Starting phenix.real_space_refine (version: dev) on Tue Apr 26 01:27:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s13_10079/04_2022/6s13_10079.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s13_10079/04_2022/6s13_10079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s13_10079/04_2022/6s13_10079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s13_10079/04_2022/6s13_10079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s13_10079/04_2022/6s13_10079.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s13_10079/04_2022/6s13_10079.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 102": "OD1" <-> "OD2" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 14": "OE1" <-> "OE2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 84": "OE1" <-> "OE2" Residue "S ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 122": "OE1" <-> "OE2" Residue "b ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f GLU 24": "OE1" <-> "OE2" Residue "f ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f GLU 51": "OE1" <-> "OE2" Residue "f PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ASP 85": "OD1" <-> "OD2" Residue "f ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h GLU 93": "OE1" <-> "OE2" Residue "h GLU 110": "OE1" <-> "OE2" Residue "h ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i GLU 39": "OE1" <-> "OE2" Residue "i PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j GLU 66": "OE1" <-> "OE2" Residue "k ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k GLU 83": "OE1" <-> "OE2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "k ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ASP 112": "OD1" <-> "OD2" Residue "l ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "p ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "p ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "p ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q GLU 83": "OE1" <-> "OE2" Residue "r PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s ASP 12": "OD1" <-> "OD2" Residue "s PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u GLU 31": "OE1" <-> "OE2" Residue "u PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v ASP 165": "OD1" <-> "OD2" Residue "v ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 233957 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 93564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2905, 93564 Classifications: {'RNA': 2905} Modifications used: {'rna3p_pyr': 1067, 'rna2p_pur': 315, 'rna3p_pur': 1350, 'rna2p_pyr': 173, '3*END': 1} Link IDs: {'rna3p': 2416, 'rna2p': 488} Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 3685 Classifications: {'RNA': 115} Modifications used: {'5*END': 1, 'rna2p_pyr': 9, '3*END': 1, 'rna3p_pur': 54, 'rna3p_pyr': 47, 'rna2p_pur': 5} Link IDs: {'rna3p': 100, 'rna2p': 14} Chain: "C" Number of atoms: 4291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4291 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3294 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3192 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 2667 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 2488 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2277 Classifications: {'peptide': 145} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1899 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2211 Classifications: {'peptide': 146} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2194 Classifications: {'peptide': 137} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1816 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1826 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1956 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1620 Classifications: {'peptide': 102} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1724 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1463 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1579 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1488 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1265 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 911 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 940 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 613 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "Z" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 718 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "1" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 784 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 782 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1107 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 635 Classifications: {'peptide': 37} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 49563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 49563 Classifications: {'RNA': 1539} Modifications used: {'rna3p_pyr': 547, 'rna2p_pur': 163, 'rna3p_pur': 705, 'rna2p_pyr': 124, '3*END': 1} Link IDs: {'rna3p': 1252, 'rna2p': 286} Chain breaks: 1 Chain: "b" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3705 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "c" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 2965 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "d" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 2946 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 83 Chain: "e" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2347 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "f" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1553 Classifications: {'peptide': 95} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2326 Classifications: {'peptide': 152} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "h" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2103 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1812 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 65 Chain: "j" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1527 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "k" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1594 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "l" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2128 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1401 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "n" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 979 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1475 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "p" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1403 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "q" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1237 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "r" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 927 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "s" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1262 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "t" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1207 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "u" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 807 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "v" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2682 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 1 Time building chain proxies: 72.69, per 1000 atoms: 0.31 Number of scatterers: 233957 At special positions: 0 Unit cell: (270.076, 243.176, 241.