Starting phenix.real_space_refine on Sun Mar 17 23:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw5_10022/03_2024/6rw5_10022_trim_updated.pdb" } resolution = 3.14 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= 0.008 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: 10 Type Number sf(0) Gaussians K 17 8.98 5 Fe 4 7.16 5 Zn 1 6.06 5 P 966 5.49 5 Mg 61 5.21 5 S 254 5.16 5 C 42626 2.51 5 N 13188 2.21 5 O 16218 1.98 5 H 63716 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B ARG 264": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 268": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ARG 264": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 318": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 351": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 419": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ARG 222": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 231": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 145": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 264": "OE1" <-> "OE2" Residue "G ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 362": "OE1" <-> "OE2" Residue "G ARG 365": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 377": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 378": "OE1" <-> "OE2" Residue "G GLU 385": "OE1" <-> "OE2" Residue "G ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "I PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 188": "OE1" <-> "OE2" Residue "L ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 171": "OE1" <-> "OE2" Residue "O GLU 212": "OE1" <-> "OE2" Residue "O ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 176": "OE1" <-> "OE2" Residue "R ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 213": "OE1" <-> "OE2" Residue "R ARG 216": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 263": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 343": "OE1" <-> "OE2" Residue "S ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 43": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "S ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 105": "OE1" <-> "OE2" Residue "S GLU 120": "OE1" <-> "OE2" Residue "S ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 100": "OE1" <-> "OE2" Residue "T ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 117": "OE1" <-> "OE2" Residue "T ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 144": "OE1" <-> "OE2" Residue "T ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 73": "OE1" <-> "OE2" Residue "U GLU 84": "OE1" <-> "OE2" Residue "U ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 138": "OE1" <-> "OE2" Residue "U GLU 144": "OE1" <-> "OE2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 194": "OE1" <-> "OE2" Residue "U ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 201": "OE1" <-> "OE2" Residue "V ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 235": "OE1" <-> "OE2" Residue "V ARG 241": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 264": "OE1" <-> "OE2" Residue "V GLU 271": "OE1" <-> "OE2" Residue "V ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 320": "OE1" <-> "OE2" Residue "V GLU 321": "OE1" <-> "OE2" Residue "V ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 362": "OE1" <-> "OE2" Residue "V GLU 370": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 128": "OE1" <-> "OE2" Residue "W TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 148": "OE1" <-> "OE2" Residue "X GLU 53": "OE1" <-> "OE2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 196": "OE1" <-> "OE2" Residue "X ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 214": "OE1" <-> "OE2" Residue "X GLU 246": "OE1" <-> "OE2" Residue "X GLU 285": "OE1" <-> "OE2" Residue "X ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 327": "OE1" <-> "OE2" Residue "X GLU 354": "OE1" <-> "OE2" Residue "X GLU 362": "OE1" <-> "OE2" Residue "X GLU 369": "OE1" <-> "OE2" Residue "X GLU 375": "OE1" <-> "OE2" Residue "X ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 300": "OE1" <-> "OE2" Residue "Y GLU 318": "OE1" <-> "OE2" Residue "Y GLU 327": "OE1" <-> "OE2" Residue "Y GLU 335": "OE1" <-> "OE2" Residue "Y GLU 352": "OE1" <-> "OE2" Residue "Y ARG 377": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 6": "OE1" <-> "OE2" Residue "Z TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 39": "OE1" <-> "OE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "0 ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 GLU 23": "OE1" <-> "OE2" Residue "0 ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 GLU 91": "OE1" <-> "OE2" Residue "0 ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 GLU 130": "OE1" <-> "OE2" Residue "0 GLU 146": "OE1" <-> "OE2" Residue "0 ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "1 GLU 100": "OE1" <-> "OE2" Residue "1 GLU 104": "OE1" <-> "OE2" Residue "1 GLU 124": "OE1" <-> "OE2" Residue "1 GLU 132": "OE1" <-> "OE2" Residue "1 GLU 141": "OE1" <-> "OE2" Residue "1 GLU 144": "OE1" <-> "OE2" Residue "1 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 GLU 237": "OE1" <-> "OE2" Residue "1 GLU 240": "OE1" <-> "OE2" Residue "1 GLU 249": "OE1" <-> "OE2" Residue "1 GLU 250": "OE1" <-> "OE2" Residue "1 GLU 259": "OE1" <-> "OE2" Residue "1 GLU 277": "OE1" <-> "OE2" Residue "1 GLU 282": "OE1" <-> "OE2" Residue "1 GLU 290": "OE1" <-> "OE2" Residue "1 GLU 302": "OE1" <-> "OE2" Residue "1 GLU 303": "OE1" <-> "OE2" Residue "1 GLU 304": "OE1" <-> "OE2" Residue "1 TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 42": "OE1" <-> "OE2" Residue "2 ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 95": "OE1" <-> "OE2" Residue "2 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 154": "OE1" <-> "OE2" Residue "4 GLU 162": "OE1" <-> "OE2" Residue "4 ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 245": "OE1" <-> "OE2" Residue "4 ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 311": "OE1" <-> "OE2" Residue "4 ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 359": "OE1" <-> "OE2" Residue "4 GLU 366": "OE1" <-> "OE2" Residue "4 ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 469": "OE1" <-> "OE2" Residue "4 ARG 537": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 543": "OE1" <-> "OE2" Residue "4 ARG 565": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 591": "OE1" <-> "OE2" Residue "4 GLU 609": "OE1" <-> "OE2" Residue "4 GLU 613": "OE1" <-> "OE2" Residue "4 GLU 643": "OE1" <-> "OE2" Residue "7 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 271": "OE1" <-> "OE2" Residue "7 GLU 294": "OE1" <-> "OE2" Residue "7 GLU 298": "OE1" <-> "OE2" Residue "7 GLU 312": "OE1" <-> "OE2" Residue "7 GLU 361": "OE1" <-> "OE2" Residue "7 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 402": "OE1" <-> "OE2" Residue "7 GLU 409": "OE1" <-> "OE2" Residue "7 ARG 422": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 429": "OE1" <-> "OE2" Residue "7 ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 442": "OE1" <-> "OE2" Residue "7 GLU 450": "OE1" <-> "OE2" Residue "7 GLU 458": "OE1" <-> "OE2" Residue "7 GLU 465": "OE1" <-> "OE2" Residue "7 ARG 489": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 499": "OE1" <-> "OE2" Residue "7 ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 510": "OE1" <-> "OE2" Residue "7 GLU 529": "OE1" <-> "OE2" Residue "7 GLU 543": "OE1" <-> "OE2" Residue "7 TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 GLU 609": "OE1" <-> "OE2" Residue "8 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 GLU 139": "OE1" <-> "OE2" Residue "8 GLU 145": "OE1" <-> "OE2" Residue "8 GLU 147": "OE1" <-> "OE2" Residue "8 GLU 203": "OE1" <-> "OE2" Residue "8 GLU 207": "OE1" <-> "OE2" Residue "8 ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 GLU 247": "OE1" <-> "OE2" Residue "8 GLU 248": "OE1" <-> "OE2" Residue "8 GLU 253": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 137051 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 30527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 30527 Classifications: {'RNA': 955} Modifications used: {'rna2p_pur': 75, 'rna2p_pyr': 84, 'rna3p': 5, 'rna3p_pur': 419, 'rna3p_pyr': 372} Link IDs: {'rna2p': 159, 'rna3p': 795} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3644 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain: "C" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2172 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "D" Number of atoms: 5536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5536 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "E" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3495 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 194} Chain: "G" Number of atoms: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5434 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Chain: "H" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2336 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "I" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2079 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "J" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1727 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 97} Chain: "K" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1748 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "L" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 2994 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "M" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1908 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "N" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1797 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3165 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 23, 'TRANS': 170} Chain: "P" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1588 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "Q" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1494 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 4838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4838 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain: "S" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2227 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "T" Number of atoms: 2764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2764 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain: "U" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2988 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "V" Number of atoms: 5933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5933 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 9, 'TRANS': 352} Chain breaks: 1 Chain: "W" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1592 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "X" Number of atoms: 5694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5694 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 332} Chain: "Y" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2444 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 141} Chain: "Z" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1699 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "0" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3584 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 197} Chain: "1" Number of atoms: 4507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4507 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 258} Chain: "2" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1896 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1325 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 9536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 9536 Classifications: {'peptide': 588} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 558} Chain breaks: 1 Chain: "7" Number of atoms: 8936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 8936 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 21, 'TRANS': 549} Chain: "8" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3131 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 172 Unusual residues: {' K': 17, ' MG': 57, 'NAD': 1, 'SPM': 1, 'SRY': 1} Classifications: {'undetermined': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' MG': 1, 'ATP': 1, 'GNP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 68186 SG CYS O 94 128.477 90.890 139.553 1.00 20.66 S ATOM 68366 SG CYS O 105 131.032 88.697 138.333 1.00 19.60 S ATOM 68409 SG CYS O 108 129.535 87.548 141.223 1.00 21.96 S ATOM 68980 SG CYS O 143 131.843 90.795 141.455 1.00 17.96 S ATOM 43547 SG CYS E 105 163.250 140.862 63.233 1.00 61.68 S ATOM 70898 SG CYS P 68 163.525 141.628 59.102 1.00 36.15 S ATOM 70850 SG CYS P 65 158.827 142.790 58.814 1.00 34.98 S ATOM 71398 SG CYS P 100 158.176 143.321 62.554 1.00 28.42 S ATOM 63916 SG CYS M 26 147.678 106.956 159.802 1.00 19.10 S ATOM 83113 SG CYS T 149 147.491 103.728 158.402 1.00 21.30 S ATOM 82974 SG CYS T 139 154.195 104.889 159.383 1.00 20.61 S ATOM 83003 SG CYS T 141 151.996 102.537 157.509 1.00 20.32 S Time building chain proxies: 43.27, per 1000 atoms: 0.32 Number of scatterers: 137051 At special positions: 0 Unit cell: (215.8, 212.48, 252.