Starting phenix.real_space_refine on Fri Mar 15 14:45:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw4_10021/03_2024/6rw4_10021_trim_updated.pdb" } resolution = 2.97 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= 0.009 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 963 5.49 5 Mg 60 5.21 5 S 237 5.16 5 C 39831 2.51 5 N 12403 2.21 5 O 15353 1.98 5 H 59211 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 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 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 ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 "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 "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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 128080 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 30527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 30527 Classifications: {'RNA': 955} Modifications used: {'rna2p_pur': 76, 'rna2p_pyr': 84, 'rna3p': 5, 'rna3p_pur': 418, 'rna3p_pyr': 372} Link IDs: {'rna2p': 160, 'rna3p': 794} 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: "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: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} 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: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 68186 SG CYS O 94 128.041 90.924 139.337 1.00 25.01 S ATOM 68366 SG CYS O 105 130.473 88.745 137.978 1.00 22.44 S ATOM 68409 SG CYS O 108 129.142 87.445 140.941 1.00 24.91 S ATOM 68980 SG CYS O 143 131.335 90.744 141.148 1.00 20.65 S ATOM 43547 SG CYS E 105 162.430 140.949 63.049 1.00 53.99 S ATOM 70898 SG CYS P 68 162.680 141.885 58.930 1.00 36.04 S ATOM 70850 SG CYS P 65 158.011 143.076 58.727 1.00 35.07 S ATOM 71398 SG CYS P 100 157.356 143.486 62.460 1.00 28.42 S ATOM 63916 SG CYS M 26 147.137 106.771 159.664 1.00 22.73 S ATOM 83113 SG CYS T 149 147.043 103.548 158.227 1.00 24.69 S ATOM 82974 SG CYS T 139 153.711 104.708 159.279 1.00 24.19 S ATOM 83003 SG CYS T 141 151.542 102.377 157.437 1.00 23.64 S Time building chain proxies: 39.50, per 1000 atoms: 0.31 Number of scatterers: 128080 At special positions: 0 Unit cell: (215.8, 197.54, 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 237 16.00 P 963 15.00 Mg 60 11.99 O 15353 8.00 N 12403 7.00 C 39831 6.00 H 59211 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: 76.36 Conformation dependent library (CDL) restraints added in 7.2 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 E 105 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 68 " 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 143 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " Number of angles added : 6 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11246 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: 226 helices and 33 sheets defined 54.6% alpha, 9.0% beta 269 base pairs and 554 stacking pairs defined. Time for finding SS restraints: 85.24 Creating SS restraints... Processing helix chain 'B' and resid 53 through 70 removed outlier: 4.793A pdb=" N ASP B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Proline residue: B 66 - end of helix removed outlier: 4.095A pdb=" N HIS B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 4.862A pdb=" N LEU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 5.333A 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: 3.557A pdb=" N ALA B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 removed outlier: 3.932A pdb=" N GLU B 103 " --> pdb=" O HIS B 99 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 5.556A pdb=" N PHE B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 107' Processing helix chain 'B' and resid 117 through 139 removed outlier: 3.668A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 removed outlier: 4.705A pdb=" N TYR B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.517A 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: 4.079A pdb=" N ARG B 210 " --> pdb=" O HIS B 206 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 277 removed outlier: 3.855A pdb=" N LEU B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.632A pdb=" N HIS C 57 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.703A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.580A 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 removed outlier: 3.596A pdb=" N THR C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.683A pdb=" N ALA D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.636A pdb=" N LYS D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 113' Processing helix chain 'D' and resid 161 through 186 removed outlier: 3.513A pdb=" N LYS D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS D 186 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 279 removed outlier: 3.668A pdb=" N ARG D 269 " --> pdb=" O MET D 265 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.815A 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: 3.657A pdb=" N GLY D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 33 Processing helix chain 'E' and resid 71 through 86 removed outlier: 4.132A pdb=" N VAL E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER E 83 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 85 " --> pdb=" O HIS E 81 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 4.527A pdb=" N GLN E 100 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 5.685A 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: 4.375A pdb=" N TYR F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.543A pdb=" N LEU F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 54 through 59' Processing helix chain 'F' and resid 60 through 73 removed outlier: 3.708A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 5.065A 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: 3.929A pdb=" N ALA F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 138 removed outlier: 4.796A pdb=" N ALA F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU F 138 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 153 removed outlier: 3.634A pdb=" N CYS F 152 " --> pdb=" O ALA F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 193 removed outlier: 3.575A pdb=" N MET F 184 " --> pdb=" O ARG F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.516A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.938A pdb=" N ARG F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA F 235 " --> pdb=" O GLU F 231 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N HIS F 238 " --> pdb=" O ARG F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 93 removed outlier: 3.685A pdb=" N GLU G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.527A pdb=" N TYR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 123 removed outlier: 3.943A 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: 3.596A pdb=" N LEU G 170 " --> pdb=" O TYR G 166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN G 171 " --> pdb=" O GLY G 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 210 removed outlier: 3.928A 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: 3.537A pdb=" N LEU G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 232 removed outlier: 5.079A pdb=" N GLN G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 246 removed outlier: 4.082A pdb=" N PHE G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) removed outlier: 5.001A 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: 3.589A 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: 3.602A pdb=" N ALA G 341 " --> pdb=" O ARG G 337 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE G 355 " --> pdb=" O ALA G 351 " (cutoff:3.500A) removed outlier: 3.905A 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: 3.687A pdb=" N LEU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 164 Processing helix chain 'H' and resid 181 through 187 removed outlier: 3.672A pdb=" N LYS H 185 " --> pdb=" O PRO H 181 " (cutoff:3.500A) removed outlier: 4.415A 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 111 through 116 removed outlier: 3.643A pdb=" N GLY I 116 " --> pdb=" O CYS I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 124 removed outlier: 4.377A pdb=" N GLY I 123 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 4.780A 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: 3.729A pdb=" N ARG I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS I 142 " --> pdb=" O ARG I 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY I 143 " --> pdb=" O ALA I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 169 removed outlier: 3.807A pdb=" N ALA I 161 " --> pdb=" O GLY I 157 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) removed outlier: 3.826A 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: 3.589A pdb=" N GLU K 46 " --> pdb=" O LYS K 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 3.815A pdb=" N LEU K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN K 60 " --> pdb=" O SER K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 79 removed outlier: 3.593A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Proline residue: K 79 - end of helix Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 73 through 80 removed outlier: 4.287A pdb=" N ASN L 78 " --> pdb=" O LYS L 74 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) Proline residue: L 80 - end of helix Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.553A