Starting phenix.real_space_refine on Wed Mar 20 17:22:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p94_17558/03_2024/8p94_17558_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p94_17558/03_2024/8p94_17558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p94_17558/03_2024/8p94_17558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p94_17558/03_2024/8p94_17558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p94_17558/03_2024/8p94_17558_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p94_17558/03_2024/8p94_17558_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 24 5.49 5 Mg 12 5.21 5 S 331 5.16 5 C 32001 2.51 5 N 8601 2.21 5 O 9689 1.98 5 H 49452 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 275": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 313": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 334": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ARG 341": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 181": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 250": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 316": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 328": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B ARG 384": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 394": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 142": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 149": "OD1" <-> "OD2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 216": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ARG 284": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 299": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 149": "OD1" <-> "OD2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ARG 189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 279": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 163": "OE1" <-> "OE2" Residue "G ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "G ASP 40": "OD1" <-> "OD2" Residue "G ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G ARG 145": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 154": "OD1" <-> "OD2" Residue "H ASP 157": "OD1" <-> "OD2" Residue "H ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 179": "OD1" <-> "OD2" Residue "H ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 222": "OD1" <-> "OD2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 276": "OE1" <-> "OE2" Residue "H ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 311": "OD1" <-> "OD2" Residue "H ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 361": "OE1" <-> "OE2" Residue "H ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I ASP 27": "OD1" <-> "OD2" Residue "I ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 4": "OD1" <-> "OD2" Residue "J PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 72": "OE1" <-> "OE2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 154": "OD1" <-> "OD2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 195": "OE1" <-> "OE2" Residue "J ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 211": "OD1" <-> "OD2" Residue "J ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 276": "OE1" <-> "OE2" Residue "J ASP 286": "OD1" <-> "OD2" Residue "J ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 292": "OD1" <-> "OD2" Residue "J ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 316": "OE1" <-> "OE2" Residue "J ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 363": "OD1" <-> "OD2" Residue "J ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 4": "OD1" <-> "OD2" Residue "K ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 51": "OD1" <-> "OD2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 184": "OD1" <-> "OD2" Residue "K GLU 195": "OE1" <-> "OE2" Residue "K ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 224": "OE1" <-> "OE2" Residue "K TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 292": "OD1" <-> "OD2" Residue "K ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 316": "OE1" <-> "OE2" Residue "K ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 25": "OD1" <-> "OD2" Residue "N ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 72": "OE1" <-> "OE2" Residue "N ASP 81": "OD1" <-> "OD2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 179": "OD1" <-> "OD2" Residue "N ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 226": "OE1" <-> "OE2" Residue "N GLU 237": "OE1" <-> "OE2" Residue "N GLU 241": "OE1" <-> "OE2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 288": "OD1" <-> "OD2" Residue "N ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 292": "OD1" <-> "OD2" Residue "N ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 334": "OE1" <-> "OE2" Residue "N ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ASP 25": "OD1" <-> "OD2" Residue "O ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ASP 81": "OD1" <-> "OD2" Residue "O GLU 93": "OE1" <-> "OE2" Residue "O ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 100": "OE1" <-> "OE2" Residue "O ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 241": "OE1" <-> "OE2" Residue "O ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ASP 288": "OD1" <-> "OD2" Residue "O ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 184": "OD1" <-> "OD2" Residue "P GLU 195": "OE1" <-> "OE2" Residue "P ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 226": "OE1" <-> "OE2" Residue "P GLU 241": "OE1" <-> "OE2" Residue "P ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 286": "OD1" <-> "OD2" Residue "P ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 361": "OE1" <-> "OE2" Residue "P ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 51": "OD1" <-> "OD2" Residue "Q ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 72": "OE1" <-> "OE2" Residue "Q GLU 83": "OE1" <-> "OE2" Residue "Q GLU 93": "OE1" <-> "OE2" Residue "Q ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "Q ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 214": "OE1" <-> "OE2" Residue "Q GLU 237": "OE1" <-> "OE2" Residue "Q ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 361": "OE1" <-> "OE2" Residue "Q GLU 364": "OE1" <-> "OE2" Residue "Q ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 11": "OD1" <-> "OD2" Residue "R PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 80": "OD1" <-> "OD2" Residue "R ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 184": "OD1" <-> "OD2" Residue "R ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 205": "OE1" <-> "OE2" Residue "R ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 211": "OD1" <-> "OD2" Residue "R GLU 224": "OE1" <-> "OE2" Residue "R ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 286": "OD1" <-> "OD2" Residue "R ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 51": "OD1" <-> "OD2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 80": "OD1" <-> "OD2" Residue "S ASP 81": "OD1" <-> "OD2" Residue "S ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 167": "OE1" <-> "OE2" Residue "S ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 205": "OE1" <-> "OE2" Residue "S ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 224": "OE1" <-> "OE2" Residue "S ASP 244": "OD1" <-> "OD2" Residue "S ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 270": "OE1" <-> "OE2" Residue "S GLU 276": "OE1" <-> "OE2" Residue "S ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 311": "OD1" <-> "OD2" Residue "S ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 259": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 282": "OE1" <-> "OE2" Residue "V ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ASP 30": "OD1" <-> "OD2" Residue "V ASP 38": "OD1" <-> "OD2" Residue "V ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ASP 52": "OD1" <-> "OD2" Residue "V ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 99": "OE1" <-> "OE2" Residue "V ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 123": "OD1" <-> "OD2" Residue "V PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 198": "OE1" <-> "OE2" Residue "V GLU 201": "OE1" <-> "OE2" Residue "V ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "W PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 72": "OE1" <-> "OE2" Residue "W ASP 80": "OD1" <-> "OD2" Residue "W ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 253": "OE1" <-> "OE2" Residue "W ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 288": "OD1" <-> "OD2" Residue "W ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 361": "OE1" <-> "OE2" Residue "W ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 100110 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6577 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 26, 'TRANS': 387} Chain: "B" Number of atoms: 6336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6336 Classifications: {'peptide': 394} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain: "C" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5594 Classifications: {'peptide': 363} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 4817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4817 Classifications: {'peptide': 300} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain: "E" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2887 Classifications: {'peptide': 178} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 164} Chain: "F" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2781 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain: "G" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2356 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 146} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 5718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5718 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1497 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "J" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5772 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "K" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5762 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5772 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "O" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5772 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "P" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5772 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "Q" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5772 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "R" Number of atoms: 5767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5767 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5772 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "U" Number of atoms: 4336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4336 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "V" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4220 Classifications: {'peptide': 270} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 260} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5728 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "b" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "c" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "d" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "h" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "i" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "j" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "k" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "l" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "m" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 79 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 32.44, per 1000 atoms: 0.32 Number of scatterers: 100110 At special positions: 0 Unit cell: (136.576, 220.869, 320.1, 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 331 16.00 P 24 15.00 Mg 12 11.99 O 9689 8.00 N 8601 7.00 C 32001 6.00 H 49452 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.54 Conformation dependent library (CDL) restraints added in 8.5 seconds 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH a 4 " pdb=" CB DTH b 4 " pdb=" CB DTH c 4 " pdb=" CB DTH d 4 " pdb=" CB DTH h 4 " pdb=" CB DTH i 4 " pdb=" CB DTH j 4 " pdb=" CB DTH k 4 " pdb=" CB DTH l 4 " pdb=" CB DTH m 4 " Number of C-beta restraints generated: 11898 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: 266 helices and 63 sheets defined 49.