) REVERT: o 68 MET cc_start: 0.8527 (mmt) cc_final: 0.7674 (mmt) REVERT: p 10 ASP cc_start: 0.7993 (t0) cc_final: 0.7758 (t0) REVERT: p 97 GLN cc_start: 0.8957 (tp40) cc_final: 0.8516 (tp-100) REVERT: p 147 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8290 (ptmm) REVERT: r 28 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7844 (mt0) REVERT: r 33 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: A 23 TYR cc_start: 0.7951 (t80) cc_final: 0.7748 (t80) REVERT: A 25 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: B 191 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 216 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7164 (tm-30) REVERT: I 177 ASP cc_start: 0.7703 (t70) cc_final: 0.7313 (t70) REVERT: K 57 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8449 (tpp) REVERT: K 83 SER cc_start: 0.9231 (m) cc_final: 0.8997 (p) REVERT: K 86 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7743 (tmm-80) REVERT: K 132 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8100 (mm-40) REVERT: C 63 GLU cc_start: 0.8261 (pm20) cc_final: 0.7907 (pm20) REVERT: G 217 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: L 34 GLN cc_start: 0.8466 (mm110) cc_final: 0.8181 (mm-40) REVERT: M 67 MET cc_start: 0.9322 (tpt) cc_final: 0.8950 (tpt) REVERT: P 80 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8772 (mm) REVERT: E 169 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: E 439 ARG cc_start: 0.7141 (mmt90) cc_final: 0.6664 (tpt170) REVERT: t 99 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.6545 (p90) REVERT: t 252 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7187 (mp0) outliers start: 54 outliers final: 35 residues processed: 809 average time/residue: 3.2814 time to fit residues: 3465.3278 Evaluate side-chains 810 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 763 time to evaluate : 7.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 302 SER Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain i residue 26 ARG Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 101 ILE Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain h residue 240 ASP Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain l residue 205 TRP Chi-restraints excluded: chain o residue 109 GLN Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain q residue 57 ASN Chi-restraints excluded: chain r residue 33 LYS Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain H residue 242 ARG Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain i2 residue 78 ASN Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Chi-restraints excluded: chain t residue 252 GLU Chi-restraints excluded: chain t residue 292 SER Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 415 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 455 optimal weight: 1.9990 chunk 734 optimal weight: 3.9990 chunk 448 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 510 optimal weight: 0.9980 chunk 770 optimal weight: 3.9990 chunk 708 optimal weight: 0.7980 chunk 613 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 473 optimal weight: 3.9990 chunk 376 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN k 140 ASN k 147 GLN g 97 GLN h 133 GLN j 192 GLN l 7 GLN L 50 GLN Q 141 GLN S 23 GLN t 151 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 71736 Z= 0.243 Angle : 0.498 7.570 96303 Z= 0.263 Chirality : 0.039 0.151 9568 Planarity : 0.004 0.188 11938 Dihedral : 15.029 178.244 12329 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.75 % Allowed : 11.44 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.19 (0.10), residues: 7847 helix: 1.93 (0.08), residues: 3856 sheet: -0.47 (0.27), residues: 378 loop : -0.29 (0.10), residues: 3613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 139 HIS 0.006 0.001 HIS E 221 PHE 0.019 0.001 PHE i 82 TYR 0.020 0.001 TYR m 79 ARG 0.013 0.000 ARG p 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15694 Ramachandran restraints generated. 7847 Oldfield, 0 Emsley, 7847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 104 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Evaluate side-chains 821 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 768 time to evaluate : 8.116 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: a 329 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8819 (mp) REVERT: b 163 PHE cc_start: 0.7795 (t80) cc_final: 0.7000 (m-80) REVERT: f 25 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8133 (mtpp) REVERT: f 161 MET cc_start: 0.8955 (ttm) cc_final: 0.8693 (ttm) REVERT: i 13 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6864 (tp30) REVERT: i 26 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7548 (mtp-110) REVERT: i 84 MET cc_start: 0.7975 (ttm) cc_final: 0.7756 (ttm) REVERT: k 86 ARG cc_start: 