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 1 29.99 Fe 4 26.01 K 17 19.00 S 254 16.00 P 966 15.00 Mg 61 11.99 O 16218 8.00 N 13188 7.00 C 42626 6.00 H 63716 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 2 45 " - pdb=" SG CYS 2 76 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 55 " - pdb=" SG CYS 2 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 90.27 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 65 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 100 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES P 201 " - pdb=" SG CYS E 105 " pdb=" FES T 201 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 141 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " Number of angles added : 6 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12302 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: 239 helices and 43 sheets defined 52.7% alpha, 11.0% beta 258 base pairs and 563 stacking pairs defined. Time for finding SS restraints: 94.61 Creating SS restraints... Processing helix chain 'B' and resid 53 through 70 removed outlier: 4.578A pdb=" N ASP B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Proline residue: B 66 - end of helix removed outlier: 4.239A pdb=" N HIS B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 4.901A pdb=" N LEU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 74 through 80' Processing helix chain 'B' and resid 81 through 88 removed outlier: 3.535A pdb=" N ALA B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 5.564A pdb=" N PHE B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 139 removed outlier: 3.687A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 128 " --> pdb=" O HIS B 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 removed outlier: 4.730A pdb=" N TYR B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 206 through 216 removed outlier: 4.259A pdb=" N ARG B 210 " --> pdb=" O HIS B 206 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 277 removed outlier: 3.884A pdb=" N LEU B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 5.545A pdb=" N ALA C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.563A pdb=" N ARG C 85 " --> pdb=" O HIS C 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 128 through 148 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.785A pdb=" N ALA D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 113 removed outlier: 4.029A pdb=" N LYS D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 186 removed outlier: 3.536A pdb=" N LYS D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS D 186 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 279 removed outlier: 3.847A pdb=" N ARG D 269 " --> pdb=" O MET D 265 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 341 through 356 removed outlier: 3.579A pdb=" N ARG D 351 " --> pdb=" O GLN D 347 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.665A pdb=" N GLY D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 33 removed outlier: 3.501A pdb=" N ALA E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 4.027A pdb=" N VAL E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 85 " --> pdb=" O HIS E 81 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 4.654A pdb=" N GLN E 100 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 101' Processing helix chain 'F' and resid 47 through 53 removed outlier: 4.412A pdb=" N TYR F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 53' Processing helix chain 'F' and resid 54 through 59 removed outlier: 5.663A pdb=" N THR F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 73 removed outlier: 3.683A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU F 73 " --> pdb=" O LYS F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 103 through 129 removed outlier: 3.913A pdb=" N ALA F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 138 removed outlier: 4.687A pdb=" N ALA F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU F 138 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 153 removed outlier: 3.517A pdb=" N CYS F 152 " --> pdb=" O ALA F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 193 removed outlier: 3.661A pdb=" N MET F 184 " --> pdb=" O ARG F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.617A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.863A pdb=" N ARG F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA F 235 " --> pdb=" O GLU F 231 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N HIS F 238 " --> pdb=" O ARG F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 93 removed outlier: 3.717A pdb=" N GLU G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.592A pdb=" N ILE G 104 " --> pdb=" O THR G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 123 removed outlier: 4.054A pdb=" N ARG G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Proline residue: G 123 - end of helix No H-bonds generated for 'chain 'G' and resid 118 through 123' Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 155 through 176 removed outlier: 3.674A pdb=" N LEU G 170 " --> pdb=" O TYR G 166 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN G 171 " --> pdb=" O GLY G 167 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 210 removed outlier: 4.140A pdb=" N GLU G 207 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 232 removed outlier: 5.057A pdb=" N GLN G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 246 removed outlier: 3.517A pdb=" N GLU G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG G 246 " --> pdb=" O GLN G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 305 Proline residue: G 305 - end of helix Processing helix chain 'G' and resid 306 through 318 removed outlier: 3.564A pdb=" N ARG G 310 " --> pdb=" O ILE G 306 " (cutoff:3.500A) Proline residue: G 316 - end of helix Processing helix chain 'G' and resid 336 through 356 removed outlier: 3.657A pdb=" N ALA G 341 " --> pdb=" O ARG G 337 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY G 342 " --> pdb=" O SER G 338 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE G 355 " --> pdb=" O ALA G 351 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL G 356 " --> pdb=" O LEU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 368 Processing helix chain 'H' and resid 84 through 103 removed outlier: 3.707A pdb=" N LEU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 164 Processing helix chain 'H' and resid 181 through 187 removed outlier: 3.510A pdb=" N LYS H 185 " --> pdb=" O PRO H 181 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU H 186 " --> pdb=" O GLU H 182 " (cutoff:3.500A) Proline residue: H 187 - end of helix No H-bonds generated for 'chain 'H' and resid 181 through 187' Processing helix chain 'I' and resid 79 through 84 Proline residue: I 84 - end of helix Processing helix chain 'I' and resid 111 through 116 removed outlier: 3.603A pdb=" N GLY I 116 " --> pdb=" O CYS I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 124 removed outlier: 4.670A pdb=" N GLY I 123 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 119 through 124' Processing helix chain 'I' and resid 125 through 143 removed outlier: 3.674A pdb=" N ARG I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS I 142 " --> pdb=" O ARG I 138 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY I 143 " --> pdb=" O ALA I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 169 removed outlier: 3.946A pdb=" N ALA I 161 " --> pdb=" O GLY I 157 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'K' and resid 31 through 48 removed outlier: 3.545A pdb=" N GLU K 46 " --> pdb=" O LYS K 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 3.845A pdb=" N LEU K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN K 60 " --> pdb=" O SER K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 78 removed outlier: 3.620A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 73 through 79 removed outlier: 4.462A pdb=" N ASN L 78 " --> pdb=" O LYS L 74 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.529A pdb=" N SER L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 4.123A pdb=" N MET L 103 " --> pdb=" O ASN L 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS L 105 " --> pdb=" O LYS L 101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 147 removed outlier: 3.710A pdb=" N LYS L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 174 Processing helix chain 'L' and resid 175 through 186 Processing helix chain 'L' and resid 200 through 236 removed outlier: 3.512A pdb=" N LEU L 220 " --> pdb=" O GLU L 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 84 through 95 removed outlier: 3.577A pdb=" N LEU M 91 " --> pdb=" O MET M 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY M 92 " --> pdb=" O GLU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 127 removed outlier: 3.775A pdb=" N LEU M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 113 removed outlier: 5.008A pdb=" N SER N 112 " --> pdb=" O SER N 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU N 113 " --> pdb=" O PRO N 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 108 through 113' Processing helix chain 'O' and resid 54 through 61 removed outlier: 4.701A pdb=" N TYR O 58 " --> pdb=" O GLU O 54 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU O 59 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU O 60 " --> pdb=" O TRP O 56 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER O 61 " --> pdb=" O LYS O 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 54 through 61' Processing helix chain 'O' and resid 62 through 68 Processing helix chain 'O' and resid 105 through 111 removed outlier: 4.047A pdb=" N ASP O 110 " --> pdb=" O PRO O 106 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N HIS O 111 " --> pdb=" O ILE O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 128 removed outlier: 4.263A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL O 127 " --> pdb=" O LEU O 123 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N CYS O 128 " --> pdb=" O GLU O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 141 removed outlier: 3.731A pdb=" N THR O 140 " --> pdb=" O TYR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 removed outlier: 3.549A pdb=" N GLN O 152 " --> pdb=" O LYS O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 196 Processing helix chain 'O' and resid 209 through 221 Processing helix chain 'P' and resid 76 through 85 removed outlier: 4.067A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER P 85 " --> pdb=" O SER P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 98 Processing helix chain 'P' and resid 100 through 118 removed outlier: 3.658A pdb=" N GLU P 106 " --> pdb=" O LYS P 102 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY P 118 " --> pdb=" O ALA P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 131 removed outlier: 3.955A pdb=" N LEU P 130 " --> pdb=" O ASP P 126 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS P 131 " --> pdb=" O PRO P 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 126 through 131' Processing helix chain 'Q' and resid 18 through 34 Processing helix chain 'Q' and resid 35 through 45 removed outlier: 3.707A pdb=" N ARG Q 43 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR Q 44 " --> pdb=" O LYS Q 40 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR Q 45 " --> pdb=" O HIS Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 80 removed outlier: 4.893A pdb=" N ARG Q 77 " --> pdb=" O ASN Q 73 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS Q 78 " --> pdb=" O PHE Q 74 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN Q 79 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ARG Q 80 " --> pdb=" O MET Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.662A pdb=" N ILE R 78 " --> pdb=" O GLU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 92 removed outlier: 3.694A pdb=" N LYS R 92 " --> pdb=" O GLN R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 127 removed outlier: 3.725A pdb=" N LYS R 127 " --> pdb=" O LYS R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 Processing helix chain 'R' and resid 211 through 222 Processing helix chain 'R' and resid 223 through 235 removed outlier: 3.525A pdb=" N VAL R 227 " --> pdb=" O ARG R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 257 removed outlier: 3.749A pdb=" N ILE R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS R 244 " --> pdb=" O THR R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 264 removed outlier: 4.370A pdb=" N LEU R 262 " --> pdb=" O LYS R 258 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG R 263 " --> pdb=" O TYR R 259 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER R 264 " --> pdb=" O ASP R 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 258 through 264' Processing helix chain 'R' and resid 267 through 279 Processing helix chain 'R' and resid 281 through 292 removed outlier: 3.534A pdb=" N ASP R 292 " --> pdb=" O GLN R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 309 removed outlier: 3.535A pdb=" N VAL R 301 " --> pdb=" O ALA R 297 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 311 through 321 Processing helix chain 'R' and resid 324 through 335 removed outlier: 4.084A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 358 removed outlier: 3.504A pdb=" N ARG R 355 " --> pdb=" O GLU R 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 23 Processing helix chain 'S' and resid 29 through 38 removed outlier: 4.368A pdb=" N ASP S 33 " --> pdb=" O PRO S 29 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 78 removed outlier: 4.551A pdb=" N ARG S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 110 removed outlier: 3.652A pdb=" N LEU S 109 " --> pdb=" O GLU S 105 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 129 removed outlier: 3.532A pdb=" N LYS S 123 " --> pdb=" O VAL S 119 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 19 removed outlier: 3.622A pdb=" N GLN T 18 " --> pdb=" O GLN T 14 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY T 19 " --> pdb=" O TYR T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 50 removed outlier: 3.810A pdb=" N GLU T 42 " --> pdb=" O GLY T 38 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY T 43 " --> pdb=" O GLU T 39 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA T 44 " --> pdb=" O LEU T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 60 Proline residue: T 60 - end of helix Processing helix chain 'T' and resid 94 through 106 removed outlier: 3.529A pdb=" N ARG T 103 " --> pdb=" O MET T 