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 28.75 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.563A pdb=" N ARG A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 4.401A pdb=" N ASP A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N PHE A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 63 through 70 removed outlier: 3.727A pdb=" N ILE A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix No H-bonds generated for 'chain 'A' and resid 63 through 70' Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.017A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 109' Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.526A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 4.034A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 157' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 219 through 231 removed outlier: 3.646A pdb=" N ALA A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 272 through 285 removed outlier: 4.858A pdb=" N PHE A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 4.864A pdb=" N PHE A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.571A pdb=" N CYS A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 309 through 319 removed outlier: 4.461A pdb=" N ARG A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.692A pdb=" N LYS A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 318 " --> pdb=" O PRO A 314 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 319' Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.621A pdb=" N MET A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 330 through 355 Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.770A pdb=" N SER A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 removed outlier: 4.016A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.423A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N HIS A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 410' Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.960A pdb=" N ARG B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.900A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 206 through 220 removed outlier: 3.803A pdb=" N PHE B 210 " --> pdb=" O HIS B 206 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 255 through 268 removed outlier: 4.770A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Proline residue: B 262 - end of helix removed outlier: 5.229A pdb=" N LEU B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 266 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.605A pdb=" N ALA B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 4.530A pdb=" N SER B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 301 " --> pdb=" O PHE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.665A pdb=" N MET B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 310' Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.723A pdb=" N LEU B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 341' Processing helix chain 'B' and resid 349 through 366 removed outlier: 4.145A pdb=" N MET B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.953A pdb=" N TRP B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.657A pdb=" N LYS B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 390' Processing helix chain 'C' and resid 297 through 308 removed outlier: 4.057A pdb=" N LYS C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 removed outlier: 4.533A pdb=" N LYS C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 25 removed outlier: 3.684A pdb=" N GLU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 25 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 removed outlier: 3.598A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 68 " --> pdb=" O TYR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 105 through 116 removed outlier: 4.472A pdb=" N ILE D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 134 removed outlier: 4.253A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 193 removed outlier: 3.875A pdb=" N VAL D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS D 186 " --> pdb=" O MET D 182 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU D 187 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N HIS D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.978A pdb=" N ASN D 233 " --> pdb=" O PRO D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 282 removed outlier: 3.706A pdb=" N THR D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ARG D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 265 " --> pdb=" O TYR D 261 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Proline residue: D 282 - end of helix Processing helix chain 'E' and resid 40 through 50 removed outlier: 4.757A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 removed outlier: 3.993A pdb=" N PHE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS E 56 " --> pdb=" O ASN E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 51 through 56' Processing helix chain 'E' and resid 62 through 83 removed outlier: 3.643A pdb=" N ARG E 66 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 102 removed outlier: 3.989A pdb=" N LYS E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 5.215A pdb=" N ALA E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 removed outlier: 3.965A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 165 removed outlier: 3.515A pdb=" N CYS E 162 " --> pdb=" O LYS E 158 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE E 163 " --> pdb=" O TRP E 159 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL E 164 " --> pdb=" O TRP E 160 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS E 165 " --> pdb=" O THR E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 21 removed outlier: 4.394A pdb=" N ARG F 6 " --> pdb=" O THR F 2 " (cutoff:3.500A) Proline residue: F 7 - end of helix removed outlier: 3.695A pdb=" N ALA F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 43 through 48 removed outlier: 4.479A pdb=" N LEU F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU F 48 " --> pdb=" O LYS F 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 48' Processing helix chain 'F' and resid 80 through 102 removed outlier: 4.216A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU F 99 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN F 100 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 126 removed outlier: 3.737A pdb=" N THR F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 168 removed outlier: 5.119A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE F 168 " --> pdb=" O PHE F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 removed outlier: 4.625A pdb=" N ARG G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 8 through 13' Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.497A pdb=" N PHE G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 34 Processing helix chain 'G' and resid 40 through 51 Processing helix chain 'G' and resid 52 through 63 removed outlier: 3.652A pdb=" N ALA G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 88 removed outlier: 3.943A pdb=" N ASN G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE G 88 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 100 removed outlier: 4.272A pdb=" N LEU G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 removed outlier: 3.898A pdb=" N LYS G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU G 117 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 122 through 138 removed outlier: 3.636A pdb=" N VAL G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN G 129 " --> pdb=" O ALA G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 149 removed outlier: 3.874A pdb=" N ILE G 143 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 149 " --> pdb=" O ARG G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 62 removed outlier: 3.643A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 91 removed outlier: 3.767A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 102 removed outlier: 4.595A pdb=" N HIS H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Proline residue: H 102 - end of helix No H-bonds generated for 'chain 'H' and resid 97 through 102' Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.517A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 146 removed outlier: 3.867A pdb=" N LEU H 140 " --> pdb=" O ILE H 136 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 197 removed outlier: 4.485A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY H 197 " --> pdb=" O LEU H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 216 removed outlier: 3.890A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 261 removed outlier: 3.919A pdb=" N ARG H 256 " --> pdb=" O ASN H 252 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Proline residue: H 258 - end of helix removed outlier: 4.534A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 252 through 261' Processing helix chain 'H' and resid 263 through 268 removed outlier: 4.730A pdb=" N LEU H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY H 268 " --> pdb=" O PRO H 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 263 through 268' Processing helix chain 'H' and resid 273 through 286 removed outlier: 3.517A pdb=" N CYS H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP H 286 " --> pdb=" O ILE H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 297 removed outlier: 4.332A pdb=" N LYS H 291 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.511A pdb=" N MET H 305 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR H 306 " --> pdb=" O GLY H 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 301 through 306' Processing helix chain 'H' and resid 308 through 322 Proline residue: H 322 - end of helix Processing helix chain 'H' and resid 334 through 349 removed outlier: 3.917A pdb=" N SER H 338 " --> pdb=" O GLU H 334 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL H 339 " --> pdb=" O ARG H 335 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TRP H 340 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU H 349 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 356 removed outlier: 4.254A pdb=" N GLN H 354 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET H 355 " --> pdb=" O THR H 351 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TRP H 356 " --> pdb=" O PHE H 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 356' Processing helix chain 'H' and resid 358 through 366 removed outlier: 3.735A pdb=" N SER H 365 " --> pdb=" O GLU H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 374 removed outlier: 4.639A pdb=" N HIS H 371 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.545A pdb=" N GLN J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 91 Processing helix chain 'J' and resid 97 through 102 removed outlier: 4.423A pdb=" N HIS J 101 " --> pdb=" O ALA J 97 " (cutoff:3.500A) Proline residue: J 102 - end of helix No H-bonds generated for 'chain 'J' and resid 97 through 102' Processing helix chain 'J' and resid 112 through 126 removed outlier: 4.043A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 146 removed outlier: 3.685A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY J 146 " --> pdb=" O LEU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 197 removed outlier: 3.535A pdb=" N LYS J 191 " --> pdb=" O ASP J 187 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR J 194 " --> pdb=" O MET J 190 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY J 197 " --> pdb=" O LEU J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 216 removed outlier: 4.048A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 233 removed outlier: 4.233A pdb=" N ALA J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 261 removed outlier: 3.629A pdb=" N ARG J 256 " --> pdb=" O ASN J 252 " (cutoff:3.500A) Proline residue: J 258 - end of helix removed outlier: 4.970A pdb=" N LEU J 261 " --> pdb=" O CYS J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 