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 4558 15.00 O 39468 8.00 N 25987 7.00 C 70620 6.00 H 93218 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 1 9 " - pdb=" SG CYS 1 12 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.04 Simple disulfide: pdb=" SG CYS n 27 " - pdb=" SG CYS n 40 " 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: 148.55 Conformation dependent library (CDL) restraints added in 8.2 seconds 11006 Ramachandran restraints generated. 5503 Oldfield, 0 Emsley, 5503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10322 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 64 sheets defined 24.7% alpha, 10.8% beta 1273 base pairs and 1941 stacking pairs defined. Time for finding SS restraints: 89.14 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.733A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.711A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 183 through 189 Processing helix chain 'E' and resid 196 through 207 Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.743A pdb=" N THR F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 removed outlier: 3.634A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 107 removed outlier: 4.598A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 111 Processing helix chain 'F' and resid 162 through 170 removed outlier: 3.768A pdb=" N ALA F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 79 Processing helix chain 'G' and resid 140 through 152 removed outlier: 4.029A pdb=" N ARG G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 39 removed outlier: 4.794A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 96 removed outlier: 4.008A pdb=" N LEU H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 removed outlier: 3.967A pdb=" N LEU H 101 " --> pdb=" O ASN H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 122 Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'J' and resid 2 through 6 removed outlier: 4.009A pdb=" N LEU J 6 " --> pdb=" O LEU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 removed outlier: 3.934A pdb=" N THR J 25 " --> pdb=" O GLY J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 79 through 85 Processing helix chain 'J' and resid 92 through 100 Processing helix chain 'J' and resid 129 through 140 removed outlier: 3.986A pdb=" N ALA J 133 " --> pdb=" O SER J 129 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS J 139 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 59 Processing helix chain 'K' and resid 110 through 124 removed outlier: 3.695A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 28 Processing helix chain 'L' and resid 34 through 52 removed outlier: 4.451A pdb=" N SER L 42 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 66 removed outlier: 3.710A pdb=" N THR L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 89 removed outlier: 4.169A pdb=" N ILE L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.768A pdb=" N THR M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 84 removed outlier: 3.514A pdb=" N ALA M 81 " --> pdb=" O GLY M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 115 Processing helix chain 'N' and resid 5 through 12 Processing helix chain 'N' and resid 55 through 58 Processing helix chain 'N' and resid 99 through 103 removed outlier: 3.594A pdb=" N LEU N 102 " --> pdb=" O LEU N 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 21 removed outlier: 3.558A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 72 removed outlier: 5.025A pdb=" N GLN O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 91 through 102 Processing helix chain 'O' and resid 103 through 116 Processing helix chain 'Q' and resid 13 through 22 removed outlier: 5.060A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 39 Processing helix chain 'Q' and resid 42 through 61 removed outlier: 4.444A pdb=" N VAL Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 21 Processing helix chain 'R' and resid 34 through 46 removed outlier: 4.197A pdb=" N GLU R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 24 removed outlier: 3.558A pdb=" N LYS T 19 " --> pdb=" O ARG T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 56 Processing helix chain 'T' and resid 81 through 84 Processing helix chain 'V' and resid 51 through 56 removed outlier: 3.788A pdb=" N SER V 56 " --> pdb=" O ARG V 52 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 9 Processing helix chain 'W' and resid 13 through 34 Processing helix chain 'W' and resid 39 through 66 removed outlier: 3.908A pdb=" N ILE W 43 " --> pdb=" O GLU W 39 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG W 44 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL W 46 " --> pdb=" O ARG W 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN W 64 " --> pdb=" O ARG W 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 40 through 49 Processing helix chain 'X' and resid 50 through 52 No H-bonds generated for 'chain 'X' and resid 50 through 52' Processing helix chain 'Z' and resid 9 through 17 Processing helix chain 'Z' and resid 18 through 20 No H-bonds generated for 'chain 'Z' and resid 18 through 20' Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 23 Processing helix chain '2' and resid 25 through 39 removed outlier: 4.786A pdb=" N VAL 2 31 " --> pdb=" O ASN 2 27 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 28 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA 2 33 " --> pdb=" O ARG 2 29 