99 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS T 104 " --> pdb=" O GLU T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 125 removed outlier: 3.505A pdb=" N GLU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU T 116 " --> pdb=" O THR T 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS T 120 " --> pdb=" O GLU T 116 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N HIS T 125 " --> pdb=" O LYS T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 161 removed outlier: 3.640A pdb=" N ARG T 160 " --> pdb=" O PRO T 156 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY T 161 " --> pdb=" O LYS T 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 156 through 161' Processing helix chain 'T' and resid 162 through 169 Processing helix chain 'U' and resid 35 through 40 removed outlier: 3.854A pdb=" N ILE U 39 " --> pdb=" O ALA U 35 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU U 40 " --> pdb=" O LYS U 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 35 through 40' Processing helix chain 'U' and resid 50 through 135 removed outlier: 3.557A pdb=" N ALA U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU U 70 " --> pdb=" O THR U 66 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG U 86 " --> pdb=" O VAL U 82 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA U 87 " --> pdb=" O HIS U 83 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY U 88 " --> pdb=" O GLU U 84 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL U 89 " --> pdb=" O ALA U 85 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N LEU U 90 " --> pdb=" O ARG U 86 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA U 91 " --> pdb=" O ALA U 87 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS U 94 " --> pdb=" O LEU U 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS U 97 " --> pdb=" O ARG U 93 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN U 126 " --> pdb=" O ALA U 122 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN U 133 " --> pdb=" O ARG U 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 165 removed outlier: 3.653A pdb=" N ALA U 140 " --> pdb=" O ALA U 136 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN U 151 " --> pdb=" O GLN U 147 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG U 152 " --> pdb=" O ALA U 148 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 184 removed outlier: 3.510A pdb=" N ASP U 182 " --> pdb=" O GLU U 178 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG U 184 " --> pdb=" O ALA U 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 43 removed outlier: 5.790A pdb=" N SER V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N HIS V 38 " --> pdb=" O TYR V 34 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LYS V 39 " --> pdb=" O VAL V 35 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP V 40 " --> pdb=" O ASP V 36 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU V 41 " --> pdb=" O SER V 37 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA V 42 " --> pdb=" O HIS V 38 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG V 43 " --> pdb=" O LYS V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 64 removed outlier: 3.769A pdb=" N THR V 60 " --> pdb=" O LEU V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 79 removed outlier: 3.860A pdb=" N ILE V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER V 73 " --> pdb=" O SER V 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG V 74 " --> pdb=" O LEU V 70 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE V 76 " --> pdb=" O ILE V 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP V 77 " --> pdb=" O SER V 73 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE V 79 " --> pdb=" O LEU V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 99 removed outlier: 3.834A pdb=" N ASP V 86 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR V 91 " --> pdb=" O HIS V 87 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER V 98 " --> pdb=" O LYS V 94 " (cutoff:3.500A) Proline residue: V 99 - end of helix Processing helix chain 'V' and resid 105 through 120 removed outlier: 3.730A pdb=" N ILE V 109 " --> pdb=" O ARG V 105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP V 120 " --> pdb=" O CYS V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 132 Processing helix chain 'V' and resid 140 through 155 removed outlier: 3.715A pdb=" N PHE V 151 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS V 154 " --> pdb=" O SER V 150 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.702A pdb=" N LEU V 161 " --> pdb=" O TYR V 157 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER V 162 " --> pdb=" O LYS V 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 194 removed outlier: 3.524A pdb=" N SER V 182 " --> pdb=" O THR V 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS V 192 " --> pdb=" O HIS V 188 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR V 194 " --> pdb=" O LEU V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 197 through 216 removed outlier: 3.538A pdb=" N ARG V 202 " --> pdb=" O TRP V 198 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU V 209 " --> pdb=" O GLY V 205 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) Proline residue: V 211 - end of helix removed outlier: 3.831A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN V 215 " --> pdb=" O PRO V 211 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS V 216 " --> pdb=" O GLY V 212 " (cutoff:3.500A) Processing helix chain 'V' and resid 217 through 238 Processing helix chain 'V' and resid 239 through 245 removed outlier: 4.097A pdb=" N VAL V 243 " --> pdb=" O GLY V 239 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR V 244 " --> pdb=" O LEU V 240 " (cutoff:3.500A) Processing helix chain 'V' and resid 254 through 270 removed outlier: 3.797A pdb=" N VAL V 262 " --> pdb=" O ARG V 258 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET V 263 " --> pdb=" O ALA V 259 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA V 267 " --> pdb=" O MET V 263 " (cutoff:3.500A) Proline residue: V 270 - end of helix Processing helix chain 'V' and resid 276 through 293 removed outlier: 3.566A pdb=" N SER V 292 " --> pdb=" O LYS V 288 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA V 293 " --> pdb=" O ALA V 289 " (cutoff:3.500A) Processing helix chain 'V' and resid 322 through 345 removed outlier: 3.603A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU V 327 " --> pdb=" O GLU V 323 " (cutoff:3.500A) Proline residue: V 328 - end of helix Processing helix chain 'V' and resid 351 through 364 removed outlier: 3.920A pdb=" N LEU V 364 " --> pdb=" O VAL V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 365 through 405 removed outlier: 3.623A pdb=" N THR V 374 " --> pdb=" O GLU V 370 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN V 388 " --> pdb=" O LEU V 384 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU V 389 " --> pdb=" O ASP V 385 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE V 390 " --> pdb=" O LEU V 386 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN V 391 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU V 398 " --> pdb=" O GLN V 394 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN V 399 " --> pdb=" O GLN V 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN V 402 " --> pdb=" O GLU V 398 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU V 403 " --> pdb=" O GLN V 399 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR V 404 " --> pdb=" O ALA V 400 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN V 405 " --> pdb=" O LYS V 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 87 removed outlier: 3.624A pdb=" N MET W 83 " --> pdb=" O SER W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 93 Processing helix chain 'W' and resid 130 through 135 removed outlier: 4.434A pdb=" N TYR W 134 " --> pdb=" O ASP W 130 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN W 135 " --> pdb=" O GLY W 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 130 through 135' Processing helix chain 'X' and resid 71 through 78 Processing helix chain 'X' and resid 84 through 95 removed outlier: 3.933A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 115 removed outlier: 3.570A pdb=" N TYR X 111 " --> pdb=" O GLU X 107 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN X 114 " --> pdb=" O HIS X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 149 removed outlier: 3.711A pdb=" N LYS X 147 " --> pdb=" O HIS X 143 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN X 148 " --> pdb=" O PHE X 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP X 149 " --> pdb=" O CYS X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 164 removed outlier: 4.556A pdb=" N VAL X 162 " --> pdb=" O ALA X 158 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS X 163 " --> pdb=" O HIS X 159 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN X 164 " --> pdb=" O LEU X 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 158 through 164' Processing helix chain 'X' and resid 180 through 196 removed outlier: 3.633A pdb=" N THR X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP X 187 " --> pdb=" O GLU X 183 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS X 189 " --> pdb=" O SER X 185 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 202 removed outlier: 4.167A pdb=" N GLN X 201 " --> pdb=" O ARG X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 233 removed outlier: 4.230A pdb=" N VAL X 225 " --> pdb=" O PRO X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 254 removed outlier: 5.544A pdb=" N ASP X 238 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER X 252 " --> pdb=" O LYS X 248 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU X 253 " --> pdb=" O ARG X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 270 removed outlier: 4.850A pdb=" N TRP X 269 " --> pdb=" O ILE X 265 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY X 270 " --> pdb=" O ASN X 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 265 through 270' Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.645A pdb=" N LEU X 293 " --> pdb=" O LEU X 289 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG X 294 " --> pdb=" O VAL X 290 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS X 298 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASN X 299 " --> pdb=" O LYS X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 324 through 329 Processing helix chain 'X' and resid 330 through 338 Processing helix chain 'X' and resid 349 through 364 Processing helix chain 'X' and resid 373 through 385 removed outlier: 3.539A pdb=" N LYS X 378 " --> pdb=" O GLU X 374 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU X 379 " --> pdb=" O GLU X 375 " (cutoff:3.500A) Processing helix chain 'X' and resid 387 through 398 removed outlier: 3.581A pdb=" N ALA X 396 " --> pdb=" O GLU X 392 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU X 398 " --> pdb=" O HIS X 394 " (cutoff:3.500A) Processing helix chain 'Y' and resid 276 through 291 removed outlier: 3.689A pdb=" N PHE Y 282 " --> pdb=" O TRP Y 278 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS Y 284 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU Y 286 " --> pdb=" O PHE Y 282 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA Y 287 " --> pdb=" O ALA Y 283 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR Y 288 " --> pdb=" O LYS Y 284 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN Y 290 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU Y 291 " --> pdb=" O ALA Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 308 removed outlier: 3.663A pdb=" N GLU Y 300 " --> pdb=" O ASN Y 296 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 333 removed outlier: 3.835A pdb=" N HIS Y 331 " --> pdb=" O GLU Y 327 " (cutoff:3.500A) Processing helix chain 'Y' and resid 334 through 339 removed outlier: 4.411A pdb=" N LEU Y 338 " --> pdb=" O LEU Y 334 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU Y 339 " --> pdb=" O GLU Y 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 334 through 339' Processing helix chain 'Y' and resid 345 through 362 removed outlier: 3.656A pdb=" N LEU Y 353 " --> pdb=" O HIS Y 349 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS Y 356 " --> pdb=" O GLU Y 352 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN Y 361 " --> pdb=" O GLY Y 357 " (cutoff:3.500A) Proline residue: Y 362 - end of helix Processing helix chain 'Y' and resid 365 through 384 removed outlier: 3.589A pdb=" N GLU Y 371 " --> pdb=" O LYS Y 367 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS Y 372 " --> pdb=" O GLN Y 368 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU Y 382 " --> pdb=" O ASN Y 378 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS Y 384 " --> pdb=" O PHE Y 380 " (cutoff:3.500A) Processing helix chain 'Y' and resid 385 through 391 removed outlier: 3.731A pdb=" N GLU Y 389 " --> pdb=" O ASP Y 385 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER Y 390 " --> pdb=" O ILE Y 386 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Y 391 " --> pdb=" O LEU Y 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 385 through 391' Processing helix chain 'Z' and resid 5 through 20 Processing helix chain 'Z' and resid 27 through 39 removed outlier: 4.145A pdb=" N LYS Z 32 " --> pdb=" O SER Z 28 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL Z 33 " --> pdb=" O LYS Z 29 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL Z 34 " --> pdb=" O SER Z 30 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 46 removed outlier: 5.816A pdb=" N LYS Z 46 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 69 removed outlier: 3.582A pdb=" N GLN Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 90 removed outlier: 3.702A pdb=" N