268 removed outlier: 4.724A pdb=" N LEU J 267 " --> pdb=" O GLN J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 286 removed outlier: 4.251A pdb=" N CYS J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP J 286 " --> pdb=" O ILE J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 297 removed outlier: 5.052A pdb=" N LYS J 291 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP J 292 " --> pdb=" O ASP J 288 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR J 297 " --> pdb=" O LEU J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.211A pdb=" N MET J 305 " --> pdb=" O GLY J 301 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR J 306 " --> pdb=" O GLY J 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 301 through 306' Processing helix chain 'J' and resid 308 through 322 Proline residue: J 322 - end of helix Processing helix chain 'J' and resid 334 through 349 removed outlier: 3.672A pdb=" N SER J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL J 339 " --> pdb=" O ARG J 335 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP J 340 " --> pdb=" O LYS J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 356 removed outlier: 4.662A pdb=" N GLN J 354 " --> pdb=" O SER J 350 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N MET J 355 " --> pdb=" O THR J 351 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP J 356 " --> pdb=" O PHE J 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 350 through 356' Processing helix chain 'J' and resid 358 through 366 Processing helix chain 'J' and resid 367 through 374 removed outlier: 5.243A pdb=" N HIS J 371 " --> pdb=" O PRO J 367 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 62 Processing helix chain 'K' and resid 78 through 91 removed outlier: 4.099A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 102 removed outlier: 4.879A pdb=" N HIS K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Proline residue: K 102 - end of helix No H-bonds generated for 'chain 'K' and resid 97 through 102' Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.947A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 181 through 197 removed outlier: 4.083A pdb=" N THR K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 216 removed outlier: 4.029A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 252 through 261 Proline residue: K 258 - end of helix removed outlier: 5.122A pdb=" N LEU K 261 " --> pdb=" O CYS K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 268 removed outlier: 4.820A pdb=" N LEU K 267 " --> pdb=" O GLN K 263 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY K 268 " --> pdb=" O PRO K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 263 through 268' Processing helix chain 'K' and resid 273 through 286 removed outlier: 3.911A pdb=" N CYS K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASP K 286 " --> pdb=" O ILE K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 297 removed outlier: 5.470A pdb=" N LYS K 291 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR K 297 " --> pdb=" O LEU K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 306 removed outlier: 4.400A pdb=" N MET K 305 " --> pdb=" O GLY K 301 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR K 306 " --> pdb=" O GLY K 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 301 through 306' Processing helix chain 'K' and resid 308 through 322 removed outlier: 3.967A pdb=" N ARG K 312 " --> pdb=" O GLY K 308 " (cutoff:3.500A) Proline residue: K 322 - end of helix Processing helix chain 'K' and resid 334 through 349 removed outlier: 3.517A pdb=" N SER K 338 " --> pdb=" O GLU K 334 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL K 339 " --> pdb=" O ARG K 335 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP K 340 " --> pdb=" O LYS K 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU K 349 " --> pdb=" O ILE K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 356 removed outlier: 4.792A pdb=" N GLN K 354 " --> pdb=" O SER K 350 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET K 355 " --> pdb=" O THR K 351 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP K 356 " --> pdb=" O PHE K 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 350 through 356' Processing helix chain 'K' and resid 358 through 366 removed outlier: 3.573A pdb=" N SER K 365 " --> pdb=" O GLU K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 374 removed outlier: 5.085A pdb=" N HIS K 371 " --> pdb=" O PRO K 367 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 62 Processing helix chain 'N' and resid 78 through 91 Processing helix chain 'N' and resid 97 through 102 removed outlier: 4.623A pdb=" N HIS N 101 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Proline residue: N 102 - end of helix No H-bonds generated for 'chain 'N' and resid 97 through 102' Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.855A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 146 removed outlier: 3.608A pdb=" N GLY N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 197 removed outlier: 4.147A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 216 removed outlier: 4.117A pdb=" N GLU N 207 " --> pdb=" O THR N 203 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE N 208 " --> pdb=" O ALA N 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 233 Processing helix chain 'N' and resid 252 through 261 removed outlier: 3.594A pdb=" N ARG N 256 " --> pdb=" O ASN N 252 " (cutoff:3.500A) Proline residue: N 258 - end of helix removed outlier: 4.706A pdb=" N LEU N 261 " --> pdb=" O CYS N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 263 through 268 removed outlier: 4.836A pdb=" N LEU N 267 " --> pdb=" O GLN N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 286 removed outlier: 3.821A pdb=" N CYS N 285 " --> pdb=" O SER N 281 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP N 286 " --> pdb=" O ILE N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 297 removed outlier: 5.213A pdb=" N LYS N 291 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ASP N 292 " --> pdb=" O ASP N 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR N 297 " --> pdb=" O LEU N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 306 removed outlier: 4.567A pdb=" N MET N 305 " --> pdb=" O GLY N 301 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR N 306 " --> pdb=" O GLY N 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 301 through 306' Processing helix chain 'N' and resid 308 through 322 Proline residue: N 322 - end of helix Processing helix chain 'N' and resid 334 through 349 removed outlier: 4.513A pdb=" N VAL N 339 " --> pdb=" O ARG N 335 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TRP N 340 " --> pdb=" O LYS N 336 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU N 349 " --> pdb=" O ILE N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 356 removed outlier: 6.052A pdb=" N GLN N 354 " --> pdb=" O SER N 350 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N MET N 355 " --> pdb=" O THR N 351 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP N 356 " --> pdb=" O PHE N 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 350 through 356' Processing helix chain 'N' and resid 358 through 366 Processing helix chain 'N' and resid 367 through 374 removed outlier: 5.288A pdb=" N HIS N 371 " --> pdb=" O PRO N 367 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 Processing helix chain 'O' and resid 78 through 91 removed outlier: 3.624A pdb=" N MET O 82 " --> pdb=" O ASN O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 102 removed outlier: 4.562A pdb=" N HIS O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) Proline residue: O 102 - end of helix No H-bonds generated for 'chain 'O' and resid 97 through 102' Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.937A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 146 Processing helix chain 'O' and resid 181 through 197 removed outlier: 3.923A pdb=" N THR O 194 " --> pdb=" O MET O 190 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 216 removed outlier: 3.615A pdb=" N ILE O 208 " --> pdb=" O ALA O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 233 Processing helix chain 'O' and resid 252 through 261 removed outlier: 3.586A pdb=" N ARG O 256 " --> pdb=" O ASN O 252 " (cutoff:3.500A) Proline residue: O 258 - end of helix removed outlier: 4.765A pdb=" N LEU O 261 " --> pdb=" O CYS O 257 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 268 removed outlier: 4.721A pdb=" N LEU O 267 " --> pdb=" O GLN O 263 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY O 268 " --> pdb=" O PRO O 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 263 through 268' Processing helix chain 'O' and resid 273 through 286 removed outlier: 3.677A pdb=" N CYS O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP O 286 " --> pdb=" O ILE O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 297 removed outlier: 5.123A pdb=" N LYS O 291 " --> pdb=" O VAL O 287 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP O 292 " --> pdb=" O ASP O 288 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA O 295 " --> pdb=" O LYS O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 301 through 306 removed outlier: 4.816A pdb=" N MET O 305 " --> pdb=" O GLY O 301 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR O 306 " --> pdb=" O GLY O 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 301 through 306' Processing helix chain 'O' and resid 308 through 322 removed outlier: 3.765A pdb=" N ARG O 312 " --> pdb=" O GLY O 308 " (cutoff:3.500A) Proline residue: O 322 - end of helix Processing helix chain 'O' and resid 334 through 349 removed outlier: 3.719A pdb=" N SER O 338 " --> pdb=" O GLU O 334 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL O 339 " --> pdb=" O ARG O 335 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TRP O 340 " --> pdb=" O LYS O 336 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY O 343 " --> pdb=" O VAL O 339 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 356 removed outlier: 5.322A pdb=" N GLN O 354 " --> pdb=" O SER O 350 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N MET O 355 " --> pdb=" O THR O 351 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP O 356 " --> pdb=" O PHE O 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 350 through 356' Processing helix chain 'O' and resid 358 through 366 Processing helix chain 'O' and resid 367 through 374 removed outlier: 5.362A pdb=" N HIS O 371 " --> pdb=" O PRO O 367 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG O 372 " --> pdb=" O SER O 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 62 Processing helix chain 'P' and resid 78 through 91 Processing helix chain 'P' and resid 97 through 102 removed outlier: 4.298A pdb=" N HIS P 101 " --> pdb=" O ALA P 97 " (cutoff:3.500A) Proline residue: P 102 - end of helix No H-bonds generated for 'chain 'P' and resid 97 through 102' Processing helix chain 'P' and resid 112 through 126 removed outlier: 4.015A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 146 Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.983A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG P 196 " --> pdb=" O ILE P 192 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY P 197 " --> pdb=" O LEU P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 216 removed outlier: 4.310A pdb=" N GLU P 207 " --> pdb=" O THR P 203 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 233 Processing helix chain 'P' and resid 252 through 261 removed outlier: 3.579A pdb=" N ARG P 256 " --> pdb=" O ASN P 252 " (cutoff:3.500A) Proline residue: P 258 - end of helix removed outlier: 4.703A pdb=" N LEU P 261 " --> pdb=" O CYS P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 268 removed outlier: 5.159A pdb=" N LEU P 267 " --> pdb=" O GLN P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 286 removed outlier: 3.785A pdb=" N CYS P 285 " --> pdb=" O SER P 281 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP P 286 " --> pdb=" O ILE P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 