pdb=" N SER L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 4.019A pdb=" N MET L 103 " --> pdb=" O ASN L 99 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS L 105 " --> pdb=" O LYS L 101 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 147 removed outlier: 3.575A pdb=" N LYS L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.913A 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 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 84 through 95 removed outlier: 3.501A pdb=" N GLY M 92 " --> pdb=" O GLU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 128 removed outlier: 3.735A pdb=" N LEU M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 113 removed outlier: 4.812A pdb=" N SER N 112 " --> pdb=" O SER N 108 " (cutoff:3.500A) removed outlier: 3.877A 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: 4.752A pdb=" N TYR O 58 " --> pdb=" O GLU O 54 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU O 59 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU O 60 " --> pdb=" O TRP O 56 " (cutoff:3.500A) removed outlier: 3.669A 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 removed outlier: 3.612A pdb=" N ARG O 67 " --> pdb=" O GLU O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 111 removed outlier: 4.156A pdb=" N ASP O 110 " --> pdb=" O PRO O 106 " (cutoff:3.500A) removed outlier: 5.044A 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: 4.231A pdb=" N PHE O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL O 127 " --> pdb=" O LEU O 123 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS O 128 " --> pdb=" O GLU O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 141 removed outlier: 3.727A pdb=" N THR O 140 " --> pdb=" O TYR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 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: 4.112A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 5.758A 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: 3.544A pdb=" N GLU P 106 " --> pdb=" O LYS P 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY P 118 " --> pdb=" O ALA P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 131 removed outlier: 3.938A pdb=" N LEU P 130 " --> pdb=" O ASP P 126 " (cutoff:3.500A) removed outlier: 4.808A 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 removed outlier: 3.503A pdb=" N ALA Q 22 " --> pdb=" O ASN Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 45 removed outlier: 3.742A pdb=" N ARG Q 43 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR Q 44 " --> pdb=" O LYS Q 40 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR Q 45 " --> pdb=" O HIS Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 80 removed outlier: 4.921A pdb=" N ARG Q 77 " --> pdb=" O ASN Q 73 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS Q 78 " --> pdb=" O PHE Q 74 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN Q 79 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARG Q 80 " --> pdb=" O MET Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.507A pdb=" N ILE R 78 " --> pdb=" O GLU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 92 removed outlier: 3.656A pdb=" N LYS R 92 " --> pdb=" O GLN R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 127 removed outlier: 3.644A pdb=" N VAL R 124 " --> pdb=" O GLU R 120 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS R 127 " --> pdb=" O LYS R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.596A pdb=" N TYR R 196 " --> pdb=" O MET R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 222 Processing helix chain 'R' and resid 223 through 235 removed outlier: 3.520A pdb=" N VAL R 227 " --> pdb=" O ARG R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 257 removed outlier: 3.641A pdb=" N ILE R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS R 244 " --> pdb=" O THR R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 264 removed outlier: 4.294A pdb=" N LEU R 262 " --> pdb=" O LYS R 258 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG R 263 " --> pdb=" O TYR R 259 " (cutoff:3.500A) removed outlier: 5.451A 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 Processing helix chain 'R' and resid 293 through 309 removed outlier: 3.590A 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: 4.118A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 358 Processing helix chain 'S' and resid 11 through 23 Processing helix chain 'S' and resid 29 through 39 removed outlier: 4.360A pdb=" N ASP S 33 " --> pdb=" O PRO S 29 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Proline residue: S 39 - end of helix Processing helix chain 'S' and resid 65 through 78 removed outlier: 4.523A pdb=" N ARG S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 110 removed outlier: 3.639A pdb=" N LEU S 109 " --> pdb=" O GLU S 105 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 129 removed outlier: 3.550A pdb=" N LYS S 123 " --> pdb=" O VAL S 119 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 19 removed outlier: 3.712A pdb=" N GLN T 18 " --> pdb=" O GLN T 14 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY T 19 " --> pdb=" O TYR T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 60 removed outlier: 3.798A pdb=" N GLU T 42 " --> pdb=" O GLY T 38 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY T 43 " --> pdb=" O GLU T 39 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA T 44 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE T 52 " --> pdb=" O VAL T 48 " (cutoff:3.500A) Proline residue: T 53 - end of helix removed outlier: 3.554A pdb=" N LYS T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) Proline residue: T 60 - end of helix Processing helix chain 'T' and resid 94 through 106 removed outlier: 3.586A pdb=" N ARG T 103 " --> pdb=" O MET T 99 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS T 104 " --> pdb=" O GLU T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 125 removed outlier: 3.563A pdb=" N LEU T 113 " --> pdb=" O ASN T 109 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU T 116 " --> pdb=" O THR T 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N HIS T 125 " --> pdb=" O LYS T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 161 removed outlier: 3.641A pdb=" N ARG T 160 " --> pdb=" O PRO T 156 " (cutoff:3.500A) removed outlier: 5.896A 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 'T' and resid 139 through 144 removed outlier: 3.860A pdb=" N GLU T 142 " --> pdb=" O CYS T 139 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL T 143 " --> pdb=" O ILE T 140 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU T 144 " --> pdb=" O CYS T 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 139 through 144' Processing helix chain 'U' and resid 35 through 40 removed outlier: 3.879A pdb=" N ILE U 39 " --> pdb=" O ALA U 35 " (cutoff:3.500A) removed outlier: 5.470A 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 49 through 135 removed outlier: 3.720A pdb=" N ARG U 86 " --> pdb=" O VAL U 82 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY U 88 " --> pdb=" O GLU U 84 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL U 89 " --> pdb=" O ALA U 85 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LEU U 90 " --> pdb=" O ARG U 86 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA U 91 " --> pdb=" O ALA U 87 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS U 94 " --> pdb=" O LEU U 90 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS U 97 " --> pdb=" O ARG U 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN U 126 " --> pdb=" O ALA U 122 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN U 133 " --> pdb=" O ARG U 129 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN U 135 " --> pdb=" O GLN U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 165 removed outlier: 3.681A pdb=" N ALA U 140 " --> pdb=" O ALA U 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN U 151 " --> pdb=" O GLN U 147 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG U 152 " --> pdb=" O ALA U 148 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 184 removed outlier: 5.055A pdb=" N ARG U 184 " --> pdb=" O ALA U 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 36 Processing helix chain 'V' and resid 37 through 43 removed outlier: 3.777A pdb=" N GLU V 41 " --> pdb=" O SER V 37 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA V 42 " --> pdb=" O HIS V 38 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG V 43 " --> pdb=" O LYS V 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 37 through 43' Processing helix chain 'V' and resid 49 through 64 removed outlier: 3.609A pdb=" N THR V 60 " --> pdb=" O LEU V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 79 removed outlier: 3.996A pdb=" N ILE V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER V 73 " --> pdb=" O SER V 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG V 74 " --> pdb=" O LEU V 70 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP V 77 " --> pdb=" O SER V 73 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE V 79 " --> pdb=" O LEU V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 99 removed outlier: 3.935A pdb=" N ASP V 86 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS V 87 " --> pdb=" O GLU V 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR V 91 " --> pdb=" O HIS V 87 " (cutoff:3.500A) removed outlier: 