LYS Z 87 " --> pdb=" O LYS Z 83 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 26 removed outlier: 3.937A pdb=" N GLU 0 13 " --> pdb=" O ARG 0 9 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Processing helix chain '0' and resid 51 through 61 removed outlier: 3.701A pdb=" N TRP 0 55 " --> pdb=" O PRO 0 51 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA 0 56 " --> pdb=" O VAL 0 52 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP 0 57 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG 0 59 " --> pdb=" O TRP 0 55 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG 0 60 " --> pdb=" O ALA 0 56 " (cutoff:3.500A) Processing helix chain '0' and resid 63 through 72 removed outlier: 5.540A pdb=" N ARG 0 70 " --> pdb=" O GLN 0 66 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU 0 71 " --> pdb=" O LEU 0 67 " (cutoff:3.500A) Proline residue: 0 72 - end of helix Processing helix chain '0' and resid 82 through 89 Processing helix chain '0' and resid 143 through 152 removed outlier: 4.640A pdb=" N GLU 0 148 " --> pdb=" O LYS 0 144 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA 0 149 " --> pdb=" O HIS 0 145 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 182 removed outlier: 3.671A pdb=" N ARG 0 178 " --> pdb=" O ILE 0 174 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN 0 179 " --> pdb=" O ILE 0 175 " (cutoff:3.500A) Processing helix chain '0' and resid 206 through 211 removed outlier: 3.911A pdb=" N LYS 0 210 " --> pdb=" O LYS 0 206 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLY 0 211 " --> pdb=" O GLN 0 207 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 206 through 211' Processing helix chain '1' and resid 55 through 61 removed outlier: 4.623A pdb=" N LYS 1 59 " --> pdb=" O PRO 1 55 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA 1 61 " --> pdb=" O THR 1 57 " (cutoff:3.500A) Processing helix chain '1' and resid 65 through 71 removed outlier: 3.937A pdb=" N VAL 1 69 " --> pdb=" O ASP 1 65 " (cutoff:3.500A) Proline residue: 1 71 - end of helix Processing helix chain '1' and resid 77 through 82 Proline residue: 1 82 - end of helix Processing helix chain '1' and resid 102 through 109 removed outlier: 4.036A pdb=" N LEU 1 106 " --> pdb=" O ASN 1 102 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE 1 108 " --> pdb=" O GLU 1 104 " (cutoff:3.500A) Proline residue: 1 109 - end of helix Processing helix chain '1' and resid 115 through 131 removed outlier: 3.888A pdb=" N ALA 1 125 " --> pdb=" O LYS 1 121 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N CYS 1 130 " --> pdb=" O LEU 1 126 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR 1 131 " --> pdb=" O LYS 1 127 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 147 removed outlier: 3.827A pdb=" N CYS 1 143 " --> pdb=" O SER 1 139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS 1 146 " --> pdb=" O LYS 1 142 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 170 removed outlier: 4.682A pdb=" N ARG 1 169 " --> pdb=" O ASN 1 165 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL 1 170 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 165 through 170' Processing helix chain '1' and resid 176 through 181 removed outlier: 4.166A pdb=" N LEU 1 180 " --> pdb=" O LYS 1 176 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASN 1 181 " --> pdb=" O LEU 1 177 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 176 through 181' Processing helix chain '1' and resid 183 through 195 removed outlier: 3.627A pdb=" N LYS 1 192 " --> pdb=" O LYS 1 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY 1 195 " --> pdb=" O ILE 1 191 " (cutoff:3.500A) Processing helix chain '1' and resid 214 through 236 removed outlier: 3.515A pdb=" N TRP 1 234 " --> pdb=" O TYR 1 230 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN 1 235 " --> pdb=" O HIS 1 231 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THR 1 236 " --> pdb=" O GLU 1 232 " (cutoff:3.500A) Processing helix chain '1' and resid 244 through 249 removed outlier: 5.643A pdb=" N GLU 1 249 " --> pdb=" O GLU 1 245 " (cutoff:3.500A) Processing helix chain '1' and resid 256 through 274 Processing helix chain '1' and resid 279 through 286 removed outlier: 3.584A pdb=" N THR 1 286 " --> pdb=" O GLU 1 282 " (cutoff:3.500A) Processing helix chain '1' and resid 287 through 302 removed outlier: 3.616A pdb=" N ASN 1 301 " --> pdb=" O VAL 1 297 " (cutoff:3.500A) Processing helix chain '1' and resid 305 through 321 removed outlier: 3.564A pdb=" N SER 1 310 " --> pdb=" O GLU 1 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG 1 318 " --> pdb=" O GLU 1 314 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU 1 319 " --> pdb=" O SER 1 315 " (cutoff:3.500A) Processing helix chain '1' and resid 237 through 243 removed outlier: 3.968A pdb=" N GLU 1 240 " --> pdb=" O GLU 1 237 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS 1 241 " --> pdb=" O GLU 1 238 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER 1 242 " --> pdb=" O TRP 1 239 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS 1 243 " --> pdb=" O GLU 1 240 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 237 through 243' Processing helix chain '2' and resid 45 through 60 removed outlier: 3.657A pdb=" N MET 2 53 " --> pdb=" O MET 2 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP 2 56 " --> pdb=" O MET 2 52 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS 2 57 " --> pdb=" O MET 2 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN 2 58 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 91 removed outlier: 3.952A pdb=" N CYS 2 66 " --> pdb=" O ARG 2 62 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG 2 67 " --> pdb=" O ASP 2 63 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS 2 68 " --> pdb=" O ASP 2 64 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU 2 69 " --> pdb=" O ALA 2 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 2 89 " --> pdb=" O LYS 2 85 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 112 removed outlier: 3.913A pdb=" N LYS 2 106 " --> pdb=" O ASN 2 102 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU 2 107 " --> pdb=" O LYS 2 103 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG 2 110 " --> pdb=" O LYS 2 106 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE 2 111 " --> pdb=" O LEU 2 107 " (cutoff:3.500A) Proline residue: 2 112 - end of helix Processing helix chain '3' and resid 130 through 151 removed outlier: 3.800A pdb=" N ARG 3 135 " --> pdb=" O LEU 3 131 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS 3 149 " --> pdb=" O LYS 3 145 " (cutoff:3.500A) Processing helix chain '3' and resid 152 through 181 removed outlier: 3.682A pdb=" N LYS 3 156 " --> pdb=" O PHE 3 152 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG 3 164 " --> pdb=" O GLY 3 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS 3 165 " --> pdb=" O ARG 3 161 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP 3 177 " --> pdb=" O LEU 3 173 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY 3 181 " --> pdb=" O TRP 3 177 " (cutoff:3.500A) Processing helix chain '4' and resid 68 through 79 removed outlier: 3.800A pdb=" N SER 4 76 " --> pdb=" O GLN 4 72 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR 4 77 " --> pdb=" O ALA 4 73 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL 4 78 " --> pdb=" O LEU 4 74 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN 4 79 " --> pdb=" O ALA 4 75 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 125 removed outlier: 3.594A pdb=" N LEU 4 107 " --> pdb=" O SER 4 103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 4 109 " --> pdb=" O SER 4 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS 4 110 " --> pdb=" O PHE 4 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU 4 114 " --> pdb=" O LYS 4 110 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE 4 120 " --> pdb=" O VAL 4 116 " (cutoff:3.500A) Proline residue: 4 125 - end of helix Processing helix chain '4' and resid 153 through 164 removed outlier: 3.724A pdb=" N LEU 4 157 " --> pdb=" O SER 4 153 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS 4 158 " --> pdb=" O GLU 4 154 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU 4 159 " --> pdb=" O ALA 4 155 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG 4 160 " --> pdb=" O ALA 4 156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU 4 163 " --> pdb=" O GLU 4 159 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG 4 164 " --> pdb=" O ARG 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 180 removed outlier: 3.748A pdb=" N ASP 4 174 " --> pdb=" O VAL 4 170 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN 4 175 " --> pdb=" O ASP 4 171 " (cutoff:3.500A) Processing helix chain '4' and resid 184 through 199 removed outlier: 3.514A pdb=" N THR 4 188 " --> pdb=" O SER 4 184 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER 4 190 " --> pdb=" O GLU 4 186 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU 4 194 " --> pdb=" O SER 4 190 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR 4 198 " --> pdb=" O LEU 4 194 " (cutoff:3.500A) Processing helix chain '4' and resid 242 through 251 removed outlier: 3.556A pdb=" N PHE 4 248 " --> pdb=" O ALA 4 244 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 270 removed outlier: 3.892A pdb=" N TYR 4 259 " --> pdb=" O ASN 4 255 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG 4 264 " --> pdb=" O CYS 4 260 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY 4 265 " --> pdb=" O THR 4 261 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS 4 269 " --> pdb=" O GLY 4 265 " (cutoff:3.500A) Processing helix chain '4' and resid 271 through 286 removed outlier: 3.581A pdb=" N ASN 4 277 " --> pdb=" O GLU 4 273 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU 4 281 " --> pdb=" O ASN 4 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 4 282 " --> pdb=" O LEU 4 278 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG 4 286 " --> pdb=" O LEU 4 282 " (cutoff:3.500A) Processing helix chain '4' and resid 290 through 306 removed outlier: 3.506A pdb=" N ILE 4 298 " --> pdb=" O PHE 4 294 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 4 299 " --> pdb=" O ASN 4 295 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL 4 302 " --> pdb=" O ILE 4 298 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE 4 305 " --> pdb=" O THR 4 301 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN 4 306 " --> pdb=" O VAL 4 302 " (cutoff:3.500A) Processing helix chain '4' and resid 308 through 327 removed outlier: 3.663A pdb=" N LEU 4 319 " --> pdb=" O LYS 4 315 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS 4 327 " --> pdb=" O MET 4 323 " (cutoff:3.500A) Processing helix chain '4' and resid 331 through 344 removed outlier: 3.656A pdb=" N PHE 4 335 " --> pdb=" O ASN 4 331 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE 4 338 " --> pdb=" O THR 4 334 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) Processing helix chain '4' and resid 346 through 364 removed outlier: 3.754A pdb=" N ARG 4 350 " --> pdb=" O HIS 4 346 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER 4 351 " --> pdb=" O VAL 4 347 " (cutoff:3.500A) Proline residue: 4 352 - end of helix removed outlier: 3.907A pdb=" N LYS 4 361 " --> pdb=" O LEU 4 357 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA 4 362 " --> pdb=" O ARG 4 358 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 4 363 " --> pdb=" O GLU 4 359 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY 4 364 " --> pdb=" O MET 4 360 " (cutoff:3.500A) Processing helix chain '4' and resid 368 through 380 removed outlier: 3.611A pdb=" N TYR 4 372 " --> pdb=" O SER 4 368 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 4 375 " --> pdb=" O THR 4 371 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 401 removed outlier: 3.708A pdb=" N PHE 4 391 " --> pdb=" O LYS 4 387 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 427 removed outlier: 4.129A pdb=" N PHE 4 415 " --> pdb=" O ASP 4 411 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE 4 416 " --> pdb=" O ASP 4 412 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN 4 417 " --> pdb=" O ASP 4 413 " (cutoff:3.500A) Processing helix chain '4' and resid 428 through 441 removed outlier: 3.758A pdb=" N ALA 4 432 " --> pdb=" O ASP 4 428 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN 4 434 " --> pdb=" O GLU 4 430 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS 4 440 " --> pdb=" O HIS 4 436 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR 4 441 " --> pdb=" O GLY 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 450 through 468 removed outlier: 3.729A pdb=" N LEU 4 467 " --> pdb=" O ASP 4 463 " (cutoff:3.500A) Processing helix chain '4' and resid 470 through 484 removed outlier: 3.677A pdb=" N LEU 4 475 " --> pdb=" O ILE 4 471 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS 4 476 " --> pdb=" O ASP 4 472 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU 4 479 " --> pdb=" O LEU 4 475 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE 4 482 " --> pdb=" O TYR 4 478 " (cutoff:3.500A) Proline residue: 4 483 - end of helix Processing helix chain '4' and resid 489 through 504 removed outlier: 3.510A pdb=" N MET 4 493 " --> pdb=" O HIS 4 489 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA 4 499 " --> pdb=" O HIS 4 495 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL 4 502 " --> pdb=" O GLN 4 498 " (cutoff:3.500A) Processing helix chain '4' and resid 508 through 520 removed outlier: 4.183A pdb=" N LYS 4 514 " --> pdb=" O PRO 4 510 " (cutoff:3.500A) Processing helix chain '4' and resid 524 through 537 removed outlier: 3.533A pdb=" N GLU 4 530 " --> pdb=" O ASP 4 526 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET 4 533 " --> pdb=" O GLU 4 529 