297 removed outlier: 4.973A pdb=" N LYS P 291 " --> pdb=" O VAL P 287 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASP P 292 " --> pdb=" O ASP P 288 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN P 296 " --> pdb=" O ASP P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 306 removed outlier: 4.449A pdb=" N MET P 305 " --> pdb=" O GLY P 301 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR P 306 " --> pdb=" O GLY P 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 301 through 306' Processing helix chain 'P' and resid 308 through 322 removed outlier: 3.928A pdb=" N ARG P 312 " --> pdb=" O GLY P 308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA P 319 " --> pdb=" O LYS P 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) Proline residue: P 322 - end of helix Processing helix chain 'P' and resid 334 through 349 removed outlier: 4.845A pdb=" N VAL P 339 " --> pdb=" O ARG P 335 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP P 340 " --> pdb=" O LYS P 336 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU P 349 " --> pdb=" O ILE P 345 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 356 removed outlier: 4.791A pdb=" N GLN P 354 " --> pdb=" O SER P 350 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET P 355 " --> pdb=" O THR P 351 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP P 356 " --> pdb=" O PHE P 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 350 through 356' Processing helix chain 'P' and resid 358 through 366 removed outlier: 3.511A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER P 365 " --> pdb=" O GLU P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 374 removed outlier: 5.039A pdb=" N HIS P 371 " --> pdb=" O PRO P 367 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 62 Processing helix chain 'Q' and resid 78 through 91 Processing helix chain 'Q' and resid 97 through 102 removed outlier: 4.657A pdb=" N HIS Q 101 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Proline residue: Q 102 - end of helix No H-bonds generated for 'chain 'Q' and resid 97 through 102' Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.965A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 146 removed outlier: 3.555A pdb=" N GLY Q 146 " --> pdb=" O LEU Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 197 removed outlier: 4.055A pdb=" N THR Q 194 " --> pdb=" O MET Q 190 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG Q 196 " --> pdb=" O ILE Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 216 removed outlier: 4.022A pdb=" N GLU Q 207 " --> pdb=" O THR Q 203 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE Q 208 " --> pdb=" O ALA Q 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 233 Processing helix chain 'Q' and resid 252 through 261 removed outlier: 3.633A pdb=" N ARG Q 256 " --> pdb=" O ASN Q 252 " (cutoff:3.500A) Proline residue: Q 258 - end of helix removed outlier: 4.611A pdb=" N LEU Q 261 " --> pdb=" O CYS Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.731A pdb=" N LEU Q 267 " --> pdb=" O GLN Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 286 removed outlier: 3.880A pdb=" N CYS Q 285 " --> pdb=" O SER Q 281 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP Q 286 " --> pdb=" O ILE Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 287 through 297 removed outlier: 4.380A pdb=" N LYS Q 291 " --> pdb=" O VAL Q 287 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 306 removed outlier: 4.383A pdb=" N MET Q 305 " --> pdb=" O GLY Q 301 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR Q 306 " --> pdb=" O GLY Q 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 301 through 306' Processing helix chain 'Q' and resid 308 through 322 removed outlier: 3.662A pdb=" N ARG Q 312 " --> pdb=" O GLY Q 308 " (cutoff:3.500A) Proline residue: Q 322 - end of helix Processing helix chain 'Q' and resid 334 through 349 removed outlier: 5.254A pdb=" N SER Q 338 " --> pdb=" O GLU Q 334 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL Q 339 " --> pdb=" O ARG Q 335 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP Q 340 " --> pdb=" O LYS Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 350 through 356 removed outlier: 5.606A pdb=" N GLN Q 354 " --> pdb=" O SER Q 350 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N MET Q 355 " --> pdb=" O THR Q 351 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP Q 356 " --> pdb=" O PHE Q 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 350 through 356' Processing helix chain 'Q' and resid 358 through 366 Processing helix chain 'Q' and resid 367 through 374 removed outlier: 4.874A pdb=" N HIS Q 371 " --> pdb=" O PRO Q 367 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG Q 372 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 62 Processing helix chain 'R' and resid 78 through 91 removed outlier: 3.849A pdb=" N LYS R 84 " --> pdb=" O ASP R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 102 removed outlier: 4.619A pdb=" N HIS R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Proline residue: R 102 - end of helix No H-bonds generated for 'chain 'R' and resid 97 through 102' Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.884A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 146 Processing helix chain 'R' and resid 181 through 197 removed outlier: 4.131A pdb=" N THR R 194 " --> pdb=" O MET R 190 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 216 removed outlier: 3.611A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 215 " --> pdb=" O ASP R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 233 Processing helix chain 'R' and resid 252 through 261 removed outlier: 3.772A pdb=" N ARG R 256 " --> pdb=" O ASN R 252 " (cutoff:3.500A) Proline residue: R 258 - end of helix removed outlier: 4.623A pdb=" N LEU R 261 " --> pdb=" O CYS R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 268 removed outlier: 4.631A pdb=" N LEU R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 286 removed outlier: 4.000A pdb=" N CYS R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP R 286 " --> pdb=" O ILE R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 297 removed outlier: 4.608A pdb=" N LYS R 291 " --> pdb=" O VAL R 287 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP R 292 " --> pdb=" O ASP R 288 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN R 296 " --> pdb=" O ASP R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 306 removed outlier: 4.306A pdb=" N MET R 305 " --> pdb=" O GLY R 301 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TYR R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 301 through 306' Processing helix chain 'R' and resid 308 through 322 removed outlier: 3.539A pdb=" N ARG R 312 " --> pdb=" O GLY R 308 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 334 through 349 removed outlier: 3.736A pdb=" N SER R 338 " --> pdb=" O GLU R 334 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL R 339 " --> pdb=" O ARG R 335 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TRP R 340 " --> pdb=" O LYS R 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY R 343 " --> pdb=" O VAL R 339 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 356 removed outlier: 5.506A pdb=" N GLN R 354 " --> pdb=" O SER R 350 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N MET R 355 " --> pdb=" O THR R 351 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP R 356 " --> pdb=" O PHE R 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 350 through 356' Processing helix chain 'R' and resid 358 through 366 Processing helix chain 'R' and resid 367 through 374 removed outlier: 5.371A pdb=" N HIS R 371 " --> pdb=" O PRO R 367 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 62 Processing helix chain 'S' and resid 78 through 91 removed outlier: 3.707A pdb=" N LYS S 84 " --> pdb=" O ASP S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 102 removed outlier: 4.517A pdb=" N HIS S 101 " --> pdb=" O ALA S 97 " (cutoff:3.500A) Proline residue: S 102 - end of helix No H-bonds generated for 'chain 'S' and resid 97 through 102' Processing helix chain 'S' and resid 112 through 126 removed outlier: 4.316A pdb=" N ARG S 116 " --> pdb=" O PRO S 112 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU S 117 " --> pdb=" O LYS S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 146 Processing helix chain 'S' and resid 181 through 197 removed outlier: 3.886A pdb=" N THR S 194 " --> pdb=" O MET S 190 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU S 195 " --> pdb=" O LYS S 191 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG S 196 " --> pdb=" O ILE S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 202 through 216 removed outlier: 3.709A pdb=" N GLU S 207 " --> pdb=" O THR S 203 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE S 208 " --> pdb=" O ALA S 204 " (cutoff:3.500A) Processing helix chain 'S' and resid 222 through 233 Processing helix chain 'S' and resid 252 through 261 Proline residue: S 258 - end of helix removed outlier: 4.874A pdb=" N LEU S 261 " --> pdb=" O CYS S 257 " (cutoff:3.500A) Processing helix chain 'S' and resid 263 through 268 removed outlier: 4.800A pdb=" N LEU S 267 " --> pdb=" O GLN S 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY S 268 " --> pdb=" O PRO S 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 263 through 268' Processing helix chain 'S' and resid 273 through 286 removed outlier: 4.156A pdb=" N CYS S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP S 286 " --> pdb=" O ILE S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 4.782A pdb=" N LYS S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 306 removed outlier: 4.737A pdb=" N MET S 305 " --> pdb=" O GLY S 301 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR S 306 " --> pdb=" O GLY S 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 301 through 306' Processing helix chain 'S' and resid 308 through 322 removed outlier: 3.700A pdb=" N ARG S 312 " --> pdb=" O GLY S 308 " (cutoff:3.500A) Proline residue: S 322 - end of helix Processing helix chain 'S' and resid 334 through 349 removed outlier: 3.574A pdb=" N SER S 338 " --> pdb=" O GLU S 334 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL S 339 " --> pdb=" O ARG S 335 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP S 340 " --> pdb=" O LYS S 336 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU S 349 " --> pdb=" O ILE S 345 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 356 removed outlier: 5.190A pdb=" N GLN S 354 " --> pdb=" O SER S 350 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N MET S 355 " --> pdb=" O THR S 351 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP S 356 " --> pdb=" O PHE S 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 350 through 356' Processing helix chain 'S' and resid 358 through 366 Processing helix chain 'S' and resid 367 through 374 removed outlier: 5.059A pdb=" N HIS S 371 " --> pdb=" O PRO S 367 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG S 372 " --> pdb=" O SER S 368 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS S 374 " --> pdb=" O VAL S 370 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 62 removed outlier: 3.550A pdb=" N GLN W 59 " --> pdb=" O GLY W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 91 removed outlier: 3.991A pdb=" N LYS W 84 " --> pdb=" O ASP W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 102 removed outlier: 4.592A pdb=" N HIS W 101 " --> pdb=" O ALA W 97 " (cutoff:3.500A) Proline residue: W 102 - end of helix No H-bonds generated for 'chain 'W' and resid 97 through 102' Processing helix chain 'W' and resid 112 through 126 removed outlier: 3.736A pdb=" N ARG W 116 " --> pdb=" O PRO W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 146 removed outlier: 3.711A pdb=" N LEU W 140 " --> pdb=" O ILE W 136 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER W 141 " --> pdb=" O GLN W 137 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU W 142 " --> pdb=" O ALA W 138 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER W 145 " --> pdb=" O SER