3.868A 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: 3.610A pdb=" N ILE V 109 " --> pdb=" O ARG V 105 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.768A pdb=" N PHE V 151 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS V 154 " --> pdb=" O SER V 150 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.632A pdb=" N SER V 162 " --> pdb=" O LYS V 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 194 removed outlier: 3.807A pdb=" N LYS V 192 " --> pdb=" O HIS V 188 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N THR V 194 " --> pdb=" O LEU V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 197 through 216 removed outlier: 3.548A pdb=" N ARG V 202 " --> pdb=" O TRP V 198 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) Proline residue: V 211 - end of helix removed outlier: 3.726A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) removed outlier: 5.179A 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: 4.074A pdb=" N VAL V 243 " --> pdb=" O GLY V 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR V 244 " --> pdb=" O LEU V 240 " (cutoff:3.500A) Processing helix chain 'V' and resid 254 through 270 removed outlier: 3.791A pdb=" N VAL V 262 " --> pdb=" O ARG V 258 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET V 263 " --> pdb=" O ALA V 259 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA V 267 " --> pdb=" O MET V 263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA V 268 " --> pdb=" O GLU V 264 " (cutoff:3.500A) Proline residue: V 270 - end of helix Processing helix chain 'V' and resid 276 through 293 removed outlier: 4.276A pdb=" N ALA V 293 " --> pdb=" O ALA V 289 " (cutoff:3.500A) Processing helix chain 'V' and resid 322 through 345 removed outlier: 3.671A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 3.709A 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 363 removed outlier: 3.502A pdb=" N GLU V 362 " --> pdb=" O GLN V 358 " (cutoff:3.500A) Processing helix chain 'V' and resid 365 through 407 removed outlier: 3.624A pdb=" N THR V 374 " --> pdb=" O GLU V 370 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN V 388 " --> pdb=" O LEU V 384 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU V 389 " --> pdb=" O ASP V 385 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE V 390 " --> pdb=" O LEU V 386 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN V 391 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU V 398 " --> pdb=" O GLN V 394 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN V 399 " --> pdb=" O GLN V 395 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN V 402 " --> pdb=" O GLU V 398 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR V 404 " --> pdb=" O ALA V 400 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN V 405 " --> pdb=" O LYS V 401 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN V 407 " --> pdb=" O GLU V 403 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 87 removed outlier: 3.620A 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: 4.409A pdb=" N TYR W 134 " --> pdb=" O ASP W 130 " (cutoff:3.500A) removed outlier: 5.342A 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: 3.524A pdb=" N VAL X 88 " --> pdb=" O PRO X 84 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 115 removed outlier: 3.501A pdb=" N LEU X 112 " --> pdb=" O LEU X 108 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN X 114 " --> pdb=" O HIS X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 149 removed outlier: 3.683A pdb=" N LYS X 147 " --> pdb=" O HIS X 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN X 148 " --> pdb=" O PHE X 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP X 149 " --> pdb=" O CYS X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 164 removed outlier: 5.001A pdb=" N TRP X 161 " --> pdb=" O ASP X 157 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL X 162 " --> pdb=" O ALA X 158 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS X 163 " --> pdb=" O HIS X 159 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN X 164 " --> pdb=" O LEU X 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 157 through 164' Processing helix chain 'X' and resid 180 through 196 removed outlier: 3.506A pdb=" N THR X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP X 187 " --> pdb=" O GLU X 183 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS X 189 " --> pdb=" O SER X 185 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 202 removed outlier: 4.053A pdb=" N GLN X 201 " --> pdb=" O ARG X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 233 removed outlier: 4.190A pdb=" N VAL X 225 " --> pdb=" O PRO X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 254 removed outlier: 5.726A pdb=" N ASP X 238 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY X 241 " --> pdb=" O THR X 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER X 252 " --> pdb=" O LYS X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 270 removed outlier: 4.843A pdb=" N TRP X 269 " --> pdb=" O ILE X 265 " (cutoff:3.500A) removed outlier: 4.031A 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: 3.533A pdb=" N LEU X 293 " --> pdb=" O LEU X 289 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG X 294 " --> pdb=" O VAL X 290 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS X 298 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 5.741A 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: 3.608A pdb=" N LYS X 378 " --> pdb=" O GLU X 374 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU X 379 " --> pdb=" O GLU X 375 " (cutoff:3.500A) Processing helix chain 'X' and resid 387 through 398 removed outlier: 3.575A pdb=" N ALA X 396 " --> pdb=" O GLU X 392 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU X 398 " --> pdb=" O HIS X 394 " (cutoff:3.500A) Processing helix chain 'Y' and resid 276 through 291 removed outlier: 3.668A pdb=" N PHE Y 282 " --> pdb=" O TRP Y 278 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA Y 283 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS Y 284 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Y 286 " --> pdb=" O PHE Y 282 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA Y 287 " --> pdb=" O ALA Y 283 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR Y 288 " --> pdb=" O LYS Y 284 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN Y 290 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU Y 291 " --> pdb=" O ALA Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 308 removed outlier: 3.615A pdb=" N GLU Y 300 " --> pdb=" O ASN Y 296 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 333 removed outlier: 3.899A pdb=" N HIS Y 331 " --> pdb=" O GLU Y 327 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE Y 333 " --> pdb=" O HIS Y 329 " (cutoff:3.500A) Processing helix chain 'Y' and resid 334 through 339 removed outlier: 4.360A pdb=" N LEU Y 338 " --> pdb=" O LEU Y 334 " (cutoff:3.500A) removed outlier: 4.940A 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: 3.681A pdb=" N LEU Y 353 " --> pdb=" O HIS Y 349 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR Y 355 " --> pdb=" O MET Y 351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS Y 356 " --> pdb=" O GLU Y 352 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.528A pdb=" N GLU Y 371 " --> pdb=" O LYS Y 367 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.676A pdb=" N LYS Y 384 " --> pdb=" O PHE Y 380 " (cutoff:3.500A) Processing helix chain 'Y' and resid 385 through 391 removed outlier: 3.634A pdb=" N GLU Y 389 " --> pdb=" O ASP Y 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER Y 390 " --> pdb=" O ILE Y 386 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 20 removed outlier: 3.540A pdb=" N GLY Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 39 removed outlier: 4.031A pdb=" N LYS Z 32 " --> pdb=" O SER Z 28 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL Z 33 " --> pdb=" O LYS Z 29 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL Z 34 " --> pdb=" O SER Z 30 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 46 removed outlier: 5.814A pdb=" N LYS Z 46 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 69 removed outlier: 3.509A pdb=" N MET Z 62 " --> pdb=" O TYR Z 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 90 removed outlier: 3.554A pdb=" N LYS Z 83 " --> pdb=" O MET Z 79 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS Z 87 " --> pdb=" O LYS Z 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 26 removed outlier: 3.828A pdb=" N GLU 0 13 " --> pdb=" O ARG 0 9 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 0 16 " --> pdb=" O ALA 0 12 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Processing helix chain '0' and resid 51 through 61 removed outlier: 3.690A pdb=" N TRP 0 55 " --> pdb=" O PRO 0 51 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA 0 56 " --> pdb=" O VAL 0 52 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP 0 57 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG 0 59 " --> pdb=" O TRP 0 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG 0 60 " --> pdb=" O ALA 0 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU 0 61 " --> pdb=" O ASP 0 57 " (cutoff:3.500A) Processing helix chain '0' and resid 63 through 72 removed outlier: 5.475A pdb=" N ARG 0 70 " --> pdb=" O GLN 0 66 " (cutoff:3.500A) removed