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 4 534 " --> pdb=" O GLU 4 530 " (cutoff:3.500A) Processing helix chain '4' and resid 541 through 562 removed outlier: 3.729A pdb=" N ALA 4 547 " --> pdb=" O GLU 4 543 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA 4 549 " --> pdb=" O GLN 4 545 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP 4 554 " --> pdb=" O ASP 4 550 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER 4 557 " --> pdb=" O ALA 4 553 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA 4 558 " --> pdb=" O ASP 4 554 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR 4 559 " --> pdb=" O ILE 4 555 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN 4 562 " --> pdb=" O ALA 4 558 " (cutoff:3.500A) Processing helix chain '4' and resid 572 through 587 removed outlier: 3.857A pdb=" N ILE 4 581 " --> pdb=" O ASN 4 577 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE 4 583 " --> pdb=" O ILE 4 579 " (cutoff:3.500A) Processing helix chain '4' and resid 588 through 603 removed outlier: 3.978A pdb=" N LYS 4 594 " --> pdb=" O GLN 4 590 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET 4 595 " --> pdb=" O GLU 4 591 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU 4 596 " --> pdb=" O ALA 4 592 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE 4 599 " --> pdb=" O MET 4 595 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG 4 600 " --> pdb=" O LEU 4 596 " (cutoff:3.500A) Processing helix chain '4' and resid 607 through 622 removed outlier: 3.513A pdb=" N LEU 4 611 " --> pdb=" O ARG 4 607 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 4 613 " --> pdb=" O GLU 4 609 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP 4 616 " --> pdb=" O ASN 4 612 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER 4 617 " --> pdb=" O GLU 4 613 " (cutoff:3.500A) Processing helix chain '4' and resid 623 through 638 removed outlier: 3.598A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 639 through 653 removed outlier: 4.040A pdb=" N GLU 4 643 " --> pdb=" O LEU 4 639 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY 4 644 " --> pdb=" O PRO 4 640 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN 4 647 " --> pdb=" O GLU 4 643 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG 4 648 " --> pdb=" O GLY 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 666 removed outlier: 3.626A pdb=" N LYS 4 660 " --> pdb=" O ASN 4 656 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU 4 663 " --> pdb=" O GLN 4 659 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU 4 666 " --> pdb=" O ALA 4 662 " (cutoff:3.500A) Processing helix chain '4' and resid 443 through 449 removed outlier: 3.573A pdb=" N LYS 4 446 " --> pdb=" O ASP 4 443 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE 4 448 " --> pdb=" O TRP 4 445 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY 4 449 " --> pdb=" O LYS 4 446 " (cutoff:3.500A) Processing helix chain '7' and resid 172 through 177 removed outlier: 5.190A pdb=" N THR 7 177 " --> pdb=" O PRO 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 192 through 202 removed outlier: 3.822A pdb=" N LYS 7 199 " --> pdb=" O THR 7 195 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE 7 200 " --> pdb=" O LEU 7 196 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG 7 201 " --> pdb=" O LEU 7 197 " (cutoff:3.500A) Processing helix chain '7' and resid 204 through 209 removed outlier: 4.211A pdb=" N VAL 7 208 " --> pdb=" O GLN 7 204 " (cutoff:3.500A) Processing helix chain '7' and resid 241 through 252 removed outlier: 4.204A pdb=" N GLN 7 250 " --> pdb=" O ALA 7 246 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL 7 251 " --> pdb=" O ARG 7 247 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR 7 252 " --> pdb=" O GLY 7 248 " (cutoff:3.500A) Processing helix chain '7' and resid 266 through 280 Processing helix chain '7' and resid 296 through 308 removed outlier: 3.857A pdb=" N VAL 7 300 " --> pdb=" O ASP 7 296 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA 7 306 " --> pdb=" O LYS 7 302 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR 7 307 " --> pdb=" O GLU 7 303 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP 7 308 " --> pdb=" O LEU 7 304 " (cutoff:3.500A) Processing helix chain '7' and resid 330 through 346 removed outlier: 4.180A pdb=" N LEU 7 334 " --> pdb=" O ASN 7 330 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA 7 335 " --> pdb=" O LEU 7 331 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU 7 346 " --> pdb=" O ALA 7 342 " (cutoff:3.500A) Processing helix chain '7' and resid 436 through 479 removed outlier: 3.580A pdb=" N HIS 7 470 " --> pdb=" O LYS 7 466 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU 7 479 " --> pdb=" O GLN 7 475 " (cutoff:3.500A) Processing helix chain '7' and resid 485 through 500 removed outlier: 3.549A pdb=" N ILE 7 491 " --> pdb=" O LYS 7 487 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 7 492 " --> pdb=" O LYS 7 488 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS 7 498 " --> pdb=" O PHE 7 494 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU 7 499 " --> pdb=" O LEU 7 495 " (cutoff:3.500A) Processing helix chain '7' and resid 524 through 538 removed outlier: 3.599A pdb=" N ASN 7 533 " --> pdb=" O GLU 7 529 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE 7 534 " --> pdb=" O ALA 7 530 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR 7 537 " --> pdb=" O ASN 7 533 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR 7 538 " --> pdb=" O ILE 7 534 " (cutoff:3.500A) Processing helix chain '7' and resid 557 through 568 removed outlier: 3.719A pdb=" N VAL 7 561 " --> pdb=" O SER 7 557 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 590 Processing helix chain '7' and resid 598 through 615 removed outlier: 3.588A pdb=" N GLU 7 604 " --> pdb=" O TYR 7 600 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP 7 605 " --> pdb=" O ARG 7 601 " (cutoff:3.500A) Proline residue: 7 615 - end of helix Processing helix chain '8' and resid 101 through 113 removed outlier: 3.642A pdb=" N ILE 8 106 " --> pdb=" O ARG 8 102 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG 8 107 " --> pdb=" O ALA 8 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 8 108 " --> pdb=" O ASN 8 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG 8 112 " --> pdb=" O LEU 8 108 " (cutoff:3.500A) Processing helix chain '8' and resid 132 through 150 removed outlier: 3.952A pdb=" N ARG 8 140 " --> pdb=" O ILE 8 136 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU 8 145 " --> pdb=" O GLN 8 141 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU 8 147 " --> pdb=" O LEU 8 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS 8 148 " --> pdb=" O ARG 8 144 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 186 removed outlier: 3.595A pdb=" N GLN 8 180 " --> pdb=" O THR 8 176 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN 8 181 " --> pdb=" O LYS 8 177 " (cutoff:3.500A) Processing helix chain '8' and resid 202 through 218 removed outlier: 3.742A pdb=" N MET 8 206 " --> pdb=" O SER 8 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU 8 207 " --> pdb=" O GLU 8 203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU 8 208 " --> pdb=" O ASN 8 204 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE 8 209 " --> pdb=" O GLU 8 205 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE 8 210 " --> pdb=" O MET 8 206 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS 8 211 " --> pdb=" O GLU 8 207 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR 8 216 " --> pdb=" O GLN 8 212 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET 8 217 " --> pdb=" O ILE 8 213 " (cutoff:3.500A) Proline residue: 8 218 - end of helix Processing helix chain '8' and resid 244 through 260 removed outlier: 3.566A pdb=" N THR 8 257 " --> pdb=" O GLU 8 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN 8 258 " --> pdb=" O THR 8 254 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU 8 259 " --> pdb=" O GLN 8 255 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 90 through 93 removed outlier: 5.037A pdb=" N HIS B 90 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP B 114 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 164 through 168 removed outlier: 3.606A pdb=" N SER B 146 " --> pdb=" O HIS B 167 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 69 through 72 removed outlier: 5.477A pdb=" N LEU C 69 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 112 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 138 through 141 removed outlier: 5.812A pdb=" N GLY D 138 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 158 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 201 through 204 removed outlier: 4.278A pdb=" N ILE D 201 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR D 220 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU D 244 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 292 through 297 removed outlier: 7.560A pdb=" N HIS D 292 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS D 307 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN D 308 " --> pdb=" O ASP D 331 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP D 331 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 370 through 373 removed outlier: 6.961A pdb=" N VAL D 370 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 240 through 248 Processing sheet with id= 9, first strand: chain 'E' and resid 61 through 69 Processing sheet with id= 10, first strand: chain 'F' and resid 156 through 162 Processing sheet with id= 11, first strand: chain 'G' and resid 260 through 263 removed outlier: 4.596A pdb=" N MET G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA G 268 " --> pdb=" O LYS G 287 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP G 327 " --> pdb=" O TYR G 286 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS G 326 " --> pdb=" O SER G 290 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG G 292 " --> pdb=" O HIS G 326 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 105 through 111 removed outlier: 4.263A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR H 140 " --> pdb=" O PRO H 111 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG H 75 " --> pdb=" O THR H 175 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 113 through 121 Processing sheet with id= 14, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.264A pdb=" N ASN I 94 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL I 149 " --> pdb=" O ILE I 173 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 148 through 153 removed outlier: 5.434A pdb=" N GLY I 153 " --> pdb=" O ASN I 178 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 57 through 61 removed outlier: 5.030A pdb=" N LEU J 109 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY J 113 " --> pdb=" O LYS J 122 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS J 122 " --> pdb=" O GLY J 113 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 64 through 69 removed outlier: 3.581A pdb=" N ARG J 82 " --> pdb=" O CYS J 64 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS J 79 " --> pdb=" O ILE J 95 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'M' and resid 22 through 25 removed outlier: 3.870A pdb=" N LEU M 65 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'N' and resid 11 through 15 removed outlier: 7.147A pdb=" N ARG N 11 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE N 13 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU N 65 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'N' and resid 24 through 37 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'R' and resid 155 through 160 removed outlier: 5.603A pdb=" N PHE R 171 " --> pdb=" O ASP R 160 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR R 180 " --> pdb=" O GLU R 176 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'T' and resid 62 through 68 Processing sheet with id= 23, first strand: chain 'W' and resid 99 through 104 removed outlier: 4.685A pdb=" N THR W 138 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG W 139 " --> pdb=" O GLN W 173 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY W 171 " --> pdb=" O ARG W 141 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'W' and resid 111 through 115 Processing sheet with id= 25, first strand: chain 'X' and resid 66 through 70 removed outlier: 4.597A pdb=" N GLN X 66 " --> pdb=" O VAL X 101 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'X' and resid 150 through 156 removed outlier: 4.319A pdb=" N ILE X 122 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY X 128 " --> pdb=" O LEU X 310 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'X' and resid 206 through 210 removed outlier: 6.885A pdb=" N GLU X 206 " --> pdb=" O LYS X 218 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS X 218 " --> pdb=" O GLU X 206 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU X 214 " --> pdb=" O TRP X 210 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '0' and resid 77 through 81 removed outlier: 4.277A pdb=" N ARG 0 78 " --> pdb=" O LEU 0 97 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '0' and resid 99 through 103 removed outlier: 5.162A pdb=" N HIS 0 111 " --> pdb=" O ASP 0 103 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '1' and resid 149 through 153 removed outlier: 3.628A pdb=" N VAL 1 172 " --> pdb=" O ASP 1 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL 1 204 " --> pdb=" O CYS 1 199 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG 1 197 " --> pdb=" O THR 1 206 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '7' and resid 217 through 224 removed outlier: 3.648A pdb=" N GLY 7 218 " --> pdb=" O ASP 7 234 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU 7 228 " --> pdb=" O LEU 7 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR 7 235 " --> pdb=" O ILE 7 185 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLY 7 187 " --> pdb=" O THR 7 235 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE 7 254 " --> pdb=" O VAL 7 182 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET 7 186 " --> pdb=" O VAL 7 256 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN 7 319 " --> pdb=" O ILE 7 283 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU 7 285 " --> pdb=" O GLN 7 319 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 7 321 " --> pdb=" O LEU 7 285 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL 7 287 " --> pdb=" O VAL 7 321 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '7' and resid 355 through 360 removed outlier: 5.508A pdb=" N VAL 7 355 " --> pdb=" O GLU 7 433 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU 7 429 " --> pdb=" O VAL 7 359 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL 7 386 " --> pdb=" O VAL 7 434 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER 7 385 " --> pdb=" O VAL 7 396 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '7' and resid 361 through 365 Processing sheet with id= 34, first strand: chain '7' and resid 544 through 549 removed outlier: 7.689A pdb=" N ILE 7 520 " --> pdb=" O VAL 7 549 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS 7 550 " --> pdb=" O VAL 7 518 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '7' and resid 593 through 596 Processing sheet with id= 36, first strand: chain '7' and resid 616 through 623 removed outlier: 5.075A pdb=" N ASP 7 707 " --> pdb=" O ILE 7 628 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY 7 645 " --> pdb=" O LEU 7 629 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '7' and resid 668 through 671 removed outlier: 3.598A pdb=" N TRP 7 669 " --> pdb=" O LEU 7 661 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '7' and resid 674 through 678 removed outlier: 3.633A pdb=" N SER 7 675 " --> pdb=" O SER 7 695 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER 7 695 " --> pdb=" O SER 7 675 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '7' and resid 517 through 522 Processing sheet with id= 40, first strand: chain '7' and resid 643 through 649 removed outlier: 4.545A pdb=" N MET 7 690 " --> pdb=" O VAL 7 648 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '7' and resid 657 through 663 removed outlier: 3.515A pdb=" N LYS 7 658 " --> pdb=" O TYR 7 712 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '8' and resid 87 through 90 Processing sheet with id= 43, first strand: chain '8' and resid 157 through 165 removed outlier: 7.857A pdb=" N HIS 8 187 " --> pdb=" O ALA 8 242 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA 8 242 " --> pdb=" O HIS 8 187 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL 8 239 " --> pdb=" O SER 8 224 " (cutoff:3.500A) 2254 hydrogen bonds defined for protein. 6714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 631 hydrogen bonds 1132 hydrogen bond angles 0 basepair planarities 258 basepair parallelities 563 stacking parallelities Total time for adding SS restraints: 57.35 Time building geometry restraints manager: 95.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.10: 63634 1.10 - 1.38: 27489 1.38 - 1.65: 48902 1.65 - 1.92: 404 1.92 - 2.20: 8 Bond restraints: 140437 Sorted by residual: bond pdb=" C4 5MU A1076 " pdb=" C5 5MU A1076 " ideal model delta sigma weight residual 1.802 1.400 0.402 2.00e-02 2.50e+03 4.04e+02 bond pdb=" N1 5MU A1076 " pdb=" C6 5MU A1076 " ideal model delta sigma weight residual 1.635 1.361 0.274 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C1' GNP X 503 " pdb=" C2' GNP X 503 " ideal model delta sigma weight residual 1.273 1.531 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C1' GNP 7 801 " pdb=" C2' GNP 7 801 " ideal model delta sigma weight residual 1.273 1.525 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C3' GNP 7 801 " pdb=" C4' GNP 7 801 " ideal model delta sigma weight residual 1.285 1.522 -0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 140432 not shown) Histogram of bond angle deviations from ideal: 79.07 - 90.51: 10 90.51 - 101.95: 1102 101.95 - 113.39: 165103 113.39 - 124.83: 79857 124.83 - 136.26: 7583 Bond angle restraints: 253655 Sorted by residual: angle pdb=" S1 FES T 201 " pdb="FE2 FES T 201 " pdb=" S2 FES T 201 " ideal model delta sigma weight residual 104.33 90.16 14.17 1.14e+00 7.69e-01 1.55e+02 angle pdb="FE1 FES T 201 " pdb=" S2 FES T 201 " pdb="FE2 FES T 201 " ideal model delta sigma weight residual 75.66 89.70 -14.04 1.14e+00 7.69e-01 1.52e+02 angle pdb=" S1 FES T 201 " pdb="FE1 FES T 201 " pdb=" S2 FES T 201 " ideal model delta sigma weight residual 104.33 90.27 14.06 1.20e+00 6.94e-01 1.37e+02 angle pdb="FE1 FES P 201 " pdb=" S2 FES P 201 " pdb="FE2 FES P 201 " ideal model delta sigma weight residual 75.66 88.98 -13.32 1.14e+00 7.69e-01 1.36e+02 angle pdb="FE1 FES T 201 " pdb=" S1 FES T 201 " pdb="FE2 FES T 201 " ideal model delta sigma weight residual 75.66 89.65 -13.99 1.20e+00 6.94e-01 1.36e+02 ... (remaining 253650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.47: 60517 25.47 - 50.95: 3372 50.95 - 76.42: 2719 76.42 - 101.89: 22 101.89 - 127.37: 9 Dihedral angle restraints: 66639 sinusoidal: 44513 harmonic: 22126 Sorted by residual: dihedral pdb=" O4' C A 765 " pdb=" C1' C A 765 " pdb=" N1 C A 765 " pdb=" C2 C A 765 " ideal model delta sinusoidal sigma weight residual 200.00 73.55 126.45 1 1.50e+01 4.44e-03 6.80e+01 dihedral pdb=" CA HIS I 183 " pdb=" C HIS I 183 " pdb=" N ASN I 184 " pdb=" CA ASN I 184 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" O4' U A1520 " pdb=" C1' U A1520 " pdb=" N1 U A1520 " pdb=" C2 U A1520 " ideal model delta sinusoidal sigma weight residual -128.00 -49.66 -78.34 1 1.70e+01 3.46e-03 2.65e+01 ... (remaining 66636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.129: 12635 1.129 - 2.257: 0 2.257 - 3.386: 0 3.386 - 4.515: 0 4.515 - 5.643: 2 Chirality restraints: 12637 Sorted by residual: chirality pdb=" C32 SRY A1703 " pdb=" CG2 SRY A1703 " pdb=" C22 SRY A1703 " pdb=" C42 SRY A1703 " both_signs ideal model delta sigma weight residual False -2.81 2.83 -5.64 2.00e-01 2.50e+01 7.96e+02 chirality pdb=" C22 SRY A1703 " pdb=" C12 SRY A1703 " pdb=" C32 SRY A1703 " pdb=" O13 SRY A1703 " both_signs ideal model delta sigma weight residual False 2.45 -2.66 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" C12 SRY A1703 " pdb=" C22 SRY A1703 " pdb=" O41 SRY A1703 " pdb=" O42 SRY A1703 " both_signs ideal model delta sigma weight residual False 2.37 2.58 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 12634 not shown) Planarity restraints: 17205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GNP 7 801 " 0.453 2.00e-02 2.50e+03 6.16e-01 8.54e+03 pdb=" C2' GNP 7 801 " -0.711 2.00e-02 2.50e+03 pdb=" C3' GNP 7 801 " -0.263 2.00e-02 2.50e+03 pdb=" C4' GNP 7 801 " 0.248 2.00e-02 2.50e+03 pdb=" C5' GNP 7 801 " -0.887 2.00e-02 2.50e+03 pdb=" N9 GNP 7 801 " -0.003 2.00e-02 2.50e+03 pdb=" O2' GNP 7 801 " -0.555 2.00e-02 2.50e+03 pdb=" O3' GNP 7 801 " 0.889 2.00e-02 2.50e+03 pdb=" O4' GNP 7 801 " 0.830 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A1076 " -0.053 2.00e-02 2.50e+03 5.58e-01 7.00e+03 pdb=" C4' 5MU A1076 " -0.420 2.00e-02 2.50e+03 pdb=" O4' 5MU A1076 " -0.535 2.00e-02 2.50e+03 pdb=" C3' 5MU A1076 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 5MU A1076 " 0.581 2.00e-02 2.50e+03 pdb=" C2' 5MU A1076 " 0.189 2.00e-02 2.50e+03 pdb=" O2' 5MU A1076 " -0.936 2.00e-02 2.50e+03 pdb=" C1' 5MU A1076 " -0.242 2.00e-02 2.50e+03 pdb=" N1 5MU A1076 " 0.821 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GNP X 503 " 0.283 2.00e-02 2.50e+03 5.57e-01 6.97e+03 pdb=" C2' GNP X 503 " -0.257 2.00e-02 2.50e+03 pdb=" C3' GNP X 503 " -0.678 2.00e-02 2.50e+03 pdb=" C4' GNP X 503 " 0.432 2.00e-02 2.50e+03 pdb=" C5' GNP X 503 " -0.022 2.00e-02 2.50e+03 pdb=" N9 GNP X 503 " -0.768 2.00e-02 2.50e+03 pdb=" O2' GNP X 503 " 0.893 2.00e-02 2.50e+03 pdb=" O3' GNP X 503 " -0.489 2.00e-02 2.50e+03 pdb=" O4' GNP X 503 " 0.607 2.00e-02 2.50e+03 ... (remaining 17202 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.20: 7666 2.20 - 2.94: 331502 2.94 - 3.67: 473644 3.67 - 4.41: 769411 4.41 - 5.14: 1168287 Nonbonded interactions: 2750510 Sorted by model distance: nonbonded pdb=" OP1 A A1231 " pdb="HH22 ARG K 88 " model vdw 1.466 1.850 nonbonded pdb=" H3 U A1077 " pdb=" OP2 A A1080 " model vdw 1.509 1.850 nonbonded pdb=" OP1 G A1227 " pdb=" HZ1 LYS H 128 " model vdw 1.511 1.850 nonbonded pdb=" H21 G A 843 " pdb=" OP2 A A 846 " model vdw 1.514 1.850 nonbonded pdb=" OP2 C A 705 " pdb=" HH TYR 0 136 " model vdw 1.521 1.850 ... (remaining 2750505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.330 Extract box with map and model: 25.560 Check model and map are aligned: 1.620 Set scattering table: 0.900 Process input model: 483.030 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 522.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.008 0.402 76721 Z= 0.484 Angle : 0.657 32.702 108171 Z= 0.361 Chirality : 0.078 5.643 12637 Planarity : 0.013 0.616 10325 Dihedral : 17.996 127.368 35379 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -2.51 (0.09), residues: 6419 helix: -2.13 (0.08), residues: 2824 sheet: -0.84 (0.19), residues: 695 loop : -1.19 (0.10), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 32 HIS 0.008 0.002 HIS L 142 PHE 0.017 0.002 PHE V 173 TYR 0.019 0.002 TYR X 348 ARG 0.013 0.001 ARG 7 708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1256 time to evaluate : 6.912 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: B 200 ASN cc_start: 0.8082 (p0) cc_final: 0.7695 (p0) REVERT: B 204 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7203 (mt-10) REVERT: C 42 VAL cc_start: 0.8307 (t) cc_final: 0.8085 (m) REVERT: D 176 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.6910 (mtm110) REVERT: D 373 ILE cc_start: 0.8781 (mm) cc_final: 0.8401 (mt) REVERT: G 233 CYS cc_start: 0.7632 (p) cc_final: 0.6694 (p) REVERT: J 84 ARG cc_start: 0.8324 (ttt180) cc_final: 0.7729 (ttt-90) REVERT: S 104 THR cc_start: 0.9170 (m) cc_final: 0.8970 (p) REVERT: W 83 MET cc_start: 0.7923 (mtt) cc_final: 0.7664 (mtt) REVERT: W 151 SER cc_start: 0.8853 (t) cc_final: 0.8614 (m) REVERT: 0 8 PRO cc_start: 0.8193 (Cg_exo) cc_final: 0.7925 (Cg_endo) REVERT: 0 190 MET cc_start: 0.7504 (mtt) cc_final: 0.7250 (mtt) REVERT: 1 252 ILE cc_start: 0.8771 (mt) cc_final: 0.8472 (tt) REVERT: 1 269 MET cc_start: 0.8909 (mtp) cc_final: 0.8375 (mtp) REVERT: 4 185 LEU cc_start: 0.8210 (tp) cc_final: 0.7859 (tp) REVERT: 4 428 ASP cc_start: 0.7314 (t0) cc_final: 0.6753 (t0) REVERT: 7 300 VAL cc_start: 0.9210 (t) cc_final: 0.8856 (t) REVERT: 7 485 LEU cc_start: 0.4973 (tp) cc_final: 0.4605 (mt) REVERT: 7 529 GLU cc_start: 0.7533 (tt0) cc_final: 0.7332 (tt0) REVERT: 7 534 ILE cc_start: 0.9012 (mm) cc_final: 0.8795 (mt) outliers start: 3 outliers final: 2 residues processed: 1259 average time/residue: 1.9408 time to fit residues: 3825.1974 Evaluate side-chains 867 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 865 time to evaluate : 6.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 617 optimal weight: 2.9990 chunk 554 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 572 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 426 optimal weight: 9.9990 chunk 663 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 90 HIS B 178 ASN D 127 ASN H 109 HIS H 176 GLN H 183 HIS P 137 ASN Q 73 ASN R 350 GLN T 51 ASN V 399 GLN X 394 HIS Y 290 ASN 0 192 ASN 1 321 ASN 4 148 GLN 4 288 HIS 4 489 HIS 4 504 ASN 4 577 ASN 7 377 GLN 7 550 HIS 7 621 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 76721 Z= 0.277 Angle : 0.684 27.656 108171 Z= 0.341 Chirality : 0.043 1.977 12637 Planarity : 0.005 0.130 10325 Dihedral : 19.300 114.227 21714 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.26 % Favored : 98.72 % Rotamer: Outliers : 0.84 % Allowed : 6.03 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: -0.94 (0.10), residues: 6419 helix: -0.40 (0.09), residues: 2931 sheet: -0.41 (0.19), residues: 684 loop : -0.77 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 149 HIS 0.008 0.001 HIS G 175 PHE 0.016 0.001 PHE B 58 TYR 0.016 0.002 TYR V 228 ARG 0.004 0.000 ARG D 427 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 884 time to evaluate : 6.949 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: C 42 VAL cc_start: 0.8443 (t) cc_final: 0.8180 (m) REVERT: D 176 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7075 (mtm110) REVERT: D 373 ILE cc_start: 0.8922 (mm) cc_final: 0.8619 (mt) REVERT: F 84 SER cc_start: 0.8251 (t) cc_final: 0.7981 (t) REVERT: G 129 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7367 (mm-30) REVERT: G 273 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6987 (mm-30) REVERT: I 189 ARG cc_start: 0.7798 (ptm160) cc_final: 0.7517 (ptm-80) REVERT: J 84 ARG cc_start: 0.8513 (ttt180) cc_final: 0.7884 (ttt-90) REVERT: L 138 SER cc_start: 0.8497 (t) cc_final: 0.8289 (p) REVERT: U 134 ARG cc_start: 0.7195 (mtm-85) cc_final: 0.6896 (ptp-170) REVERT: W 151 SER cc_start: 0.8915 (t) cc_final: 0.8660 (m) REVERT: 0 8 PRO cc_start: 0.8264 (Cg_exo) cc_final: 0.8027 (Cg_endo) REVERT: 1 252 ILE cc_start: 0.8789 (mt) cc_final: 0.8524 (tt) REVERT: 1 263 LEU cc_start: 0.8708 (tp) cc_final: 0.8414 (tp) REVERT: 4 342 LEU cc_start: 0.8882 (mt) cc_final: 0.8603 (mt) REVERT: 7 244 MET cc_start: 0.9183 (mtt) cc_final: 0.8903 (mtt) REVERT: 7 485 LEU cc_start: 0.4807 (tp) cc_final: 0.4384 (mt) outliers start: 48 outliers final: 35 residues processed: 907 average time/residue: 1.8174 time to fit residues: 2633.3318 Evaluate side-chains 835 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 800 time to evaluate : 6.