W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 181 through 197 removed outlier: 4.181A pdb=" N GLU W 195 " --> pdb=" O LYS W 191 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG W 196 " --> pdb=" O ILE W 192 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY W 197 " --> pdb=" O LEU W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 216 removed outlier: 4.185A pdb=" N GLU W 207 " --> pdb=" O THR W 203 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE W 208 " --> pdb=" O ALA W 204 " (cutoff:3.500A) Processing helix chain 'W' and resid 222 through 233 Processing helix chain 'W' and resid 252 through 261 removed outlier: 3.660A pdb=" N CYS W 257 " --> pdb=" O GLU W 253 " (cutoff:3.500A) Proline residue: W 258 - end of helix removed outlier: 4.742A pdb=" N LEU W 261 " --> pdb=" O CYS W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 263 through 268 removed outlier: 4.568A pdb=" N LEU W 267 " --> pdb=" O GLN W 263 " (cutoff:3.500A) Processing helix chain 'W' and resid 273 through 286 removed outlier: 4.194A pdb=" N CYS W 285 " --> pdb=" O SER W 281 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP W 286 " --> pdb=" O ILE W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 287 through 297 removed outlier: 4.854A pdb=" N LYS W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP W 292 " --> pdb=" O ASP W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 306 removed outlier: 4.324A pdb=" N MET W 305 " --> pdb=" O GLY W 301 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR W 306 " --> pdb=" O GLY W 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 301 through 306' Processing helix chain 'W' and resid 308 through 322 Proline residue: W 322 - end of helix Processing helix chain 'W' and resid 334 through 349 removed outlier: 4.603A pdb=" N VAL W 339 " --> pdb=" O ARG W 335 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TRP W 340 " --> pdb=" O LYS W 336 " (cutoff:3.500A) Processing helix chain 'W' and resid 350 through 356 removed outlier: 5.938A pdb=" N GLN W 354 " --> pdb=" O SER W 350 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N MET W 355 " --> pdb=" O THR W 351 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TRP W 356 " --> pdb=" O PHE W 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 350 through 356' Processing helix chain 'W' and resid 358 through 366 Processing helix chain 'W' and resid 367 through 374 removed outlier: 4.669A pdb=" N HIS W 371 " --> pdb=" O PRO W 367 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG W 372 " --> pdb=" O SER W 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 40 removed outlier: 3.938A pdb=" N TRP I 39 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 77 removed outlier: 3.665A pdb=" N LEU I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 116 removed outlier: 4.004A pdb=" N VAL I 115 " --> pdb=" O HIS I 111 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP I 116 " --> pdb=" O CYS I 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 111 through 116' Processing helix chain 'U' and resid 9 through 24 removed outlier: 3.655A pdb=" N ALA U 24 " --> pdb=" O PHE U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 41 removed outlier: 3.653A pdb=" N ASP U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 50 Processing helix chain 'U' and resid 51 through 62 removed outlier: 3.761A pdb=" N ALA U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE U 62 " --> pdb=" O ASN U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 116 through 136 removed outlier: 4.694A pdb=" N TRP U 120 " --> pdb=" O GLY U 116 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA U 127 " --> pdb=" O SER U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 250 Processing helix chain 'U' and resid 253 through 259 removed outlier: 3.555A pdb=" N LEU U 258 " --> pdb=" O THR U 254 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG U 259 " --> pdb=" O PHE U 255 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 286 removed outlier: 4.409A pdb=" N TYR U 277 " --> pdb=" O LYS U 273 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS U 278 " --> pdb=" O ILE U 274 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE U 279 " --> pdb=" O LEU U 275 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY U 280 " --> pdb=" O SER U 276 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LYS U 281 " --> pdb=" O TYR U 277 " (cutoff:3.500A) Processing helix chain 'V' and resid 1 through 16 removed outlier: 3.649A pdb=" N MET V 13 " --> pdb=" O ALA V 9 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG V 14 " --> pdb=" O LEU V 10 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG V 15 " --> pdb=" O ASP V 11 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU V 16 " --> pdb=" O LEU V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 33 removed outlier: 4.343A pdb=" N ILE V 21 " --> pdb=" O PRO V 17 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU V 22 " --> pdb=" O PRO V 18 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS V 23 " --> pdb=" O GLN V 19 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER V 26 " --> pdb=" O GLU V 22 " (cutoff:3.500A) Proline residue: V 33 - end of helix Processing helix chain 'V' and resid 35 through 43 removed outlier: 3.642A pdb=" N LEU V 39 " --> pdb=" O LEU V 35 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU V 40 " --> pdb=" O CYS V 36 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER V 41 " --> pdb=" O GLU V 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 112 removed outlier: 3.702A pdb=" N LYS V 95 " --> pdb=" O ALA V 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 245 removed outlier: 4.065A pdb=" N GLU V 218 " --> pdb=" O GLY V 214 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR V 227 " --> pdb=" O LYS V 223 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR V 232 " --> pdb=" O LEU V 228 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR V 236 " --> pdb=" O TYR V 232 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS V 237 " --> pdb=" O PHE V 233 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP V 238 " --> pdb=" O GLY V 234 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL V 240 " --> pdb=" O THR V 236 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG V 244 " --> pdb=" O VAL V 240 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER V 245 " --> pdb=" O ASN V 241 " (cutoff:3.500A) Processing helix chain 'V' and resid 252 through 270 removed outlier: 3.763A pdb=" N ARG V 268 " --> pdb=" O GLU V 264 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.754A pdb=" N TYR A 16 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 113 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N CYS A 12 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= 3, first strand: chain 'A' and resid 164 through 171 removed outlier: 4.544A pdb=" N VAL A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 254 through 261 removed outlier: 3.919A pdb=" N LYS A 265 " --> pdb=" O ASN A 260 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 68 through 72 removed outlier: 6.170A pdb=" N LYS B 19 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 7 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN B 13 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 135 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 154 through 159 Processing sheet with id= 7, first strand: chain 'B' and resid 242 through 245 Processing sheet with id= 8, first strand: chain 'C' and resid 1 through 6 removed outlier: 7.790A pdb=" N GLY C 352 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE C 345 " --> pdb=" O TRP C 357 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN C 344 " --> pdb=" O LEU C 335 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 13 through 16 removed outlier: 5.244A pdb=" N CYS C 13 " --> pdb=" O CYS C 26 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR C 21 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 34 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.771A pdb=" N ARG C 66 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.071A pdb=" N LYS C 110 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.697A pdb=" N SER C 147 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 156 " --> pdb=" O HIS C 151 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL C 155 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 207 through 211 removed outlier: 3.871A pdb=" N GLY C 207 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG C 216 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER C 224 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 248 through 252 removed outlier: 5.954A pdb=" N ASN C 256 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C 278 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 31 through 34 Processing sheet with id= 16, first strand: chain 'D' and resid 32 through 35 Processing sheet with id= 17, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.754A pdb=" N GLN D 197 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 50 through 55 removed outlier: 6.904A pdb=" N GLU F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 8 through 11 removed outlier: 4.068A pdb=" N THR H 106 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 15 through 19 removed outlier: 5.190A pdb=" N GLY H 15 " --> pdb=" O SER H 33 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 149 through 156 removed outlier: 5.459A pdb=" N VAL H 159 " --> pdb=" O GLY H 156 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 237 through 242 removed outlier: 4.560A pdb=" N GLN H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 8 through 11 removed outlier: 3.912A pdb=" N THR J 106 " --> pdb=" O VAL J 10 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.318A pdb=" N GLY J 15 " --> pdb=" O SER J 33 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 149 through 156 removed outlier: 4.269A pdb=" N VAL J 159 " --> pdb=" O GLY J 156 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 237 through 242 removed outlier: 4.687A pdb=" N GLN J 246 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 8 through 11 removed outlier: 4.123A pdb=" N THR K 106 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 15 through 19 removed outlier: 5.056A pdb=" N GLY K 15 " --> pdb=" O SER K 33 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 149 through 156 removed outlier: 5.040A pdb=" N VAL K 159 " --> pdb=" O GLY K 156 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 237 through 242 removed outlier: 4.298A pdb=" N GLN K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 8 through 11 removed outlier: 3.856A pdb=" N THR N 106 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 15 through 19 removed outlier: 4.911A pdb=" N GLY N 15 " --> pdb=" O SER N 33 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'N' and resid 149 through 156 removed outlier: 4.104A pdb=" N VAL N 159 " --> pdb=" O GLY N 156 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 237 through 242 removed outlier: 4.240A pdb=" N GLN N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'O' and resid 8 through 11 removed outlier: 3.883A pdb=" N THR O 106 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'O' and resid 15 through 19 removed outlier: 5.673A pdb=" N GLY O 15 " --> pdb=" O SER O 33 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'O' and resid 149 through 156 removed outlier: 4.360A pdb=" N VAL O 159 " --> pdb=" O GLY O 156 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 237 through 242 removed outlier: 4.395A pdb=" N GLN O 246 " --> pdb=" O LEU O 242 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 8 through 11 removed outlier: 3.943A pdb=" N THR P 106 " --> pdb=" O VAL P 10 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'P' and resid 15 through 19 removed outlier: 5.596A pdb=" N GLY P 15 " --> pdb=" O SER P 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG P 37 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'P' and resid 149 through 156 removed outlier: 4.888A pdb=" N VAL P 159 " --> pdb=" O GLY P 156 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 