outlier: 4.495A 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: 4.530A pdb=" N GLU 0 148 " --> pdb=" O LYS 0 144 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA 0 149 " --> pdb=" O HIS 0 145 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR 0 151 " --> pdb=" O GLU 0 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA 0 152 " --> pdb=" O GLU 0 148 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 182 removed outlier: 3.534A pdb=" N GLN 0 179 " --> pdb=" O ILE 0 175 " (cutoff:3.500A) Processing helix chain '0' and resid 206 through 211 removed outlier: 3.976A pdb=" N LYS 0 210 " --> pdb=" O LYS 0 206 " (cutoff:3.500A) removed outlier: 5.693A 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: 4.618A pdb=" N LYS 1 59 " --> pdb=" O PRO 1 55 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA 1 61 " --> pdb=" O THR 1 57 " (cutoff:3.500A) Processing helix chain '1' and resid 65 through 71 removed outlier: 3.852A 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: 4.005A pdb=" N LEU 1 106 " --> pdb=" O ASN 1 102 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.828A pdb=" N ALA 1 125 " --> pdb=" O LYS 1 121 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS 1 127 " --> pdb=" O CYS 1 123 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N CYS 1 130 " --> pdb=" O LEU 1 126 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR 1 131 " --> pdb=" O LYS 1 127 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 147 removed outlier: 3.753A pdb=" N CYS 1 143 " --> pdb=" O SER 1 139 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS 1 146 " --> pdb=" O LYS 1 142 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 170 removed outlier: 4.694A pdb=" N ARG 1 169 " --> pdb=" O ASN 1 165 " (cutoff:3.500A) removed outlier: 4.896A 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: 4.105A pdb=" N LEU 1 180 " --> pdb=" O LYS 1 176 " (cutoff:3.500A) removed outlier: 5.465A 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: 3.692A pdb=" N LYS 1 192 " --> pdb=" O LYS 1 188 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY 1 195 " --> pdb=" O ILE 1 191 " (cutoff:3.500A) Processing helix chain '1' and resid 214 through 236 removed outlier: 3.548A pdb=" N TRP 1 234 " --> pdb=" O TYR 1 230 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN 1 235 " --> pdb=" O HIS 1 231 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR 1 236 " --> pdb=" O GLU 1 232 " (cutoff:3.500A) Processing helix chain '1' and resid 244 through 249 removed outlier: 3.531A pdb=" N MET 1 248 " --> pdb=" O THR 1 244 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLU 1 249 " --> pdb=" O GLU 1 245 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 244 through 249' Processing helix chain '1' and resid 256 through 274 removed outlier: 3.534A pdb=" N LYS 1 270 " --> pdb=" O LEU 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 286 removed outlier: 3.534A pdb=" N THR 1 286 " --> pdb=" O GLU 1 282 " (cutoff:3.500A) Processing helix chain '1' and resid 287 through 301 removed outlier: 3.643A pdb=" N SER 1 298 " --> pdb=" O LYS 1 294 " (cutoff:3.500A) Processing helix chain '1' and resid 305 through 321 removed outlier: 3.654A pdb=" N SER 1 310 " --> pdb=" O GLU 1 306 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU 1 319 " --> pdb=" O SER 1 315 " (cutoff:3.500A) Processing helix chain '1' and resid 237 through 243 removed outlier: 3.946A pdb=" N GLU 1 240 " --> pdb=" O GLU 1 237 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS 1 241 " --> pdb=" O GLU 1 238 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER 1 242 " --> pdb=" O TRP 1 239 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.708A pdb=" N MET 2 53 " --> pdb=" O MET 2 49 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP 2 56 " --> pdb=" O MET 2 52 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS 2 57 " --> pdb=" O MET 2 53 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN 2 58 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 91 removed outlier: 4.015A pdb=" N CYS 2 66 " --> pdb=" O ARG 2 62 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG 2 67 " --> pdb=" O ASP 2 63 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS 2 68 " --> pdb=" O ASP 2 64 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU 2 69 " --> pdb=" O ALA 2 65 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE 2 89 " --> pdb=" O LYS 2 85 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 112 removed outlier: 3.705A pdb=" N LYS 2 106 " --> pdb=" O ASN 2 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU 2 107 " --> pdb=" O LYS 2 103 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG 2 110 " --> pdb=" O LYS 2 106 " (cutoff:3.500A) removed outlier: 3.764A 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: 3.835A pdb=" N ARG 3 135 " --> pdb=" O LEU 3 131 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS 3 149 " --> pdb=" O LYS 3 145 " (cutoff:3.500A) Processing helix chain '3' and resid 152 through 181 removed outlier: 3.703A pdb=" N LYS 3 156 " --> pdb=" O PHE 3 152 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP 3 177 " --> pdb=" O LEU 3 173 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY 3 181 " --> pdb=" O TRP 3 177 " (cutoff:3.500A) Processing helix chain '4' and resid 68 through 79 removed outlier: 3.648A pdb=" N SER 4 76 " --> pdb=" O GLN 4 72 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR 4 77 " --> pdb=" O ALA 4 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL 4 78 " --> pdb=" O LEU 4 74 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN 4 79 " --> pdb=" O ALA 4 75 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 125 removed outlier: 3.526A pdb=" N LYS 4 110 " --> pdb=" O PHE 4 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY 4 113 " --> pdb=" O ALA 4 109 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.688A pdb=" N LEU 4 157 " --> pdb=" O SER 4 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS 4 158 " --> pdb=" O GLU 4 154 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU 4 159 " --> pdb=" O ALA 4 155 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG 4 160 " --> pdb=" O ALA 4 156 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 4 162 " --> pdb=" O LYS 4 158 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 4 163 " --> pdb=" O GLU 4 159 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG 4 164 " --> pdb=" O ARG 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 180 removed outlier: 3.539A pdb=" N ASP 4 174 " --> pdb=" O VAL 4 170 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN 4 175 " --> pdb=" O ASP 4 171 " (cutoff:3.500A) Processing helix chain '4' and resid 184 through 199 removed outlier: 3.644A pdb=" N THR 4 188 " --> pdb=" O SER 4 184 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER 4 190 " --> pdb=" O GLU 4 186 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU 4 194 " --> pdb=" O SER 4 190 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR 4 198 " --> pdb=" O LEU 4 194 " (cutoff:3.500A) Processing helix chain '4' and resid 242 through 251 Processing helix chain '4' and resid 255 through 270 removed outlier: 3.853A pdb=" N TYR 4 259 " --> pdb=" O ASN 4 255 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG 4 264 " --> pdb=" O CYS 4 260 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY 4 265 " --> pdb=" O THR 4 261 " (cutoff:3.500A) Processing helix chain '4' and resid 271 through 286 removed outlier: 3.534A pdb=" N ASN 4 277 " --> pdb=" O GLU 4 273 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU 4 281 " --> pdb=" O ASN 4 277 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 4 282 " --> pdb=" O LEU 4 278 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU 4 283 " --> pdb=" O TYR 4 279 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG 4 286 " --> pdb=" O LEU 4 282 " (cutoff:3.500A) Processing helix chain '4' and resid 290 through 306 removed outlier: 3.668A pdb=" N GLU 4 299 " --> pdb=" O ASN 4 295 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 4 302 " --> pdb=" O ILE 4 298 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE 4 305 " --> pdb=" O THR 4 301 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN 4 306 " --> pdb=" O VAL 4 302 " (cutoff:3.500A) Processing helix chain '4' and resid 308 through 327 removed outlier: 4.062A pdb=" N LYS 4 327 " --> pdb=" O MET 4 323 " (cutoff:3.500A) Processing helix chain '4' and resid 331 through 344 removed outlier: 3.615A pdb=" N PHE 4 335 " --> pdb=" O ASN 4 331 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE 4 338 " --> pdb=" O THR 4 334 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) Processing helix chain '4' and resid 347 through 364 removed outlier: 4.722A pdb=" N SER 4 351 " --> pdb=" O VAL 4 347 " (cutoff:3.500A) Proline residue: 4 352 - end of helix removed outlier: 3.891A pdb=" N LYS 4 361 " --> pdb=" O LEU 4 357 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA 4 362 " --> pdb=" O ARG 4 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE 4 363 " --> pdb=" O GLU 4 359 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY 4 364 " --> pdb=" O MET 4 360 " (cutoff:3.500A) Processing helix chain '4' and resid 368 through 380 removed outlier: 3.635A pdb=" N TYR 4 372 " --> pdb=" O SER 4 368 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 401 removed outlier: 