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 171 GLU Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain 0 residue 79 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 1 residue 183 ASP Chi-restraints excluded: chain 1 residue 255 ASN Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 181 THR Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 577 ASN Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 7 residue 344 MET Chi-restraints excluded: chain 7 residue 423 ASP Chi-restraints excluded: chain 8 residue 238 CYS Chi-restraints excluded: chain 8 residue 246 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 368 optimal weight: 0.0970 chunk 206 optimal weight: 2.9990 chunk 552 optimal weight: 2.9990 chunk 452 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 665 optimal weight: 9.9990 chunk 718 optimal weight: 9.9990 chunk 592 optimal weight: 2.9990 chunk 659 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 533 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN P 137 ASN Y 290 ASN 1 321 ASN 4 489 HIS 4 577 ASN 7 550 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 76721 Z= 0.268 Angle : 0.616 25.860 108171 Z= 0.306 Chirality : 0.042 2.101 12637 Planarity : 0.005 0.131 10325 Dihedral : 18.948 117.033 21714 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.29 % Rotamer: Outliers : 0.96 % Allowed : 6.48 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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 (0.10), residues: 6419 helix: 0.56 (0.10), residues: 2939 sheet: -0.29 (0.19), residues: 682 loop : -0.54 (0.11), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 177 HIS 0.007 0.001 HIS G 175 PHE 0.016 0.001 PHE N 50 TYR 0.014 0.001 TYR R 242 ARG 0.006 0.000 ARG 2 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 831 time to evaluate : 6.927 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: C 42 VAL cc_start: 0.8505 (t) cc_final: 0.8281 (m) REVERT: D 176 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7008 (mtm110) REVERT: D 373 ILE cc_start: 0.8964 (mm) cc_final: 0.8693 (mt) REVERT: I 189 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7521 (ptm-80) REVERT: J 84 ARG cc_start: 0.8524 (ttt180) cc_final: 0.7846 (ttt-90) REVERT: R 306 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8670 (m) REVERT: U 134 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.6899 (ptp-170) REVERT: V 166 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6555 (mm-30) REVERT: Y 262 MET cc_start: 0.6913 (tmm) cc_final: 0.6702 (tmm) REVERT: 0 8 PRO cc_start: 0.8281 (Cg_exo) cc_final: 0.8057 (Cg_endo) REVERT: 1 183 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7597 (p0) REVERT: 1 252 ILE cc_start: 0.8811 (mt) cc_final: 0.8547 (tt) REVERT: 1 263 LEU cc_start: 0.8724 (tp) cc_final: 0.8473 (tp) REVERT: 2 67 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6559 (mtt-85) REVERT: 4 341 CYS cc_start: 0.7741 (p) cc_final: 0.7473 (p) REVERT: 7 244 MET cc_start: 0.9183 (mtt) cc_final: 0.8926 (mtt) REVERT: 7 455 LYS cc_start: 0.7791 (tttt) cc_final: 0.7560 (ttpt) REVERT: 7 485 LEU cc_start: 0.4839 (tp) cc_final: 0.4361 (mt) outliers start: 55 outliers final: 39 residues processed: 854 average time/residue: 1.8072 time to fit residues: 2452.6136 Evaluate side-chains 832 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 790 time to evaluate : 6.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain O residue 171 GLU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 299 GLU Chi-restraints excluded: chain 0 residue 79 LEU Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 1 residue 183 ASP Chi-restraints excluded: chain 1 residue 255 ASN Chi-restraints excluded: chain 1 residue 260 ARG Chi-restraints excluded: chain 2 residue 67 ARG Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 181 THR Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 399 GLU Chi-restraints excluded: chain 4 residue 576 LEU Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 7 residue 344 MET Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 657 optimal weight: 8.9990 chunk 499 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 446 optimal weight: 5.9990 chunk 667 optimal weight: 3.9990 chunk 706 optimal weight: 9.9990 chunk 348 optimal weight: 2.9990 chunk 632 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN D 127 ASN G 130 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN H 147 HIS O 155 GLN Y 290 ASN 4 489 HIS 7 550 HIS 7 649 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 76721 Z= 0.434 Angle : 0.681 26.785 108171 Z= 0.337 Chirality : 0.046 1.960 12637 Planarity : 0.005 0.133 10325 Dihedral : 18.811 120.573 21714 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.07 % Rotamer: Outliers : 1.19 % Allowed : 7.45 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 0.17 (0.10), residues: 6419 helix: 0.91 (0.10), residues: 2940 sheet: -0.39 (0.19), residues: 692 loop : -0.53 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 104 HIS 0.010 0.002 HIS C 57 PHE 0.015 0.002 PHE B 107 TYR 0.017 0.002 TYR R 242 ARG 0.009 0.001 ARG D 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 825 time to evaluate : 7.040 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: D 176 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.6931 (mtm110) REVERT: D 373 ILE cc_start: 0.9026 (mm) cc_final: 0.8770 (mt) REVERT: I 66 ILE cc_start: 0.8258 (pt) cc_final: 0.8021 (mm) REVERT: I 189 ARG cc_start: 0.7828 (ptm160) cc_final: 0.7516 (ptm-80) REVERT: J 84 ARG cc_start: 0.8593 (ttt180) cc_final: 0.7875 (ttt-90) REVERT: O 65 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7728 (tm-30) REVERT: R 341 TYR cc_start: 0.8021 (t80) cc_final: 0.7703 (t80) REVERT: V 166 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6706 (mm-30) REVERT: X 379 GLU cc_start: 0.7244 (mt-10) cc_final: 0.7028 (mt-10) REVERT: Y 262 MET cc_start: 0.6966 (tmm) cc_final: 0.6722 (tmm) REVERT: Y 335 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: 0 8 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.8160 (Cg_endo) REVERT: 1 183 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7824 (p0) REVERT: 1 252 ILE cc_start: 0.8889 (mt) cc_final: 0.8633 (tt) REVERT: 1 263 LEU cc_start: 0.8912 (tp) cc_final: 0.8530 (tp) REVERT: 1 267 LEU cc_start: 0.9255 (mp) cc_final: 0.9045 (mp) REVERT: 4 341 CYS cc_start: 0.7886 (p) cc_final: 0.7674 (p) REVERT: 4 493 MET cc_start: 0.8362 (mmm) cc_final: 0.8072 (mmt) REVERT: 7 244 MET cc_start: 0.9206 (mtt) cc_final: 0.8962 (mtt) REVERT: 7 455 LYS cc_start: 0.7848 (tttt) cc_final: 0.7600 (ttpt) REVERT: 7 485 LEU cc_start: 0.5129 (tp) cc_final: 0.4662 (mt) outliers start: 68 outliers final: 48 residues processed: 862 average time/residue: 1.8039 time to fit residues: 2466.5111 Evaluate side-chains 838 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 788 time to evaluate : 6.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 196 HIS Chi-restraints excluded: chain G residue 243 ARG Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 281 ASP Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 114 ASN Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 251 SER Chi-restraints excluded: chain X residue 278 ASP Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 299 GLU Chi-restraints excluded: chain Y residue 335 GLU Chi-restraints excluded: chain 0 residue 93 CYS Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 1 residue 183 ASP Chi-restraints excluded: chain 2 residue 59 ASN Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 178 GLN Chi-restraints excluded: chain 4 residue 181 THR Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 7 residue 344 MET Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 588 optimal weight: 0.6980 chunk 401 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 526 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 602 optimal weight: 2.9990 chunk 488 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 634 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 130 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN U 133 GLN Y 290 ASN 1 321 ASN 4 489 HIS 7 550 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 76721 Z= 0.286 Angle : 0.611 26.704 108171 Z= 0.302 Chirality : 0.042 1.996 12637 Planarity : 0.005 0.128 10325 Dihedral : 18.707 116.480 21714 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.89 % Favored : 98.10 % Rotamer: Outliers : 1.16 % Allowed : 8.25 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 0.49 (0.10), residues: 6419 helix: 1.26 (0.10), residues: 2928 sheet: -0.44 (0.19), residues: 729 loop : -0.39 (0.11), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 104 HIS 0.008 0.001 HIS C 57 PHE 0.014 0.001 PHE B 58 TYR 0.018 0.001 TYR 7 600 ARG 0.008 0.000 ARG G 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 814 time to evaluate : 7.122 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: C 42 VAL cc_start: 0.8654 (t) cc_final: 0.8400 (m) REVERT: D 176 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.6977 (mtm110) REVERT: D 373 ILE cc_start: 0.8986 (mm) cc_final: 0.8750 (mt) REVERT: I 66 ILE cc_start: 0.8280 (pt) cc_final: 0.8021 (mm) REVERT: I 189 ARG cc_start: 0.7776 (ptm160) cc_final: 0.7531 (ptm-80) REVERT: J 84 ARG cc_start: 0.8584 (ttt180) cc_final: 0.7849 (ttt-90) REVERT: L 179 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7465 (mt-10) REVERT: O 65 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7763 (tm-30) REVERT: V 166 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6662 (mm-30) REVERT: X 234 ARG cc_start: 0.8051 (tmm-80) cc_final: 0.7821 (ttm170) REVERT: X 379 GLU cc_start: 0.7233 (mt-10) cc_final: 0.7001 (mt-10) REVERT: Y 262 MET cc_start: 0.6952 (tmm) cc_final: 0.6706 (tmm) REVERT: Y 335 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7093 (tp30) REVERT: 1 183 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7824 (p0) REVERT: 1 184 ASP cc_start: 0.7866 (m-30) cc_final: 0.7557 (m-30) REVERT: 1 252 ILE cc_start: 0.8876 (mt) cc_final: 0.8635 (tt) REVERT: 1 263 LEU cc_start: 0.8902 (tp) cc_final: 0.8534 (tp) REVERT: 1 267 LEU cc_start: 0.9265 (mp) cc_final: 0.9052 (mp) REVERT: 7 244 MET cc_start: 0.9214 (mtt) cc_final: 0.8974 (mtt) REVERT: 7 455 LYS cc_start: 0.7758 (tttt) cc_final: 0.7537 (ttpt) outliers start: 66 outliers final: 46 residues processed: 850 average time/residue: 1.7910 time to fit residues: 2415.0684 Evaluate side-chains 832 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 784 time to evaluate : 6.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 196 HIS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 214 SER Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 335 GLU Chi-restraints excluded: chain 0 residue 84 SER Chi-restraints excluded: chain 0 residue 93 CYS Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 183 ASP Chi-restraints excluded: chain 2 residue 59 ASN Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 178 GLN Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 465 ILE Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 8 residue 228 GLN Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 237 optimal weight: 1.9990 chunk 636 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 414 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 707 optimal weight: 40.0000 chunk 587 optimal weight: 0.9990 chunk 327 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN F 233 ASN G 130 GLN P 137 ASN 1 321 ASN 4 489 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 76721 Z= 0.280 Angle : 0.604 26.908 108171 Z= 0.299 Chirality : 0.042 1.969 12637 Planarity : 0.005 0.128 10325 Dihedral : 18.608 117.842 21714 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 1.00 % Allowed : 8.72 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 0.70 (0.10), residues: 6419 helix: 1.48 (0.10), residues: 2930 sheet: -0.44 (0.19), residues: 729 loop : -0.30 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 177 HIS 0.008 0.001 HIS C 57 PHE 0.013 0.001 PHE B 58 TYR 0.015 0.001 TYR R 242 ARG 0.008 0.000 ARG 2 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 805 time to evaluate : 8.510 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: C 42 VAL cc_start: 0.8675 (t) cc_final: 0.8429 (m) REVERT: D 176 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.6990 (mtm110) REVERT: D 373 ILE cc_start: 0.8993 (mm) cc_final: 0.8754 (mt) REVERT: I 189 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7520 (ptm-80) REVERT: J 84 ARG cc_start: 0.8572 (ttt180) cc_final: 0.7854 (ttt-90) REVERT: L 179 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7499 (mt-10) REVERT: O 65 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7821 (tm-30) REVERT: X 379 GLU cc_start: 0.7244 (mt-10) cc_final: 0.7011 (mt-10) REVERT: Y 262 MET cc_start: 0.6957 (tmm) cc_final: 0.6736 (tmm) REVERT: Y 335 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7085 (tp30) REVERT: 1 183 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7835 (p0) REVERT: 1 252 ILE cc_start: 0.8894 (mt) cc_final: 0.8531 (tt) REVERT: 1 267 LEU cc_start: 0.9271 (mp) cc_final: 0.9043 (mp) REVERT: 3 190 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7645 (mm-40) REVERT: 7 244 MET cc_start: 0.9243 (mtt) cc_final: 0.8966 (mtt) REVERT: 7 455 LYS cc_start: 0.7811 (tttt) cc_final: 0.7544 (ttpt) REVERT: 7 529 GLU cc_start: 0.7529 (tt0) cc_final: 0.7270 (tt0) outliers start: 57 outliers final: 44 residues processed: 837 average time/residue: 1.7867 time to fit residues: 2365.5903 Evaluate side-chains 833 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 787 time to evaluate : 6.