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG 2 34 " --> pdb=" O LYS 2 30 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 Processing helix chain '3' and resid 37 through 44 Processing helix chain '3' and resid 51 through 59 Processing helix chain '3' and resid 60 through 62 No H-bonds generated for 'chain '3' and resid 60 through 62' Processing helix chain 'b' and resid 6 through 11 Processing helix chain 'b' and resid 24 through 28 removed outlier: 3.592A pdb=" N LYS b 28 " --> pdb=" O PRO b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 47 through 62 removed outlier: 3.625A pdb=" N GLN b 59 " --> pdb=" O ASN b 55 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL b 60 " --> pdb=" O PHE b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 88 Processing helix chain 'b' and resid 109 through 123 removed outlier: 4.008A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 145 removed outlier: 4.361A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP b 142 " --> pdb=" O LYS b 138 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ARG b 143 " --> pdb=" O LYS b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 177 removed outlier: 6.707A pdb=" N ASN b 171 " --> pdb=" O ARG b 167 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA b 172 " --> pdb=" O LYS b 168 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE b 173 " --> pdb=" O GLU b 169 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU b 175 " --> pdb=" O ASN b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 178 through 180 No H-bonds generated for 'chain 'b' and resid 178 through 180' Processing helix chain 'b' and resid 206 through 212 removed outlier: 3.842A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 213 through 221 Processing helix chain 'c' and resid 30 through 37 removed outlier: 3.553A pdb=" N ASP c 35 " --> pdb=" O LEU c 31 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 41 removed outlier: 3.542A pdb=" N PHE c 41 " --> pdb=" O ILE c 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 38 through 41' Processing helix chain 'c' and resid 81 through 90 removed outlier: 3.646A pdb=" N ASN c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 111 Processing helix chain 'c' and resid 114 through 124 removed outlier: 4.493A pdb=" N ASN c 118 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN c 122 " --> pdb=" O ASN c 118 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 140 Processing helix chain 'd' and resid 53 through 59 Processing helix chain 'd' and resid 67 through 78 removed outlier: 3.725A pdb=" N LYS d 78 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 91 removed outlier: 4.460A pdb=" N LEU d 89 " --> pdb=" O ASN d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 197 Processing helix chain 'e' and resid 58 through 68 removed outlier: 3.955A pdb=" N ALA e 66 " --> pdb=" O LYS e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 116 Processing helix chain 'e' and resid 133 through 146 removed outlier: 3.612A pdb=" N VAL e 137 " --> pdb=" O PRO e 133 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY e 143 " --> pdb=" O ALA e 139 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU e 144 " --> pdb=" O THR e 140 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN e 146 " --> pdb=" O ASP e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.769A pdb=" N VAL e 153 " --> pdb=" O ASN e 149 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 24 removed outlier: 4.052A pdb=" N LEU f 22 " --> pdb=" O ALA f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 removed outlier: 4.118A pdb=" N GLY f 28 " --> pdb=" O GLU f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 32 No H-bonds generated for 'chain 'f' and resid 30 through 32' Processing helix chain 'f' and resid 73 through 78 Processing helix chain 'g' and resid 21 through 29 removed outlier: 3.663A pdb=" N LEU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 44 Processing helix chain 'g' and resid 47 through 54 removed outlier: 4.074A pdb=" N GLU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 Processing helix chain 'h' and resid 10 through 18 removed outlier: 4.735A pdb=" N ASN h 16 " --> pdb=" O THR h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 44 Processing helix chain 'h' and resid 97 through 101 Processing helix chain 'h' and resid 115 through 119 removed outlier: 3.579A pdb=" N ALA h 118 " --> pdb=" O ASP h 115 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG h 119 " --> pdb=" O LYS h 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 115 through 119' Processing helix chain 'i' and resid 47 through 49 No H-bonds generated for 'chain 'i' and resid 47 through 49' Processing helix chain 'i' and resid 50 through 55 Processing helix chain 'i' and resid 56 through 58 No H-bonds generated for 'chain 'i' and resid 56 through 58' Processing helix chain 'i' and resid 80 through 93 removed outlier: 3.602A pdb=" N ARG i 87 " --> pdb=" O HIS i 83 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA i 88 " --> pdb=" O GLY i 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU i 91 " --> pdb=" O ARG i 87 " (cutoff:3.500A) Processing helix chain 'j' and resid 17 through 29 removed outlier: 4.455A pdb=" N GLU j 23 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU j 27 " --> pdb=" O GLU j 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 63 removed outlier: 4.104A pdb=" N ALA k 62 " --> pdb=" O THR k 59 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 75 removed outlier: 3.686A pdb=" N THR k 69 " --> pdb=" O MET k 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA k 70 " --> pdb=" O ALA k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 100 removed outlier: 3.718A pdb=" N ALA k 99 " --> pdb=" O ALA k 96 " (cutoff:3.500A) Processing helix chain 'm' and resid 51 through 56 Processing helix chain 'm' and resid 57 through 60 removed outlier: 3.541A pdb=" N VAL m 60 " --> pdb=" O ARG m 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 57 through 60' Processing helix chain 'm' and resid 74 through 83 removed outlier: 4.108A pdb=" N ILE m 77 " --> pdb=" O ASN m 74 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG m 79 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU m 82 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE m 83 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 88 through 93 Processing helix chain 'n' and resid 42 through 47 Processing helix