3.810A pdb=" N PHE 4 391 " --> pdb=" O LYS 4 387 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 427 Processing helix chain '4' and resid 428 through 441 removed outlier: 3.666A pdb=" N ALA 4 432 " --> pdb=" O ASP 4 428 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN 4 434 " --> pdb=" O GLU 4 430 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS 4 440 " --> pdb=" O HIS 4 436 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR 4 441 " --> pdb=" O GLY 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 450 through 468 removed outlier: 3.608A pdb=" N LEU 4 467 " --> pdb=" O ASP 4 463 " (cutoff:3.500A) Processing helix chain '4' and resid 470 through 484 removed outlier: 3.542A pdb=" N LEU 4 475 " --> pdb=" O ILE 4 471 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS 4 476 " --> pdb=" O ASP 4 472 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU 4 479 " --> pdb=" O LEU 4 475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP 4 480 " --> pdb=" O LYS 4 476 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.569A pdb=" N MET 4 493 " --> pdb=" O HIS 4 489 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 4 499 " --> pdb=" O HIS 4 495 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL 4 502 " --> pdb=" O GLN 4 498 " (cutoff:3.500A) Processing helix chain '4' and resid 508 through 520 removed outlier: 4.216A pdb=" N LYS 4 514 " --> pdb=" O PRO 4 510 " (cutoff:3.500A) Processing helix chain '4' and resid 524 through 537 removed outlier: 4.115A pdb=" N MET 4 533 " --> pdb=" O GLU 4 529 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU 4 534 " --> pdb=" O GLU 4 530 " (cutoff:3.500A) Processing helix chain '4' and resid 542 through 562 removed outlier: 3.727A pdb=" N ALA 4 547 " --> pdb=" O GLU 4 543 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA 4 549 " --> pdb=" O GLN 4 545 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP 4 550 " --> pdb=" O VAL 4 546 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP 4 554 " --> pdb=" O ASP 4 550 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR 4 559 " --> pdb=" O ILE 4 555 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN 4 562 " --> pdb=" O ALA 4 558 " (cutoff:3.500A) Processing helix chain '4' and resid 572 through 587 removed outlier: 3.741A pdb=" N ILE 4 581 " --> pdb=" O ASN 4 577 " (cutoff:3.500A) Processing helix chain '4' and resid 588 through 603 removed outlier: 3.847A pdb=" N LYS 4 594 " --> pdb=" O GLN 4 590 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET 4 595 " --> pdb=" O GLU 4 591 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU 4 596 " --> pdb=" O ALA 4 592 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE 4 599 " --> pdb=" O MET 4 595 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG 4 600 " --> pdb=" O LEU 4 596 " (cutoff:3.500A) Processing helix chain '4' and resid 607 through 622 removed outlier: 3.539A pdb=" N GLU 4 613 " --> pdb=" O GLU 4 609 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP 4 616 " --> pdb=" O ASN 4 612 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER 4 617 " --> pdb=" O GLU 4 613 " (cutoff:3.500A) Processing helix chain '4' and resid 623 through 638 removed outlier: 3.708A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 639 through 653 removed outlier: 4.093A pdb=" N GLU 4 643 " --> pdb=" O LEU 4 639 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY 4 644 " --> pdb=" O PRO 4 640 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN 4 647 " --> pdb=" O GLU 4 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG 4 648 " --> pdb=" O GLY 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 666 removed outlier: 3.674A pdb=" N LYS 4 660 " --> pdb=" O ASN 4 656 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 4 663 " --> pdb=" O GLN 4 659 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU 4 666 " --> pdb=" O ALA 4 662 " (cutoff:3.500A) Processing helix chain '4' and resid 443 through 449 removed outlier: 3.580A pdb=" N LYS 4 446 " --> pdb=" O ASP 4 443 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE 4 448 " --> pdb=" O TRP 4 445 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY 4 449 " --> pdb=" O LYS 4 446 " (cutoff:3.500A) Processing helix chain '8' and resid 101 through 113 removed outlier: 3.754A pdb=" N ILE 8 106 " --> pdb=" O ARG 8 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 8 107 " --> pdb=" O ALA 8 103 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU 8 108 " --> pdb=" O ASN 8 104 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 8 112 " --> pdb=" O LEU 8 108 " (cutoff:3.500A) Processing helix chain '8' and resid 132 through 150 removed outlier: 3.784A pdb=" N ARG 8 140 " --> pdb=" O ILE 8 136 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU 8 145 " --> pdb=" O GLN 8 141 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 8 147 " --> pdb=" O LEU 8 143 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS 8 148 " --> pdb=" O ARG 8 144 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 186 removed outlier: 3.608A pdb=" N GLN 8 180 " --> pdb=" O THR 8 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN 8 181 " --> pdb=" O LYS 8 177 " (cutoff:3.500A) Processing helix chain '8' and resid 202 through 218 removed outlier: 3.790A pdb=" N MET 8 206 " --> pdb=" O SER 8 202 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU 8 207 " --> pdb=" O GLU 8 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU 8 208 " --> pdb=" O ASN 8 204 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE 8 209 " --> pdb=" O GLU 8 205 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE 8 210 " --> pdb=" O MET 8 206 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS 8 211 " --> pdb=" O GLU 8 207 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR 8 216 " --> pdb=" O GLN 8 212 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.513A pdb=" N THR 8 257 " --> pdb=" O GLU 8 253 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN 8 258 " --> pdb=" O THR 8 254 " (cutoff:3.500A) removed outlier: 3.803A 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: 4.940A pdb=" N HIS B 90 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.737A 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: 3.593A 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: 5.591A pdb=" N LEU C 69 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 125 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 138 through 141 removed outlier: 5.782A pdb=" N GLY D 138 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 3.553A 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: 4.232A pdb=" N ILE D 201 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR D 220 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.572A 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: 7.558A pdb=" N HIS D 292 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS D 307 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN D 308 " --> pdb=" O ASP D 331 " (cutoff:3.500A) removed outlier: 5.994A 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: 7.033A 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: 4.649A pdb=" N MET G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ALA G 268 " --> pdb=" O LYS G 287 " (cutoff:3.500A) removed outlier: 3.879A 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: 3.610A 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: 4.307A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR H 140 " --> pdb=" O PRO H 111 " (cutoff:3.500A) removed outlier: 3.804A 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 84 through 91 removed outlier: 4.285A pdb=" N ASN I 94 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 148 through 153 removed outlier: 5.447A 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: 4.967A pdb=" N LEU J 109 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY J 113 " --> pdb=" O LYS J 122 " (cutoff:3.500A) removed outlier: 5.031A 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: 5.058A 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: 3.850A 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: 7.099A pdb=" N ARG N 11 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE N 63 " --> pdb=" O VAL N 85 " (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: 5.467A pdb=" N PHE R 171 " --> pdb=" O ASP R 160 " (cutoff:3.500A) removed outlier: 4.207A 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: 4.510A pdb=" N THR W 138 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG W 139 " --> pdb=" O GLN W 173 " (cutoff:3.500A) removed outlier: 3.958A 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: 4.495A pdb=" N GLN X 66 " --> pdb=" O VAL X 101 " (cutoff:3.500A) removed outlier: 4.481A 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: 4.304A pdb=" N ILE X 122 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.181A 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: 6.843A pdb=" N GLU X 206 " --> pdb=" O LYS X 218 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS X 218 " --> pdb=" O GLU X 206 " (cutoff:3.500A) removed outlier: 6.583A 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: 4.329A 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: 5.066A pdb=" N HIS 0 111 " --> pdb=" O ASP 0 103 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA 0 114 " --> pdb=" O ILE 0 131 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '1' and resid 149 through 153 removed outlier: 3.553A pdb=" N VAL 1 204 " --> pdb=" O CYS 1 199 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG 1 197 " --> pdb=" O THR 1 206 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '8' and resid 87 through 90 Processing sheet with id= 32, first strand: chain '8' and resid 157 through 163 removed outlier: 7.785A pdb=" N HIS 8 187 " --> pdb=" O ALA 8 242 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA 8 242 " --> pdb=" O HIS 8 187 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL 8 239 " --> pdb=" O SER 8 224 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '8' and resid 227 through 230 removed outlier: 6.974A pdb=" N ALA 8 235 " --> pdb=" O VAL 8 230 " (cutoff:3.500A) 2070 hydrogen bonds defined for protein. 