237 through 242 removed outlier: 4.473A pdb=" N GLN P 246 " --> pdb=" O LEU P 242 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 8 through 11 removed outlier: 4.051A pdb=" N THR Q 106 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA Q 135 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 15 through 19 removed outlier: 5.518A pdb=" N GLY Q 15 " --> pdb=" O SER Q 33 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 149 through 156 removed outlier: 4.547A pdb=" N VAL Q 159 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 237 through 242 removed outlier: 4.274A pdb=" N GLN Q 246 " --> pdb=" O LEU Q 242 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'R' and resid 8 through 11 removed outlier: 3.868A pdb=" N THR R 106 " --> pdb=" O VAL R 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'R' and resid 15 through 19 removed outlier: 5.999A pdb=" N GLY R 15 " --> pdb=" O SER R 33 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R' and resid 149 through 156 Processing sheet with id= 50, first strand: chain 'R' and resid 237 through 242 removed outlier: 4.270A pdb=" N GLN R 246 " --> pdb=" O LEU R 242 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'S' and resid 8 through 11 removed outlier: 3.607A pdb=" N VAL S 10 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR S 106 " --> pdb=" O VAL S 10 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'S' and resid 15 through 19 removed outlier: 6.203A pdb=" N GLY S 15 " --> pdb=" O SER S 33 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'S' and resid 149 through 156 removed outlier: 4.908A pdb=" N VAL S 159 " --> pdb=" O GLY S 156 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'S' and resid 237 through 242 removed outlier: 4.436A pdb=" N GLN S 246 " --> pdb=" O LEU S 242 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'W' and resid 8 through 11 removed outlier: 4.003A pdb=" N THR W 106 " --> pdb=" O VAL W 10 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 15 through 19 removed outlier: 5.238A pdb=" N GLY W 15 " --> pdb=" O SER W 33 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 149 through 156 removed outlier: 3.643A pdb=" N VAL W 159 " --> pdb=" O GLY W 156 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 237 through 242 removed outlier: 4.402A pdb=" N GLN W 246 " --> pdb=" O LEU W 242 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'U' and resid 63 through 66 removed outlier: 3.530A pdb=" N THR U 63 " --> pdb=" O ILE U 76 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 80 through 83 removed outlier: 5.626A pdb=" N GLY U 80 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG U 86 " --> pdb=" O LEU U 82 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER U 85 " --> pdb=" O PHE U 98 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU U 104 " --> pdb=" O ASP U 99 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 139 through 147 removed outlier: 4.912A pdb=" N GLN U 152 " --> pdb=" O ILE U 181 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE U 168 " --> pdb=" O TYR U 199 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR U 180 " --> pdb=" O GLN U 187 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN U 187 " --> pdb=" O THR U 180 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'V' and resid 48 through 53 removed outlier: 4.813A pdb=" N LYS V 48 " --> pdb=" O LEU V 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU V 61 " --> pdb=" O LYS V 48 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP V 52 " --> pdb=" O LYS V 57 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS V 57 " --> pdb=" O ASP V 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'V' and resid 115 through 123 removed outlier: 3.614A pdb=" N PHE V 128 " --> pdb=" O VAL V 156 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY V 146 " --> pdb=" O GLY V 138 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS V 145 " --> pdb=" O GLN V 178 " (cutoff:3.500A) 2185 hydrogen bonds defined for protein. 6489 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: 37.71 Time building geometry restraints manager: 65.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 49339 1.03 - 1.23: 1310 1.23 - 1.43: 20386 1.43 - 1.63: 29628 1.63 - 1.82: 548 Bond restraints: 101211 Sorted by residual: bond pdb=" C4 ADP S 402 " pdb=" C5 ADP S 402 " ideal model delta sigma weight residual 1.490 1.353 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C GLY O 156 " pdb=" O GLY O 156 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.02e-02 9.61e+03 2.87e+01 bond pdb=" CD2 HIS I 49 " pdb=" NE2 HIS I 49 " ideal model delta sigma weight residual 1.374 1.315 0.059 1.10e-02 8.26e+03 2.86e+01 bond pdb=" C5 ADP S 402 " pdb=" C6 ADP S 402 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" ND1 HIS P 101 " pdb=" CE1 HIS P 101 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.67e+01 ... (remaining 101206 not shown) Histogram of bond angle deviations from ideal: 96.94 - 105.05: 1482 105.05 - 113.15: 118397 113.15 - 121.26: 42468 121.26 - 129.37: 20109 129.37 - 137.47: 358 Bond angle restraints: 182814 Sorted by residual: angle pdb=" N ILE V 231 " pdb=" CA ILE V 231 " pdb=" C ILE V 231 " ideal model delta sigma weight residual 111.90 101.85 10.05 8.10e-01 1.52e+00 1.54e+02 angle pdb=" N ILE V 239 " pdb=" CA ILE V 239 " pdb=" C ILE V 239 " ideal model delta sigma weight residual 110.82 103.54 7.28 9.70e-01 1.06e+00 5.63e+01 angle pdb=" CB HIS I 49 " pdb=" CG HIS I 49 " pdb=" CD2 HIS I 49 " ideal model delta sigma weight residual 131.20 122.29 8.91 1.30e+00 5.92e-01 4.70e+01 angle pdb=" CB HIS P 101 " pdb=" CG HIS P 101 " pdb=" CD2 HIS P 101 " ideal model delta sigma weight residual 131.20 122.61 8.59 1.30e+00 5.92e-01 4.36e+01 angle pdb=" O1B ADP S 402 " pdb=" PB ADP S 402 " pdb=" O2B ADP S 402 " ideal model delta sigma weight residual 119.90 100.10 19.80 3.00e+00 1.11e-01 4.35e+01 ... (remaining 182809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 46199 34.78 - 69.57: 1428 69.57 - 104.35: 98 104.35 - 139.14: 8 139.14 - 173.92: 5 Dihedral angle restraints: 47738 sinusoidal: 26071 harmonic: 21667 Sorted by residual: dihedral pdb=" C5' ADP Q 401 " pdb=" O5' ADP Q 401 " pdb=" PA ADP Q 401 " pdb=" O2A ADP Q 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.92 -173.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP N 401 " pdb=" O3A ADP N 401 " pdb=" PA ADP N 401 " pdb=" PB ADP N 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.18 -168.18 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP R 401 " pdb=" O5' ADP R 401 " pdb=" PA ADP R 401 " pdb=" O2A ADP R 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.73 -163.72 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 47735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 6487 0.069 - 0.137: 1162 0.137 - 0.206: 103 0.206 - 0.275: 6 0.275 - 0.343: 3 Chirality restraints: 7761 Sorted by residual: chirality pdb=" CA LEU V 243 " pdb=" N LEU V 243 " pdb=" C LEU V 243 " pdb=" CB LEU V 243 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C2' ADP S 402 " pdb=" C1' ADP S 402 " pdb=" C3' ADP S 402 " pdb=" O2' ADP S 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.81 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ASP U 201 " pdb=" N ASP U 201 " pdb=" C ASP U 201 " pdb=" CB ASP U 201 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 7758 not shown) Planarity restraints: 15014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 38 " -0.235 9.50e-02 1.11e+02 3.67e-01 2.90e+03 pdb=" NE ARG I 38 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG I 38 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG I 38 " -0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG I 38 " 0.053 2.00e-02 2.50e+03 pdb="HH11 ARG I 38 " 0.347 2.00e-02 2.50e+03 pdb="HH12 ARG I 38 " -0.502 2.00e-02 2.50e+03 pdb="HH21 ARG I 38 " 0.689 2.00e-02 2.50e+03 pdb="HH22 ARG I 38 " -0.550 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN U 93 " 0.230 2.00e-02 2.50e+03 3.95e-01 2.34e+03 pdb=" CD GLN U 93 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN U 93 " -0.217 2.00e-02 2.50e+03 pdb=" NE2 GLN U 93 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN U 93 " -0.641 2.00e-02 2.50e+03 pdb="HE22 GLN U 93 " 0.652 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN I 37 " -0.224 2.00e-02 2.50e+03 2.54e-01 9.71e+02 pdb=" CD GLN I 37 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN I 37 " 0.207 2.00e-02 2.50e+03 pdb=" NE2 GLN I 37 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN I 37 " 0.380 2.00e-02 2.50e+03 pdb="HE22 GLN I 37 " -0.388 2.00e-02 2.50e+03 ... (remaining 15011 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.89: 765 1.89 - 2.57: 97957 2.57 - 3.25: 307633 3.25 - 3.92: 393608 3.92 - 4.60: 630977 Nonbonded interactions: 1430940 Sorted by model distance: nonbonded pdb=" HE1 TYR J 198 " pdb="HG22 ILE J 248 " model vdw 1.218 2.270 nonbonded pdb=" HZ2 LYS F 77 " pdb=" OE2 GLU R 99 " model vdw 1.221 1.850 nonbonded pdb=" HB ILE B 78 " pdb=" HB1 ALA a 7 " model vdw 1.247 2.440 nonbonded pdb=" OE2 GLU F 148 " pdb=" CE1 HIS R 87 " model vdw 1.298 3.150 nonbonded pdb=" HE1 HIS H 173 " pdb=" OG1 THR U 267 " model vdw 1.308 2.450 ... (remaining 1430935 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 'H' and (resid 4 through 146 or (resid 147 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 148 through 152 or (res \ id 153 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 154 through 156 or (resid 157 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 158 through 289 or (resid 290 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 291 through 324 or (resid 325 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 326 through 375)) selection = (chain 'J' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 158 through 1 \ 82 or (resid 183 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 184 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 207 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 211 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 291 through 324 or (resid \ 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 326 through 375)) selection = (chain 'K' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 158 through 1 \ 82 or (resid 183 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 184 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 207 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 211 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 291 through 375)) selection = (chain 'N' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 158 through 1 \ 82 or (resid 183 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 184 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 207 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 211 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 291 through 324 or (resid \ 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 326 through 375)) selection = (chain 'O' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 158 through 1 \ 82 or (resid 183 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 184 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 207 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 211 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 291 through 324 or (resid \ 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 326 through 375)) selection = (chain 'P' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 158 through 1 \ 82 or (resid 183 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 184 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 207 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 211 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 291 through 324 or (resid \ 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 326 through 375)) selection = (chain 'Q' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 158 through 1 \ 82 or (resid 183 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 184 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 207 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 