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 196 HIS Chi-restraints excluded: chain G residue 330 CYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 278 ASP Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 299 GLU Chi-restraints excluded: chain Y residue 335 GLU Chi-restraints excluded: chain 0 residue 84 SER Chi-restraints excluded: chain 0 residue 93 CYS Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 183 ASP Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 399 GLU Chi-restraints excluded: chain 4 residue 465 ILE Chi-restraints excluded: chain 7 residue 304 LEU Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 8 residue 228 GLN Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 681 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 402 optimal weight: 0.0370 chunk 516 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 chunk 595 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 704 optimal weight: 20.0000 chunk 440 optimal weight: 7.9990 chunk 429 optimal weight: 0.2980 chunk 325 optimal weight: 1.9990 overall best weight: 1.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 ASN G 130 GLN P 137 ASN 1 321 ASN 4 489 HIS 7 550 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 76721 Z= 0.218 Angle : 0.582 27.199 108171 Z= 0.287 Chirality : 0.041 1.967 12637 Planarity : 0.004 0.125 10325 Dihedral : 18.556 115.891 21714 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.79 % Favored : 98.18 % Rotamer: Outliers : 0.95 % Allowed : 8.95 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 0.90 (0.10), residues: 6419 helix: 1.69 (0.10), residues: 2926 sheet: -0.41 (0.19), residues: 728 loop : -0.24 (0.11), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 177 HIS 0.007 0.001 HIS C 57 PHE 0.013 0.001 PHE B 58 TYR 0.017 0.001 TYR 7 600 ARG 0.007 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 802 time to evaluate : 7.203 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: D 176 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7003 (mtm110) REVERT: G 238 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6951 (mm-30) REVERT: I 189 ARG cc_start: 0.7739 (ptm160) cc_final: 0.7503 (ptm-80) REVERT: J 84 ARG cc_start: 0.8566 (ttt180) cc_final: 0.7847 (ttt-90) REVERT: L 179 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7484 (mt-10) REVERT: X 379 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6940 (mt-10) REVERT: Y 262 MET cc_start: 0.6955 (tmm) cc_final: 0.6744 (tmm) REVERT: Y 335 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: 1 252 ILE cc_start: 0.8852 (mt) cc_final: 0.8619 (tt) REVERT: 3 190 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7648 (mm-40) REVERT: 7 244 MET cc_start: 0.9243 (mtt) cc_final: 0.8961 (mtt) REVERT: 7 455 LYS cc_start: 0.7799 (tttt) cc_final: 0.7560 (ttpt) REVERT: 7 529 GLU cc_start: 0.7547 (tt0) cc_final: 0.7239 (tt0) outliers start: 54 outliers final: 45 residues processed: 831 average time/residue: 1.7779 time to fit residues: 2330.8615 Evaluate side-chains 835 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 789 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain G residue 330 CYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 133 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 335 GLU Chi-restraints excluded: chain 0 residue 84 SER Chi-restraints excluded: chain 0 residue 93 CYS Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 399 GLU Chi-restraints excluded: chain 4 residue 465 ILE Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 8 residue 228 GLN Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 435 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 420 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 447 optimal weight: 4.9990 chunk 480 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 553 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 ASN G 130 GLN P 137 ASN 1 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 76721 Z= 0.306 Angle : 0.607 26.904 108171 Z= 0.299 Chirality : 0.042 1.968 12637 Planarity : 0.005 0.128 10325 Dihedral : 18.536 118.783 21714 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 1.00 % Allowed : 9.29 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 0.91 (0.10), residues: 6419 helix: 1.73 (0.10), residues: 2933 sheet: -0.39 (0.19), residues: 728 loop : -0.27 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 104 HIS 0.009 0.001 HIS C 57 PHE 0.012 0.001 PHE X 198 TYR 0.015 0.001 TYR R 242 ARG 0.009 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 795 time to evaluate : 7.056 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: D 176 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.7004 (mtm110) REVERT: D 373 ILE cc_start: 0.9044 (mm) cc_final: 0.8761 (mp) REVERT: G 238 GLU cc_start: 0.7234 (mm-30) cc_final: 0.7014 (mm-30) REVERT: I 189 ARG cc_start: 0.7760 (ptm160) cc_final: 0.7504 (ptm-80) REVERT: J 84 ARG cc_start: 0.8586 (ttt180) cc_final: 0.7859 (ttt-90) REVERT: X 379 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6965 (mt-10) REVERT: Y 262 MET cc_start: 0.6999 (tmm) cc_final: 0.6769 (tmm) REVERT: Y 335 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7117 (tp30) REVERT: 1 183 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7839 (p0) REVERT: 1 252 ILE cc_start: 0.8879 (mt) cc_final: 0.8645 (tt) REVERT: 1 263 LEU cc_start: 0.8958 (tp) cc_final: 0.8743 (tt) REVERT: 3 190 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7640 (mm-40) REVERT: 7 244 MET cc_start: 0.9251 (mtt) cc_final: 0.8980 (mtt) REVERT: 7 455 LYS cc_start: 0.7831 (tttt) cc_final: 0.7589 (ttpt) REVERT: 7 529 GLU cc_start: 0.7537 (tt0) cc_final: 0.7243 (tt0) outliers start: 57 outliers final: 49 residues processed: 829 average time/residue: 1.7865 time to fit residues: 2334.5128 Evaluate side-chains 826 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 775 time to evaluate : 6.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 196 HIS Chi-restraints excluded: chain G residue 330 CYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 133 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 335 GLU Chi-restraints excluded: chain 0 residue 84 SER Chi-restraints excluded: chain 0 residue 93 CYS Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 183 ASP Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 178 GLN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 399 GLU Chi-restraints excluded: chain 4 residue 465 ILE Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 8 residue 228 GLN Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 640 optimal weight: 3.9990 chunk 674 optimal weight: 3.9990 chunk 615 optimal weight: 5.9990 chunk 656 optimal weight: 6.9990 chunk 395 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 515 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 593 optimal weight: 2.9990 chunk 620 optimal weight: 6.9990 chunk 654 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 ASN G 130 GLN P 137 ASN 1 321 ASN 7 550 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 76721 Z= 0.399 Angle : 0.648 26.687 108171 Z= 0.320 Chirality : 0.045 1.960 12637 Planarity : 0.005 0.130 10325 Dihedral : 18.604 119.678 21714 Min Nonbonded Distance : 1.581 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.80 % Rotamer: Outliers : 1.09 % Allowed : 9.51 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 0.80 (0.10), residues: 6419 helix: 1.63 (0.10), residues: 2946 sheet: -0.41 (0.19), residues: 731 loop : -0.35 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 104 HIS 0.011 0.001 HIS C 57 PHE 0.014 0.001 PHE Z 37 TYR 0.021 0.002 TYR 7 600 ARG 0.010 0.001 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 783 time to evaluate : 6.939 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: D 176 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7027 (mtm110) REVERT: G 238 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7006 (mm-30) REVERT: H 53 ASP cc_start: 0.8116 (t0) cc_final: 0.7912 (t0) REVERT: I 189 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7508 (ptm-80) REVERT: J 84 ARG cc_start: 0.8618 (ttt180) cc_final: 0.7873 (ttt-90) REVERT: Y 335 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: 1 183 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7906 (p0) REVERT: 1 252 ILE cc_start: 0.8894 (mt) cc_final: 0.8669 (tt) REVERT: 3 190 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7668 (mm-40) REVERT: 7 244 MET cc_start: 0.9253 (mtt) cc_final: 0.8981 (mtt) REVERT: 7 455 LYS cc_start: 0.7855 (tttt) cc_final: 0.7577 (ttpt) REVERT: 7 529 GLU cc_start: 0.7543 (tt0) cc_final: 0.7213 (tt0) outliers start: 62 outliers final: 52 residues processed: 818 average time/residue: 1.7688 time to fit residues: 2285.4832 Evaluate side-chains 828 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 774 time to evaluate : 6.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 196 HIS Chi-restraints excluded: chain G residue 330 CYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 133 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 251 SER Chi-restraints excluded: chain X residue 278 ASP Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 335 GLU Chi-restraints excluded: chain 0 residue 84 SER Chi-restraints excluded: chain 0 residue 93 CYS Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 126 SER Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 183 ASP Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 178 GLN Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 399 GLU Chi-restraints excluded: chain 4 residue 465 ILE Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 8 residue 228 GLN Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 431 optimal weight: 0.6980 chunk 694 optimal weight: 0.9990 chunk 423 optimal weight: 0.9990 chunk 329 optimal weight: 2.9990 chunk 482 optimal weight: 2.9990 chunk 728 optimal weight: 7.9990 chunk 670 optimal weight: 9.9990 chunk 579 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 447 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 347 GLN F 233 ASN G 130 GLN P 137 ASN 1 321 ASN 7 550 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 76721 Z= 0.154 Angle : 0.572 27.619 108171 Z= 0.282 Chirality : 0.039 1.962 12637 Planarity : 0.004 0.122 10325 Dihedral : 18.551 113.581 21714 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 0.74 % Allowed : 9.88 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 1.12 (0.11), residues: 6419 helix: 1.93 (0.10), residues: 2943 sheet: -0.36 (0.19), residues: 722 loop : -0.18 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 0 139 HIS 0.007 0.001 HIS P 95 PHE 0.015 0.001 PHE B 58 TYR 0.011 0.001 TYR R 242 ARG 0.008 0.000 ARG T 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12838 Ramachandran restraints generated. 6419 Oldfield, 0 Emsley, 6419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 788 time to evaluate : 7.010 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: D 176 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7100 (mtm110) REVERT: I 189 ARG cc_start: 0.7710 (ptm160) cc_final: 0.7479 (ptm-80) REVERT: J 84 ARG cc_start: 0.8589 (ttt180) cc_final: 0.7852 (ttt-90) REVERT: O 65 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7949 (tm-30) REVERT: U 134 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7430 (ttp-110) REVERT: Y 262 MET cc_start: 0.6829 (tmm) cc_final: 0.6591 (tmm) REVERT: Y 335 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: 1 252 ILE cc_start: 0.8880 (mt) cc_final: 0.8654 (tt) REVERT: 7 244 MET cc_start: 0.9245 (mtt) cc_final: 0.8971 (mtt) REVERT: 7 455 LYS cc_start: 0.7788 (tttt) cc_final: 0.7541 (ttpt) REVERT: 7 529 GLU cc_start: 0.7515 (tt0) cc_final: 0.7212 (tt0) outliers start: 42 outliers final: 34 residues processed: 812 average time/residue: 1.7308 time to fit residues: 2209.8066 Evaluate side-chains 805 residues out of total 5708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 770 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain G residue 330 CYS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 133 ILE Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 98 SER Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain X residue 76 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 165 CYS Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 335 GLU Chi-restraints excluded: chain 0 residue 84 SER Chi-restraints excluded: chain 0 residue 93 CYS Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 138 ASP Chi-restraints excluded: chain 2 residue 118 SER Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 399 GLU Chi-restraints excluded: chain 4 residue 465 ILE Chi-restraints excluded: chain 7 residue 311 CYS Chi-restraints excluded: chain 7 residue 329 ASP Chi-restraints excluded: chain 8 residue 228 GLN Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 460 optimal weight: 4.9990 chunk 617 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 534 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 580 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 596 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 ASN G 130 GLN 1 321 ASN 7 550 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.076077 restraints weight = 312514.831| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.96 r_work: 0.2472 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 76721 Z= 0.288 Angle : 0.599 27.134 108171 Z= 0.295 Chirality : 0.042 1.969 12637 Planarity : 0.005 0.127 10325 Dihedral : 18.511 118.157 21714 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 0.72 % Allowed : 9.99 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % 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: 1.09 (0.11), residues: 6419 helix: 1.90 (0.10), residues: 2941 sheet: -0.36 (0.19), residues: 728 loop : -0.19 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 104 HIS 0.009 0.001 HIS 7 550 PHE 0.011 0.001 PHE B 58 TYR 0.017 0.001 TYR 7 600 ARG 0.012 0.000 ARG 4 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39921.66 seconds wall clock time: 685 minutes 31.40 seconds (41131.40 seconds total)