6183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 657 hydrogen bonds 1168 hydrogen bond angles 0 basepair planarities 269 basepair parallelities 554 stacking parallelities Total time for adding SS restraints: 55.38 Time building geometry restraints manager: 80.93 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: 59137 1.10 - 1.38: 25621 1.38 - 1.65: 46254 1.65 - 1.92: 377 1.92 - 2.20: 8 Bond restraints: 131397 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 4.05e+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 1.88e+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 1.66e+02 bond pdb=" C3' GNP X 503 " pdb=" C4' GNP X 503 " ideal model delta sigma weight residual 1.285 1.518 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C3' ATP X 501 " pdb=" C4' ATP X 501 " ideal model delta sigma weight residual 1.305 1.511 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 131392 not shown) Histogram of bond angle deviations from ideal: 79.24 - 90.60: 10 90.60 - 101.96: 1092 101.96 - 113.32: 153429 113.32 - 124.68: 74668 124.68 - 136.04: 8011 Bond angle restraints: 237210 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 90.20 14.13 1.14e+00 7.69e-01 1.54e+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 89.67 -14.01 1.14e+00 7.69e-01 1.51e+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 90.29 14.04 1.20e+00 6.94e-01 1.37e+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 89.59 -13.93 1.20e+00 6.94e-01 1.35e+02 angle pdb=" S1 FES P 201 " pdb="FE2 FES P 201 " pdb=" S2 FES P 201 " ideal model delta sigma weight residual 104.33 91.17 13.16 1.14e+00 7.69e-01 1.33e+02 ... (remaining 237205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.28: 56655 26.28 - 52.55: 3233 52.55 - 78.83: 2539 78.83 - 105.11: 22 105.11 - 131.38: 8 Dihedral angle restraints: 62457 sinusoidal: 42153 harmonic: 20304 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 74.30 125.70 1 1.50e+01 4.44e-03 6.76e+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 -145.61 -34.39 0 5.00e+00 4.00e-02 4.73e+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 -47.52 -80.48 1 1.70e+01 3.46e-03 2.77e+01 ... (remaining 62454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.125: 11942 1.125 - 2.251: 0 2.251 - 3.376: 0 3.376 - 4.502: 0 4.502 - 5.627: 2 Chirality restraints: 11944 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 2.81 -5.63 2.00e-01 2.50e+01 7.92e+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 -2.67 5.12 2.00e-01 2.50e+01 6.55e+02 chirality pdb=" C3' C A1531 " pdb=" C4' C A1531 " pdb=" O3' C A1531 " pdb=" C2' C A1531 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 11941 not shown) Planarity restraints: 15866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GNP X 503 " 0.275 2.00e-02 2.50e+03 5.72e-01 7.36e+03 pdb=" C2' GNP X 503 " -0.254 2.00e-02 2.50e+03 pdb=" C3' GNP X 503 " -0.686 2.00e-02 2.50e+03 pdb=" C4' GNP X 503 " 0.436 2.00e-02 2.50e+03 pdb=" C5' GNP X 503 " -0.021 2.00e-02 2.50e+03 pdb=" N9 GNP X 503 " -0.799 2.00e-02 2.50e+03 pdb=" O2' GNP X 503 " 0.905 2.00e-02 2.50e+03 pdb=" O3' GNP X 503 " -0.509 2.00e-02 2.50e+03 pdb=" O4' GNP X 503 " 0.654 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A1076 " -0.052 2.00e-02 2.50e+03 5.69e-01 7.28e+03 pdb=" C4' 5MU A1076 " -0.421 2.00e-02 2.50e+03 pdb=" O4' 5MU A1076 " -0.570 2.00e-02 2.50e+03 pdb=" C3' 5MU A1076 " 0.600 2.00e-02 2.50e+03 pdb=" O3' 5MU A1076 " 0.590 2.00e-02 2.50e+03 pdb=" C2' 5MU A1076 " 0.189 2.00e-02 2.50e+03 pdb=" O2' 5MU A1076 " -0.946 2.00e-02 2.50e+03 pdb=" C1' 5MU A1076 " -0.234 2.00e-02 2.50e+03 pdb=" N1 5MU A1076 " 0.845 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP X 501 " 0.275 2.00e-02 2.50e+03 5.10e-01 5.85e+03 pdb=" C2' ATP X 501 " -0.268 2.00e-02 2.50e+03 pdb=" C3' ATP X 501 " -0.567 2.00e-02 2.50e+03 pdb=" C4' ATP X 501 " 0.436 2.00e-02 2.50e+03 pdb=" C5' ATP X 501 " -0.081 2.00e-02 2.50e+03 pdb=" N9 ATP X 501 " -0.775 2.00e-02 2.50e+03 pdb=" O2' ATP X 501 " 0.696 2.00e-02 2.50e+03 pdb=" O3' ATP X 501 " -0.383 2.00e-02 2.50e+03 pdb=" O4' ATP X 501 " 0.666 2.00e-02 2.50e+03 ... (remaining 15863 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.17: 4517 2.17 - 2.91: 301102 2.91 - 3.65: 443339 3.65 - 4.40: 728919 4.40 - 5.14: 1103887 Nonbonded interactions: 2581764 Sorted by model distance: nonbonded pdb=" H3 U A1077 " pdb=" OP2 A A1080 " model vdw 1.427 1.850 nonbonded pdb=" OP1 A A1231 " pdb="HH22 ARG K 88 " model vdw 1.474 1.850 nonbonded pdb=" O GLY O 182 " pdb=" HZ3 LYS R 183 " model vdw 1.484 1.850 nonbonded pdb=" O GLY J 99 " pdb="HH22 ARG J 127 " model vdw 1.504 1.850 nonbonded pdb=" O LEU 4 481 " pdb=" H ALA 4 485 " model vdw 1.529 1.850 ... (remaining 2581759 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 1.240 Extract box with map and model: 24.570 Check model and map are aligned: 1.340 Set scattering table: 0.820 Process input model: 425.130 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 469.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 72186 Z= 0.486 Angle : 0.666 31.915 102044 Z= 0.366 Chirality : 0.080 5.627 11944 Planarity : 0.012 0.572 9535 Dihedral : 18.289 131.383 33644 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.09), residues: 5850 helix: -2.23 (0.08), residues: 2679 sheet: -0.69 (0.21), residues: 545 loop : -1.15 (0.10), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 32 HIS 0.008 0.002 HIS D 317 PHE 0.017 0.002 PHE O 135 TYR 0.018 0.002 TYR X 348 ARG 0.008 0.001 ARG H 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1081 time to evaluate : 6.384 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: B 200 ASN cc_start: 0.8045 (p0) cc_final: 0.7705 (p0) REVERT: B 204 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7095 (mt-10) REVERT: D 226 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7801 (tpp80) REVERT: D 424 ASN cc_start: 0.8177 (m-40) cc_final: 0.7954 (m110) REVERT: P 56 ASN cc_start: 0.8785 (t0) cc_final: 0.8569 (t0) REVERT: R 116 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7838 (ttm110) REVERT: T 124 SER cc_start: 0.8949 (p) cc_final: 0.8620 (t) REVERT: V 81 SER cc_start: 0.7972 (t) cc_final: 0.7089 (p) REVERT: W 103 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7497 (ttm170) REVERT: 1 311 GLN cc_start: 0.8413 (tt0) cc_final: 0.8117 (tt0) REVERT: 4 360 MET cc_start: 0.7097 (mtp) cc_final: 0.6862 (mtp) REVERT: 4 546 VAL cc_start: 0.8412 (t) cc_final: 0.8198 (p) outliers start: 3 outliers final: 4 residues processed: 1084 average time/residue: 3.8764 time to fit residues: 5172.8701 Evaluate side-chains 758 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 754 time to evaluate : 6.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain V residue 52 ASP 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: 674 random chunks: chunk 569 optimal weight: 1.9990 chunk 510 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 344 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 528 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 321 optimal weight: 0.6980 chunk 393 optimal weight: 2.9990 chunk 612 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS B 148 ASN B 178 ASN C 115 ASN D 127 ASN D 175 GLN D 415 GLN H 109 HIS H 176 GLN K 119 GLN O 152 GLN S 47 GLN T 51 ASN U 188 ASN V 38 HIS V 134 GLN V 380 GLN V 391 GLN X 69 ASN X 110 HIS X 292 ASN Y 290 ASN Y 295 GLN 0 108 ASN 4 285 ASN 4 288 HIS 4 504 ASN 8 198 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 72186 Z= 0.232 Angle : 0.677 30.673 102044 Z= 0.337 Chirality : 0.041 1.825 11944 Planarity : 0.005 0.135 9535 Dihedral : 19.649 125.849 21089 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.18 % Favored : 98.80 % Rotamer: Outliers : 1.15 % Allowed : 10.68 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.10), residues: 5850 helix: -0.24 (0.09), residues: 2749 sheet: -0.27 (0.21), residues: 544 loop : -0.64 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 0 95 HIS 0.014 0.001 HIS V 38 PHE 0.018 0.001 PHE S 118 TYR 0.017 0.002 TYR R 242 ARG 0.009 0.001 ARG 2 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 767 time to evaluate : 6.365 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: D 226 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7826 (tpp80) REVERT: D 424 ASN cc_start: 0.8259 (m-40) cc_final: 0.8029 (m110) REVERT: E 77 SER cc_start: 0.8948 (t) cc_final: 0.8745 (m) REVERT: G 131 ILE cc_start: 0.8923 (mt) cc_final: 0.8704 (mm) REVERT: G 173 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: Q 66 MET cc_start: 0.8366 (mtt) cc_final: 0.8128 (mtt) REVERT: R 116 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7781 (ttm110) REVERT: U 44 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7420 (mpt) REVERT: V 398 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: 1 311 GLN cc_start: 0.8271 (tt0) cc_final: 0.8037 (tt0) REVERT: 4 468 MET cc_start: 0.7429 (mmm) cc_final: 0.7226 (mmt) outliers start: 60 outliers final: 29 residues processed: 798 average time/residue: 3.6986 time to fit residues: 3672.8835 Evaluate side-chains 729 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 697 time to evaluate : 6.