211 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 291 through 324 or (resid \ 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 326 through 375)) selection = (chain 'R' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 182 or (resid 183 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 184 through 2 \ 05 or (resid 206 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 207 through 209 or (resid 210 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 211 through 289 or \ (resid 290 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 291 through 324 or (resid 325 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 326 through 375)) selection = (chain 'S' and (resid 4 through 112 or (resid 113 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 resid 114 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 148 thr \ ough 152 or (resid 153 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 154 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 158 through 1 \ 82 or (resid 183 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 184 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 207 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 211 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 291 through 324 or (resid \ 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 326 through 375)) selection = (chain 'W' and (resid 4 through 112 or (resid 113 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 resid 114 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 158 thr \ ough 182 or (resid 183 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 184 through 205 or (resid 206 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 207 through 2 \ 09 or (resid 210 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 211 through 324 or (resid 325 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 326 through 375)) } ncs_group { reference = (chain 'a' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'b' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'c' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = chain 'd' selection = (chain 'h' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'i' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'j' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'k' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'l' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'm' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or resid 2 or (resid 3 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or nam \ e C or name O or name CB or name SG )) or resid 6 or (resid 7 and (name N or nam \ e CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.120 Extract box with map and model: 20.250 Check model and map are aligned: 1.140 Set scattering table: 0.800 Process input model: 266.740 Find NCS groups from input model: 3.900 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 300.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.006 0.137 51759 Z= 0.379 Angle : 0.901 19.796 70147 Z= 0.569 Chirality : 0.051 0.343 7761 Planarity : 0.006 0.126 8979 Dihedral : 14.679 173.919 19295 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -2.56 (0.09), residues: 6286 helix: -1.63 (0.09), residues: 2415 sheet: -1.49 (0.14), residues: 1266 loop : -1.68 (0.11), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP U 271 HIS 0.011 0.001 HIS U 135 PHE 0.033 0.002 PHE U 140 TYR 0.079 0.002 TYR U 247 ARG 0.008 0.001 ARG V 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 569 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 78 GLN cc_start: 0.7804 (tt0) cc_final: 0.7434 (tt0) REVERT: I 70 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7624 (mmtt) REVERT: I 95 MET cc_start: 0.6986 (mmm) cc_final: 0.6641 (tpp) REVERT: J 313 MET cc_start: 0.7795 (mmm) cc_final: 0.7587 (mmm) REVERT: K 132 MET cc_start: 0.8696 (ppp) cc_final: 0.8432 (ppp) REVERT: K 190 MET cc_start: 0.8731 (mtm) cc_final: 0.8496 (mtm) REVERT: N 44 MET cc_start: 0.8280 (mtm) cc_final: 0.7907 (tpt) REVERT: O 75 ILE cc_start: 0.8527 (mt) cc_final: 0.8282 (mm) REVERT: P 283 MET cc_start: 0.8857 (mmm) cc_final: 0.8533 (mmt) REVERT: Q 82 MET cc_start: 0.9097 (tpt) cc_final: 0.8646 (tpp) REVERT: R 283 MET cc_start: 0.8605 (mmm) cc_final: 0.8342 (mmt) REVERT: S 123 MET cc_start: 0.9326 (mmt) cc_final: 0.9110 (mmt) REVERT: S 211 ASP cc_start: 0.8868 (t0) cc_final: 0.8441 (t0) REVERT: W 374 CYS cc_start: 0.4417 (m) cc_final: 0.3701 (m) outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 1.5785 time to fit residues: 1393.9197 Evaluate side-chains 403 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 6.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 529 optimal weight: 0.9990 chunk 475 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 491 optimal weight: 3.9990 chunk 190 optimal weight: 0.2980 chunk 298 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 569 optimal weight: 40.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS C 14 HIS G 98 GLN H 92 ASN I 37 GLN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 354 GLN ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN V 212 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 51759 Z= 0.297 Angle : 0.621 7.589 70147 Z= 0.316 Chirality : 0.044 0.200 7761 Planarity : 0.004 0.067 8979 Dihedral : 8.090 161.589 7185 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.39 % Allowed : 6.64 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.51 (0.10), residues: 6286 helix: -0.45 (0.10), residues: 2443 sheet: -1.27 (0.14), residues: 1220 loop : -1.24 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 378 HIS 0.007 0.001 HIS R 87 PHE 0.018 0.001 PHE H 375 TYR 0.017 0.001 TYR J 198 ARG 0.011 0.001 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 396 time to evaluate : 6.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 TYR cc_start: 0.7964 (t80) cc_final: 0.7544 (t80) REVERT: K 190 MET cc_start: 0.8798 (mtm) cc_final: 0.8581 (mtm) REVERT: N 12 ASN cc_start: 0.8800 (t0) cc_final: 0.8377 (t0) REVERT: N 44 MET cc_start: 0.8381 (mtm) cc_final: 0.7899 (tpt) REVERT: P 283 MET cc_start: 0.8873 (mmm) cc_final: 0.8556 (mmt) REVERT: R 283 MET cc_start: 0.8583 (mmm) cc_final: 0.8362 (mmt) outliers start: 21 outliers final: 10 residues processed: 406 average time/residue: 1.4083 time to fit residues: 916.1884 Evaluate side-chains 382 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 372 time to evaluate : 6.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 272 CYS Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain U residue 226 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 316 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 473 optimal weight: 3.9990 chunk 387 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 570 optimal weight: 0.2980 chunk 616 optimal weight: 10.0000 chunk 508 optimal weight: 5.9990 chunk 565 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 457 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 GLN O 12 ASN Q 12 ASN Q 252 ASN R 296 ASN U 93 GLN W 87 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 51759 Z= 0.171 Angle : 0.551 6.807 70147 Z= 0.273 Chirality : 0.043 0.172 7761 Planarity : 0.003 0.042 8979 Dihedral : 7.378 158.242 7185 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.39 % Allowed : 7.58 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -0.73 (0.11), residues: 6286 helix: 0.22 (0.11), residues: 2427 sheet: -0.98 (0.14), residues: 1219 loop : -0.74 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 271 HIS 0.007 0.001 HIS U 161 PHE 0.016 0.001 PHE J 375 TYR 0.026 0.001 TYR H 166 ARG 0.006 0.000 ARG U 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 386 time to evaluate : 6.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.1943 (OUTLIER) cc_final: 0.1063 (tpt) REVERT: C 278 MET cc_start: 0.6584 (ppp) cc_final: 0.6279 (ptt) REVERT: H 166 TYR cc_start: 0.7581 (t80) cc_final: 0.7322 (t80) REVERT: H 269 MET cc_start: 0.7228 (mtm) cc_final: 0.6876 (ttp) REVERT: K 132 MET cc_start: 0.8606 (ppp) cc_final: 0.8323 (ppp) REVERT: K 190 MET cc_start: 0.8772 (mtm) cc_final: 0.8530 (mtm) REVERT: N 44 MET cc_start: 0.8389 (mtm) cc_final: 0.7899 (tpt) REVERT: O 360 GLN cc_start: 0.9102 (mp10) cc_final: 0.8834 (mp10) REVERT: P 283 MET cc_start: 0.8782 (mmm) cc_final: 0.8462 (mmt) REVERT: R 283 MET cc_start: 0.8544 (mmm) cc_final: 0.8334 (mmt) REVERT: R 360 GLN cc_start: 0.8745 (pp30) cc_final: 0.8265 (pp30) REVERT: S 211 ASP cc_start: 0.8844 (t0) cc_final: 0.8495 (t0) outliers start: 21 outliers final: 12 residues processed: 396 average time/residue: 1.4103 time to fit residues: 904.4916 Evaluate side-chains 382 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 369 time to evaluate : 6.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain U residue 226 LYS Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 563 optimal weight: 30.0000 chunk 428 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 383 optimal weight: 1.9990 chunk 572 optimal weight: 20.0000 chunk 606 optimal weight: 8.9990 chunk 299 optimal weight: 0.7980 chunk 542 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 294 GLN C 33 HIS S 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 51759 Z= 0.313 Angle : 0.572 7.095 70147 Z= 0.287 Chirality : 0.043 0.211 7761 Planarity : 0.004 0.073 8979 Dihedral : 7.045 137.872 7185 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.48 % Allowed : 8.18 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -0.50 (0.11), residues: 6286 helix: 0.45 (0.11), residues: 2433 sheet: -0.94 (0.14), residues: 1231 loop : -0.61 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 169 HIS 0.005 0.001 HIS U 161 PHE 0.017 0.001 PHE H 375 TYR 0.022 0.001 TYR H 166 ARG 0.008 0.000 ARG V 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 367 time to evaluate : 6.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.6614 (ppp) cc_final: 0.6346 (ptt) REVERT: E 169 MET cc_start: 0.8144 (mmm) cc_final: 0.7910 (mmt) REVERT: K 132 MET cc_start: 0.8657 (ppp) cc_final: 0.8343 (ppp) REVERT: K 153 MET cc_start: 0.8379 (tpp) cc_final: 0.7379 (tpp) REVERT: K 190 MET cc_start: 0.8777 (mtm) cc_final: 0.8572 (mtm) REVERT: N 44 MET cc_start: 0.8431 (mtm) cc_final: 0.7897 (tpt) REVERT: N 355 MET cc_start: 0.8640 (mtm) cc_final: 0.8356 (mtm) REVERT: P 283 MET cc_start: 0.8783 (mmm) cc_final: 0.8457 (mmt) REVERT: R 360 GLN cc_start: 0.8733 (pp30) cc_final: 0.8254 (pp30) REVERT: U 59 MET cc_start: 0.2288 (OUTLIER) cc_final: 0.1544 (tmm) outliers start: 26 outliers final: 20 residues processed: 383 average time/residue: 1.3595 time to fit residues: 834.6281 Evaluate side-chains 383 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 362 time to evaluate : 6.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 190 MET Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 358 SER Chi-restraints excluded: chain U residue 59 MET Chi-restraints excluded: chain U residue 226 LYS Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 504 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 451 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 chunk 517 optimal weight: 1.9990 chunk 418 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 543 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN J 161 HIS O 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 51759 Z= 0.200 Angle : 0.533 6.612 70147 Z= 0.263 Chirality : 0.043 0.166 7761 Planarity : 0.003 0.050 8979 Dihedral : 6.587 121.087 7185 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.50 % Allowed : 8.55 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -0.08 (0.11), residues: 6286 helix: 0.78 (0.11), residues: 2437 sheet: -0.77 (0.15), residues: 1229 loop : -0.32 (0.13), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP U 169 HIS 0.005 0.001 HIS U 161 PHE 0.014 0.001 PHE D 165 TYR 0.014 0.001 TYR D 43 ARG 0.005 0.000 ARG V 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 398 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 371 time to evaluate : 6.