0.8483 (ttm110) cc_final: 0.8257 (ttp-110) REVERT: k 90 ASP cc_start: 0.8483 (t70) cc_final: 0.8062 (t0) REVERT: l 25 MET cc_start: 0.9326 (tpp) cc_final: 0.8943 (tpp) REVERT: l 69 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.8000 (tmm160) REVERT: o 68 MET cc_start: 0.8530 (mmt) cc_final: 0.7680 (mmt) REVERT: p 10 ASP cc_start: 0.7995 (t0) cc_final: 0.7739 (t0) REVERT: p 54 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8250 (mm-30) REVERT: p 97 GLN cc_start: 0.8957 (tp40) cc_final: 0.8515 (tp-100) REVERT: p 147 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8292 (ptmm) REVERT: r 28 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7856 (mt0) REVERT: r 33 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8190 (ttmt) REVERT: A 23 TYR cc_start: 0.7953 (t80) cc_final: 0.7749 (t80) REVERT: A 25 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: B 191 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7735 (tm-30) REVERT: I 177 ASP cc_start: 0.7709 (t70) cc_final: 0.7317 (t70) REVERT: K 83 SER cc_start: 0.9254 (m) cc_final: 0.8969 (p) REVERT: K 86 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7810 (ttp80) REVERT: K 132 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8111 (mm-40) REVERT: C 63 GLU cc_start: 0.8252 (pm20) cc_final: 0.7901 (pm20) REVERT: G 217 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: L 34 GLN cc_start: 0.8466 (mm110) cc_final: 0.8181 (mm-40) REVERT: M 67 MET cc_start: 0.9325 (tpt) cc_final: 0.8954 (tpt) REVERT: P 80 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8774 (mm) REVERT: E 109 MET cc_start: 0.8601 (tpp) cc_final: 0.8350 (ttt) REVERT: E 169 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: E 439 ARG cc_start: 0.7138 (mmt90) cc_final: 0.6658 (tpt170) REVERT: t 99 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.6612 (p90) REVERT: t 252 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7187 (mp0) outliers start: 53 outliers final: 38 residues processed: 802 average time/residue: 3.4272 time to fit residues: 3636.0673 Evaluate side-chains 815 residues out of total 7046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 766 time to evaluate : 8.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 302 SER Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain b residue 112 ARG Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain i residue 26 ARG Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain g residue 217 PHE Chi-restraints excluded: chain h residue 240 ASP Chi-restraints excluded: chain j residue 198 ASP Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain l residue 205 TRP Chi-restraints excluded: chain m residue 71 THR Chi-restraints excluded: chain o residue 109 GLN Chi-restraints excluded: chain p residue 147 LYS Chi-restraints excluded: chain q residue 57 ASN Chi-restraints excluded: chain r residue 33 LYS Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain G residue 217 PHE Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 242 ARG Chi-restraints excluded: chain J residue 198 ASP Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain i2 residue 78 ASN Chi-restraints excluded: chain t residue 99 HIS Chi-restraints excluded: chain t residue 173 ARG Chi-restraints excluded: chain t residue 252 GLU Chi-restraints excluded: chain t residue 292 SER Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 415 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 773 random chunks: chunk 487 optimal weight: 4.9990 chunk 653 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 565 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 614 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 630 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN f 8 GLN i 167 ASN k 140 ASN k 147 GLN g 97 GLN h 133 GLN j 192 GLN l 7 GLN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 254 GLN L 50 GLN S 23 GLN t 151 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.072767 restraints weight = 297969.930| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.56 r_work: 0.2755 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 71736 Z= 0.224 Angle : 0.492 7.598 96303 Z= 0.260 Chirality : 0.038 0.152 9568 Planarity : 0.004 0.186 11938 Dihedral : 14.865 178.680 12329 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.74 % Allowed : 11.48 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.23 (0.10), residues: 7847 helix: 1.96 (0.08), residues: 3856 sheet: -0.45 (0.27), residues: 378 loop : -0.27 (0.10), residues: 3613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 139 HIS 0.006 0.001 HIS E 221 PHE 0.019 0.001 PHE A 426 TYR 0.019 0.001 TYR m 79 ARG 0.014 0.000 ARG P 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51323.59 seconds wall clock time: 877 minutes 37.28 seconds (52657.28 seconds total)