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 269 SER Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 196 GLU Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain X residue 370 LYS Chi-restraints excluded: chain Y residue 340 SER Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 0 residue 110 ASP Chi-restraints excluded: chain 0 residue 127 GLU Chi-restraints excluded: chain 1 residue 150 GLU Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 273 GLU Chi-restraints excluded: chain 4 residue 324 VAL Chi-restraints excluded: chain 4 residue 479 GLU Chi-restraints excluded: chain 4 residue 531 ILE Chi-restraints excluded: chain 4 residue 561 SER Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 509 optimal weight: 0.9980 chunk 416 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 613 optimal weight: 10.0000 chunk 662 optimal weight: 1.9990 chunk 546 optimal weight: 10.0000 chunk 608 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 491 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 227 ASN H 133 GLN ** R 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 161 GLN X 69 ASN X 292 ASN Y 290 ASN Y 295 GLN 0 24 GLN 4 602 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 72186 Z= 0.377 Angle : 0.660 25.439 102044 Z= 0.331 Chirality : 0.046 2.068 11944 Planarity : 0.006 0.135 9535 Dihedral : 19.223 129.896 21089 Min Nonbonded Distance : 1.591 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.88 % Favored : 98.10 % Rotamer: Outliers : 1.74 % Allowed : 11.06 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 5850 helix: 0.50 (0.10), residues: 2771 sheet: -0.04 (0.21), residues: 540 loop : -0.46 (0.11), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 0 95 HIS 0.008 0.001 HIS F 146 PHE 0.014 0.002 PHE G 54 TYR 0.018 0.002 TYR D 281 ARG 0.008 0.001 ARG W 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 763 time to evaluate : 6.350 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: C 126 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: D 226 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7829 (tpp80) REVERT: E 113 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7281 (mt) REVERT: G 173 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: H 174 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: R 116 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7696 (ttp-110) REVERT: R 152 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: U 44 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7487 (mpt) REVERT: X 234 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7438 (ttm110) REVERT: X 249 ARG cc_start: 0.8541 (ptp90) cc_final: 0.8324 (ptp90) REVERT: X 253 LEU cc_start: 0.9132 (mt) cc_final: 0.8853 (mp) REVERT: Y 312 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: 0 17 ARG cc_start: 0.6848 (mtm110) cc_final: 0.6637 (ttp-170) REVERT: 1 311 GLN cc_start: 0.8356 (tt0) cc_final: 0.8088 (tt0) REVERT: 4 468 MET cc_start: 0.7696 (mmm) cc_final: 0.7320 (mmt) outliers start: 91 outliers final: 39 residues processed: 806 average time/residue: 3.7058 time to fit residues: 3715.5090 Evaluate side-chains 780 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 733 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 233 CYS Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 269 SER Chi-restraints excluded: chain V residue 272 ASP Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 114 ASN Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 149 ASP Chi-restraints excluded: chain X residue 196 GLU Chi-restraints excluded: chain X residue 234 ARG Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 312 GLU Chi-restraints excluded: chain Y residue 340 SER Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 0 residue 127 GLU Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 258 SER Chi-restraints excluded: chain 4 residue 280 THR Chi-restraints excluded: chain 4 residue 324 VAL Chi-restraints excluded: chain 4 residue 561 SER Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 2.9990 chunk 461 optimal weight: 7.9990 chunk 318 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 411 optimal weight: 0.0980 chunk 615 optimal weight: 4.9990 chunk 651 optimal weight: 5.9990 chunk 321 optimal weight: 0.9990 chunk 583 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 227 ASN I 129 GLN ** R 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 135 GLN W 173 GLN X 69 ASN X 292 ASN Y 290 ASN Y 295 GLN Y 378 ASN 0 24 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 72186 Z= 0.280 Angle : 0.616 27.201 102044 Z= 0.307 Chirality : 0.042 1.947 11944 Planarity : 0.005 0.129 9535 Dihedral : 19.030 114.096 21087 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.52 % Favored : 98.44 % Rotamer: Outliers : 1.55 % Allowed : 12.40 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 5850 helix: 1.01 (0.10), residues: 2764 sheet: 0.01 (0.21), residues: 541 loop : -0.30 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 0 95 HIS 0.006 0.001 HIS D 288 PHE 0.012 0.001 PHE B 58 TYR 0.017 0.001 TYR 4 198 ARG 0.010 0.000 ARG 2 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 751 time to evaluate : 6.374 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: B 175 MET cc_start: 0.7559 (mmp) cc_final: 0.7239 (mmp) REVERT: B 181 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8704 (mp) REVERT: C 126 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: D 226 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7846 (tpp80) REVERT: E 113 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7369 (mt) REVERT: G 173 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: H 174 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8429 (mttp) REVERT: R 116 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7708 (ttp-110) REVERT: R 152 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: T 124 SER cc_start: 0.9105 (p) cc_final: 0.8850 (t) REVERT: U 44 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7445 (mpt) REVERT: U 141 ARG cc_start: 0.7103 (tmm-80) cc_final: 0.6840 (tmm-80) REVERT: V 169 MET cc_start: 0.8253 (mmm) cc_final: 0.8050 (mmt) REVERT: X 234 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7479 (ttm110) REVERT: X 253 LEU cc_start: 0.9033 (mt) cc_final: 0.8818 (mp) REVERT: Y 312 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: 1 220 ASP cc_start: 0.7926 (m-30) cc_final: 0.7705 (m-30) REVERT: 1 311 GLN cc_start: 0.8383 (tt0) cc_final: 0.8075 (tt0) REVERT: 4 262 MET cc_start: 0.8321 (tpt) cc_final: 0.7996 (tpt) REVERT: 4 468 MET cc_start: 0.7738 (mmm) cc_final: 0.7287 (mmt) outliers start: 81 outliers final: 37 residues processed: 788 average time/residue: 3.7947 time to fit residues: 3725.2214 Evaluate side-chains 765 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 719 time to evaluate : 6.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 233 CYS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 269 SER Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 214 GLU Chi-restraints excluded: chain X residue 234 ARG Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 312 GLU Chi-restraints excluded: chain Y residue 340 SER Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 0 residue 127 GLU Chi-restraints excluded: chain 4 residue 162 GLU Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 258 SER Chi-restraints excluded: chain 4 residue 280 THR Chi-restraints excluded: chain 4 residue 324 VAL Chi-restraints excluded: chain 4 residue 531 ILE Chi-restraints excluded: chain 4 residue 561 SER Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 485 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 555 optimal weight: 0.5980 chunk 450 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 584 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN I 141 GLN L 77 GLN X 69 ASN ** X 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 292 ASN Y 295 GLN Y 381 ASN 0 24 GLN 4 612 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 72186 Z= 0.358 Angle : 0.639 26.835 102044 Z= 0.319 Chirality : 0.044 1.954 11944 Planarity : 0.005 0.133 9535 Dihedral : 18.960 119.346 21087 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 1.70 % Allowed : 12.61 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.11), residues: 5850 helix: 1.13 (0.10), residues: 2779 sheet: -0.06 (0.21), residues: 567 loop : -0.29 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 593 HIS 0.007 0.001 HIS D 317 PHE 0.014 0.001 PHE G 54 TYR 0.017 0.002 TYR R 242 ARG 0.010 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 735 time to evaluate : 6.372 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: B 175 MET cc_start: 0.7595 (mmp) cc_final: 0.7154 (mmp) REVERT: B 181 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8784 (mp) REVERT: C 126 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: D 226 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7846 (tpp80) REVERT: E 113 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7470 (mt) REVERT: G 173 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: H 174 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8430 (mttp) REVERT: R 116 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7762 (ttp-110) REVERT: T 124 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8853 (t) REVERT: U 44 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7475 (mpt) REVERT: X 234 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7528 (ttm110) REVERT: X 253 LEU cc_start: 0.9002 (mt) cc_final: 0.8795 (mp) REVERT: Y 312 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: 4 262 MET cc_start: 0.8275 (tpt) cc_final: 0.7973 (tpt) REVERT: 4 468 MET cc_start: 0.7768 (mmm) cc_final: 0.7331 (mmt) REVERT: 8 197 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6951 (ttmt) outliers start: 89 outliers final: 44 residues processed: 782 average time/residue: 3.6999 time to fit residues: 3593.8858 Evaluate side-chains 776 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 722 time to evaluate : 6.