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.6605 (ppp) cc_final: 0.6317 (ptt) REVERT: E 169 MET cc_start: 0.8083 (mmm) cc_final: 0.7856 (mmt) REVERT: K 132 MET cc_start: 0.8670 (ppp) cc_final: 0.8315 (ppp) REVERT: K 190 MET cc_start: 0.8787 (mtm) cc_final: 0.8581 (mtm) REVERT: N 12 ASN cc_start: 0.8703 (t0) cc_final: 0.8242 (t0) REVERT: N 44 MET cc_start: 0.8451 (mtm) cc_final: 0.7906 (tpt) REVERT: N 355 MET cc_start: 0.8606 (mtm) cc_final: 0.8309 (mtm) REVERT: O 360 GLN cc_start: 0.9091 (mp10) cc_final: 0.8822 (mp10) REVERT: R 360 GLN cc_start: 0.8682 (pp30) cc_final: 0.8283 (pp30) REVERT: U 59 MET cc_start: 0.2039 (OUTLIER) cc_final: 0.1461 (tmm) outliers start: 27 outliers final: 20 residues processed: 387 average time/residue: 1.4409 time to fit residues: 907.3839 Evaluate side-chains 384 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 363 time to evaluate : 6.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 358 SER Chi-restraints excluded: chain U residue 59 MET Chi-restraints excluded: chain U residue 226 LYS Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 203 optimal weight: 4.9990 chunk 545 optimal weight: 30.0000 chunk 119 optimal weight: 3.9990 chunk 355 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 606 optimal weight: 20.0000 chunk 503 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 129 GLN P 360 GLN P 371 HIS V 270 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 51759 Z= 0.509 Angle : 0.635 8.361 70147 Z= 0.325 Chirality : 0.046 0.166 7761 Planarity : 0.004 0.074 8979 Dihedral : 6.670 135.721 7185 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.75 % Allowed : 8.98 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 6286 helix: 0.63 (0.11), residues: 2438 sheet: -0.90 (0.14), residues: 1240 loop : -0.48 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 169 HIS 0.005 0.001 HIS I 52 PHE 0.018 0.001 PHE D 165 TYR 0.016 0.001 TYR F 8 ARG 0.005 0.001 ARG Q 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 395 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 354 time to evaluate : 6.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.6624 (ppp) cc_final: 0.6406 (ptt) REVERT: K 132 MET cc_start: 0.8715 (ppp) cc_final: 0.8362 (ppp) REVERT: K 153 MET cc_start: 0.8415 (tpp) cc_final: 0.7409 (tpp) REVERT: N 12 ASN cc_start: 0.8759 (t0) cc_final: 0.8298 (t0) REVERT: N 44 MET cc_start: 0.8502 (mtm) cc_final: 0.7943 (tpt) REVERT: N 355 MET cc_start: 0.8777 (mtm) cc_final: 0.8470 (mtm) REVERT: R 360 GLN cc_start: 0.8764 (pp30) cc_final: 0.8265 (pp30) REVERT: U 59 MET cc_start: 0.2047 (OUTLIER) cc_final: 0.1440 (tmm) REVERT: U 226 LYS cc_start: 0.4398 (OUTLIER) cc_final: 0.3414 (mmmt) outliers start: 41 outliers final: 29 residues processed: 379 average time/residue: 1.3701 time to fit residues: 839.6996 Evaluate side-chains 378 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 347 time to evaluate : 6.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 358 SER Chi-restraints excluded: chain U residue 59 MET Chi-restraints excluded: chain U residue 226 LYS Chi-restraints excluded: chain V residue 13 MET Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 584 optimal weight: 40.0000 chunk 68 optimal weight: 0.8980 chunk 345 optimal weight: 2.9990 chunk 443 optimal weight: 1.9990 chunk 343 optimal weight: 2.9990 chunk 510 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 604 optimal weight: 20.0000 chunk 378 optimal weight: 1.9990 chunk 368 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.003 0.035 51759 Z= 0.230 Angle : 0.542 7.212 70147 Z= 0.270 Chirality : 0.043 0.171 7761 Planarity : 0.003 0.043 8979 Dihedral : 6.475 131.658 7185 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.50 % Allowed : 9.40 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: 0.04 (0.11), residues: 6286 helix: 0.89 (0.11), residues: 2434 sheet: -0.76 (0.15), residues: 1231 loop : -0.25 (0.13), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 169 HIS 0.005 0.001 HIS A 192 PHE 0.016 0.001 PHE D 165 TYR 0.014 0.001 TYR D 43 ARG 0.005 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 385 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 358 time to evaluate : 6.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 132 MET cc_start: 0.8711 (ppp) cc_final: 0.8321 (ppp) REVERT: K 153 MET cc_start: 0.8355 (tpp) cc_final: 0.7365 (tpp) REVERT: N 12 ASN cc_start: 0.8700 (t0) cc_final: 0.8212 (t0) REVERT: N 44 MET cc_start: 0.8485 (mtm) cc_final: 0.7934 (tpt) REVERT: N 355 MET cc_start: 0.8726 (mtm) cc_final: 0.8382 (mtm) REVERT: R 360 GLN cc_start: 0.8713 (pp30) cc_final: 0.8172 (pp30) outliers start: 27 outliers final: 24 residues processed: 376 average time/residue: 1.4091 time to fit residues: 865.7440 Evaluate side-chains 380 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 356 time to evaluate : 6.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 358 SER Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 373 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 360 optimal weight: 4.9990 chunk 182 optimal weight: 0.0870 chunk 118 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 475 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 280 ASN ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 51759 Z= 0.231 Angle : 0.532 7.398 70147 Z= 0.263 Chirality : 0.042 0.168 7761 Planarity : 0.003 0.042 8979 Dihedral : 6.202 130.681 7185 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.55 % Allowed : 9.47 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: 0.29 (0.11), residues: 6286 helix: 1.09 (0.11), residues: 2434 sheet: -0.62 (0.15), residues: 1234 loop : -0.09 (0.13), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 169 HIS 0.004 0.001 HIS D 254 PHE 0.017 0.001 PHE D 165 TYR 0.020 0.001 TYR I 84 ARG 0.003 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 361 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 132 MET cc_start: 0.7072 (ppp) cc_final: 0.6778 (ppp) REVERT: H 227 MET cc_start: 0.7492 (mmm) cc_final: 0.7100 (mmm) REVERT: K 132 MET cc_start: 0.8690 (ppp) cc_final: 0.8264 (ppp) REVERT: K 153 MET cc_start: 0.8338 (tpp) cc_final: 0.7395 (tpp) REVERT: N 12 ASN cc_start: 0.8708 (t0) cc_final: 0.8258 (t0) REVERT: N 44 MET cc_start: 0.8466 (mtm) cc_final: 0.7904 (tpt) REVERT: N 355 MET cc_start: 0.8717 (mtm) cc_final: 0.8380 (mtm) REVERT: R 360 GLN cc_start: 0.8692 (pp30) cc_final: 0.8234 (pp30) outliers start: 30 outliers final: 26 residues processed: 381 average time/residue: 1.3974 time to fit residues: 867.5281 Evaluate side-chains 374 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 348 time to evaluate : 6.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 358 SER Chi-restraints excluded: chain V residue 13 MET Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 549 optimal weight: 40.0000 chunk 578 optimal weight: 2.9990 chunk 528 optimal weight: 3.9990 chunk 563 optimal weight: 30.0000 chunk 338 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 442 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 508 optimal weight: 1.9990 chunk 532 optimal weight: 0.7980 chunk 561 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 51759 Z= 0.318 Angle : 0.561 8.489 70147 Z= 0.280 Chirality : 0.043 0.170 7761 Planarity : 0.003 0.042 8979 Dihedral : 6.163 135.366 7185 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.55 % Allowed : 9.64 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: 0.27 (0.11), residues: 6286 helix: 1.09 (0.11), residues: 2438 sheet: -0.62 (0.15), residues: 1235 loop : -0.13 (0.13), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 169 HIS 0.004 0.001 HIS A 192 PHE 0.024 0.001 PHE D 165 TYR 0.021 0.001 TYR I 84 ARG 0.013 0.000 ARG V 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 384 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 354 time to evaluate : 6.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 132 MET cc_start: 0.7221 (ppp) cc_final: 0.6904 (ppp) REVERT: K 132 MET cc_start: 0.8706 (ppp) cc_final: 0.8293 (ppp) REVERT: K 153 MET cc_start: 0.8379 (tpp) cc_final: 0.7420 (tpp) REVERT: N 12 ASN cc_start: 0.8768 (t0) cc_final: 0.8302 (t0) REVERT: N 44 MET cc_start: 0.8508 (mtm) cc_final: 0.7936 (tpt) REVERT: N 355 MET cc_start: 0.8756 (mtm) cc_final: 0.8412 (mtm) REVERT: R 360 GLN cc_start: 0.8715 (pp30) cc_final: 0.8190 (pp30) outliers start: 30 outliers final: 27 residues processed: 375 average time/residue: 1.3427 time to fit residues: 821.0780 Evaluate side-chains 380 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 353 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 358 SER Chi-restraints excluded: chain V residue 13 MET Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 369 optimal weight: 0.6980 chunk 595 optimal weight: 9.9990 chunk 363 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 413 optimal weight: 3.9990 chunk 624 optimal weight: 30.0000 chunk 574 optimal weight: 30.0000 chunk 497 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 384 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 188 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 51759 Z= 0.163 Angle : 0.521 8.389 70147 Z= 0.255 Chirality : 0.042 0.175 7761 Planarity : 0.003 0.042 8979 Dihedral : 5.963 131.484 7185 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.46 % Allowed : 9.75 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: 0.51 (0.11), residues: 6286 helix: 1.26 (0.11), residues: 2433 sheet: -0.52 (0.15), residues: 1240 loop : 0.06 (0.13), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 169 HIS 0.004 0.001 HIS D 254 PHE 0.019 0.001 PHE D 165 TYR 0.014 0.001 TYR I 84 ARG 0.004 0.000 ARG G 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 93 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue MET 153 is missing expected H atoms. Skipping. Evaluate side-chains 386 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 361 time to evaluate : 6.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 227 MET cc_start: 0.7465 (mmm) cc_final: 0.7092 (mmm) REVERT: K 132 MET cc_start: 0.8670 (ppp) cc_final: 0.8235 (ppp) REVERT: K 153 MET cc_start: 0.8349 (tpp) cc_final: 0.7461 (tpp) REVERT: N 12 ASN cc_start: 0.8723 (t0) cc_final: 0.8254 (t0) REVERT: N 44 MET cc_start: 0.8474 (mtm) cc_final: 0.7906 (tpt) REVERT: N 355 MET cc_start: 0.8706 (mtm) cc_final: 0.8361 (mtm) REVERT: O 360 GLN cc_start: 0.9076 (mp10) cc_final: 0.8820 (mp10) REVERT: R 360 GLN cc_start: 0.8672 (pp30) cc_final: 0.8307 (pp30) outliers start: 25 outliers final: 24 residues processed: 377 average time/residue: 1.3252 time to fit residues: 813.7205 Evaluate side-chains 383 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 359 time to evaluate : 6.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 272 CYS Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain S residue 257 CYS Chi-restraints excluded: chain S residue 358 SER Chi-restraints excluded: chain V residue 13 MET Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 395 optimal weight: 3.9990 chunk 529 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 458 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 498 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 511 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 188 ASN ** W 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.078908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.052599 restraints weight = 451776.907| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.91 r_work: 0.2702 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 51759 Z= 0.256 Angle : 0.539 8.615 70147 Z= 0.266 Chirality : 0.043 0.170 7761 Planarity : 0.003 0.042 8979 Dihedral : 5.921 134.900 7185 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.44 % Allowed : 9.84 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: 0.48 (0.11), residues: 6286 helix: 1.21 (0.11), residues: 2464 sheet: -0.53 (0.15), residues: 1240 loop : 0.04 (0.13), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 169 HIS 0.004 0.001 HIS D 254 PHE 0.023 0.001 PHE D 165 TYR 0.026 0.001 TYR I 84 ARG 0.003 0.000 ARG V 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18295.84 seconds wall clock time: 326 minutes 3.13 seconds (19563.13 seconds total)