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 233 CYS Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain T residue 124 SER Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 269 SER Chi-restraints excluded: chain V residue 272 ASP Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 234 ARG Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 279 ASP Chi-restraints excluded: chain Y residue 312 GLU Chi-restraints excluded: chain Y residue 340 SER Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 0 residue 127 GLU Chi-restraints excluded: chain 4 residue 162 GLU Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 258 SER Chi-restraints excluded: chain 4 residue 273 GLU Chi-restraints excluded: chain 4 residue 280 THR Chi-restraints excluded: chain 4 residue 324 VAL Chi-restraints excluded: chain 4 residue 561 SER Chi-restraints excluded: chain 8 residue 197 LYS Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 1.9990 chunk 586 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 382 optimal weight: 1.9990 chunk 160 optimal weight: 0.2980 chunk 652 optimal weight: 20.0000 chunk 541 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 342 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN E 92 ASN F 72 GLN I 141 GLN L 77 GLN R 320 GLN W 135 GLN X 211 ASN Y 295 GLN Y 378 ASN 0 24 GLN 1 311 GLN ** 4 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 72186 Z= 0.197 Angle : 0.582 27.434 102044 Z= 0.290 Chirality : 0.040 1.934 11944 Planarity : 0.005 0.127 9535 Dihedral : 18.896 114.408 21087 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.22 % Rotamer: Outliers : 1.24 % Allowed : 13.37 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.11), residues: 5850 helix: 1.42 (0.10), residues: 2780 sheet: -0.07 (0.21), residues: 572 loop : -0.17 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 177 HIS 0.005 0.001 HIS D 317 PHE 0.012 0.001 PHE B 58 TYR 0.012 0.001 TYR R 242 ARG 0.010 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11700 Ramachandran restraints generated. 5850 Oldfield, 0 Emsley, 5850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 733 time to evaluate : 6.354 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: B 77 GLU cc_start: 0.7495 (pt0) cc_final: 0.7291 (pt0) REVERT: B 181 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8747 (mp) REVERT: C 126 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: D 226 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7825 (tpp80) REVERT: E 77 SER cc_start: 0.9070 (t) cc_final: 0.8841 (m) REVERT: E 113 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7392 (mt) REVERT: H 174 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8423 (mttp) REVERT: R 116 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7749 (ttp-110) REVERT: T 124 SER cc_start: 0.9053 (p) cc_final: 0.8835 (t) REVERT: U 44 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7464 (mpt) REVERT: X 234 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7497 (ttm110) REVERT: Y 312 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: 0 17 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6765 (ttp-170) REVERT: 4 246 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7406 (ttm170) REVERT: 4 262 MET cc_start: 0.8267 (tpt) cc_final: 0.7965 (tpt) REVERT: 4 468 MET cc_start: 0.7723 (mmm) cc_final: 0.7278 (mmt) outliers start: 65 outliers final: 40 residues processed: 768 average time/residue: 3.8047 time to fit residues: 3655.7992 Evaluate side-chains 754 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 707 time to evaluate : 6.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 233 CYS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 269 SER Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 149 ASP Chi-restraints excluded: chain X residue 196 GLU Chi-restraints excluded: chain X residue 234 ARG Chi-restraints excluded: chain X residue 308 SER Chi-restraints excluded: chain Y residue 312 GLU Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 0 residue 160 SER Chi-restraints excluded: chain 4 residue 162 GLU Chi-restraints excluded: chain 4 residue 243 ASN Chi-restraints excluded: chain 4 residue 258 SER Chi-restraints excluded: chain 4 residue 324 VAL Chi-restraints excluded: chain 4 residue 561 SER Chi-restraints excluded: chain 8 residue 238 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3827 > 50: distance: 234 - 277: 31.120 distance: 240 - 287: 34.449 distance: 251 - 304: 35.611 distance: 261 - 277: 31.169 distance: 277 - 278: 20.085 distance: 277 - 282: 7.896 distance: 278 - 279: 32.024 distance: 278 - 281: 24.058 distance: 278 - 283: 21.762 distance: 279 - 280: 40.528 distance: 279 - 287: 56.146 distance: 281 - 285: 8.274 distance: 287 - 288: 56.318 distance: 287 - 296: 30.232 distance: 288 - 289: 39.840 distance: 288 - 291: 51.419 distance: 288 - 297: 40.200 distance: 289 - 304: 69.769 distance: 291 - 292: 4.611 distance: 291 - 298: 26.293 distance: 291 - 299: 47.505 distance: 292 - 293: 16.180 distance: 292 - 300: 32.033 distance: 292 - 301: 28.559 distance: 293 - 294: 16.321 distance: 293 - 295: 10.364 distance: 295 - 302: 14.486 distance: 295 - 303: 6.590 distance: 305 - 306: 57.664 distance: 305 - 308: 30.185 distance: 306 - 324: 57.544 distance: 308 - 309: 8.705 distance: 308 - 317: 40.861 distance: 308 - 318: 41.206 distance: 309 - 310: 19.840 distance: 309 - 311: 19.338 distance: 310 - 312: 17.754 distance: 310 - 319: 18.804 distance: 311 - 313: 12.348 distance: 311 - 320: 23.605 distance: 312 - 314: 15.750 distance: 312 - 321: 8.898 distance: 313 - 314: 3.856 distance: 313 - 322: 7.118 distance: 314 - 323: 18.527 distance: 324 - 325: 39.974 distance: 324 - 333: 40.176 distance: 325 - 326: 57.329 distance: 325 - 328: 67.897 distance: 325 - 334: 39.568 distance: 326 - 327: 56.862 distance: 326 - 339: 38.832 distance: 329 - 330: 40.578 distance: 329 - 337: 40.125 distance: 329 - 338: 17.366 distance: 339 - 340: 62.299 distance: 339 - 345: 42.468 distance: 340 - 341: 48.852 distance: 340 - 343: 46.994 distance: 340 - 346: 61.924 distance: 341 - 342: 55.873 distance: 341 - 353: 61.591 distance: 344 - 345: 49.151 distance: 344 - 350: 40.106 distance: 345 - 351: 11.839 distance: 345 - 352: 13.400 distance: 353 - 354: 48.731 distance: 353 - 361: 25.413 distance: 354 - 355: 62.221 distance: 354 - 357: 39.952 distance: 354 - 362: 40.276 distance: 355 - 356: 46.606 distance: 355 - 365: 15.159 distance: 357 - 363: 10.683 distance: 357 - 364: 30.802 distance: 358 - 359: 37.317 distance: 358 - 360: 11.486 distance: 365 - 366: 56.926 distance: 366 - 367: 61.636 distance: 366 - 369: 32.958 distance: 366 - 372: 39.186 distance: 367 - 368: 14.634 distance: 367 - 376: 43.873 distance: 369 - 370: 9.342 distance: 369 - 373: 7.598 distance: 369 - 374: 7.809 distance: 370 - 375: 41.877 distance: 376 - 377: 57.564 distance: 376 - 383: 17.351 distance: 377 - 378: 47.951 distance: 377 - 380: 47.198 distance: 377 - 384: 39.516 distance: 378 - 379: 29.239 distance: 378 - 390: 27.216 distance: 380 - 381: 25.495 distance: 380 - 382: 27.252 distance: 380 - 385: 43.724 distance: 381 - 386: 39.930 distance: 382 - 387: 17.980 distance: 382 - 388: 8.593 distance: 382 - 389: 7.722 distance: 390 - 391: 41.345 distance: 391 - 392: 37.766 distance: 391 - 394: 36.534 distance: 391 - 400: 34.233 distance: 392 - 393: 46.757 distance: 392 - 405: 44.065 distance: 393 - 458: 25.965 distance: 394 - 395: 6.564 distance: 394 - 401: 30.540 distance: 394 - 402: 6.560 distance: 395 - 396: 30.571 distance: 395 - 404: 33.565 distance: 396 - 397: 27.738 distance: 396 - 398: 43.960 distance: 405 - 406: 14.024 distance: 405 - 417: 44.910 distance: 406 - 407: 40.500 distance: 406 - 409: 24.748 distance: 406 - 418: 15.950 distance: 407 - 408: 47.854 distance: 407 - 426: 26.539 distance: 408 - 472: 28.723 distance: 409 - 419: 4.505 distance: 410 - 411: 5.195 distance: 410 - 412: 7.112 distance: 411 - 413: 28.334 distance: 411 - 421: 3.565 distance: 412 - 414: 23.307 distance: 412 - 422: 8.730 distance: 413 - 415: 39.107 distance: 413 - 423: 18.091 distance: 414 - 415: 35.275 distance: 414 - 424: 26.391 distance: 415 - 416: 10.453 distance: 416 - 425: 30.543