chain 'n' and resid 48 through 50 No H-bonds generated for 'chain 'n' and resid 48 through 50' Processing helix chain 'o' and resid 11 through 16 Processing helix chain 'o' and resid 30 through 34 removed outlier: 3.964A pdb=" N THR o 33 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA o 34 " --> pdb=" O VAL o 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 30 through 34' Processing helix chain 'o' and resid 37 through 45 removed outlier: 4.098A pdb=" N THR o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 74 removed outlier: 3.699A pdb=" N ASN o 68 " --> pdb=" O ARG o 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR o 69 " --> pdb=" O HIS o 65 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 83 removed outlier: 3.861A pdb=" N TYR o 78 " --> pdb=" O ASP o 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 59 removed outlier: 3.607A pdb=" N ALA p 57 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU p 58 " --> pdb=" O ALA p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 77 removed outlier: 3.685A pdb=" N ILE p 74 " --> pdb=" O THR p 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER p 76 " --> pdb=" O HIS p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 80 through 90 removed outlier: 3.544A pdb=" N ASP p 85 " --> pdb=" O MET p 81 " (cutoff:3.500A) Processing helix chain 'r' and resid 55 through 63 Processing helix chain 'r' and resid 64 through 69 Processing helix chain 's' and resid 15 through 23 removed outlier: 3.653A pdb=" N GLU s 20 " --> pdb=" O MET s 16 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) Processing helix chain 't' and resid 9 through 18 Processing helix chain 't' and resid 25 through 34 removed outlier: 3.900A pdb=" N ALA t 31 " --> pdb=" O ALA t 27 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS t 33 " --> pdb=" O ARG t 29 " (cutoff:3.500A) Processing helix chain 't' and resid 34 through 40 Processing helix chain 't' and resid 52 through 57 Processing helix chain 'u' and resid 28 through 33 removed outlier: 3.944A pdb=" N ARG u 33 " --> pdb=" O ILE u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 42 through 48 removed outlier: 3.592A pdb=" N LYS u 46 " --> pdb=" O VAL u 43 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS u 48 " --> pdb=" O ARG u 45 " (cutoff:3.500A) Processing helix chain 'v' and resid 22 through 27 removed outlier: 4.361A pdb=" N GLY v 26 " --> pdb=" O GLU v 22 " (cutoff:3.500A) Processing helix chain 'v' and resid 78 through 82 Processing helix chain 'v' and resid 149 through 153 removed outlier: 3.704A pdb=" N GLN v 152 " --> pdb=" O ALA v 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 74 through 75 removed outlier: 3.909A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 83 removed outlier: 4.513A pdb=" N VAL C 78 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA7, first strand: chain 'D' and resid 115 through 116 removed outlier: 5.328A pdb=" N GLU D 184 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU D 196 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 88 through 91 removed outlier: 6.691A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN D 33 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.595A pdb=" N VAL D 178 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 128 Processing sheet with id=AB2, first strand: chain 'E' and resid 13 through 18 removed outlier: 11.532A pdb=" N LEU E 123 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP E 5 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL E 125 " --> pdb=" O ASP E 5 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 153 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 91 Processing sheet with id=AB4, first strand: chain 'F' and resid 69 through 70 Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.825A pdb=" N HIS G 23 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 122 through 125 Processing sheet with id=AB7, first strand: chain 'G' and resid 95 through 98 Processing sheet with id=AB8, first strand: chain 'H' and resid 54 through 57 removed outlier: 6.381A pdb=" N TRP H 16 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 75 through 78 Processing sheet with id=AC1, first strand: chain 'I' and resid 7 through 9 removed outlier: 6.173A pdb=" N ALA I 16 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA I 46 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU I 18 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 76 through 79 removed outlier: 6.389A pdb=" N THR N 60 " --> pdb=" O ARG N 52 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG N 52 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR N 62 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE N 66 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLU N 46 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG N 29 " --> pdb=" O VAL N 88 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL N 88 " --> pdb=" O ARG N 29 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS N 31 " --> pdb=" O ILE N 86 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE N 86 " --> pdb=" O HIS N 31 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ARG N 33 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU N 84 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 75 through 77 removed outlier: 6.061A pdb=" N ALA J 75 " --> pdb=" O LYS J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 63 through 66 removed outlier: 6.511A pdb=" N LEU K 34 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU K 105 " --> pdb=" O PHE K 32 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE K 32 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 72 through 75 removed outlier: 6.392A pdb=" N THR K 72 " --> pdb=" O TRP K 93 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TRP K 93 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR K 74 " --> pdb=" O GLU K 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 30 through 32 Processing sheet with id=AC7, first strand: chain 'L' and resid 71 through 73 Processing sheet with id=AC8, first strand: chain 'M' and resid 30 through 35 Processing sheet with id=AC9, first strand: chain 'M' and resid 30 through 35 Processing sheet with id=AD1, first strand: chain 'P' and resid 10 through 14 removed outlier: 6.572A pdb=" N ILE P 4 " --> pdb=" O LEU P 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 19 through 22 removed outlier: 6.966A pdb=" N TYR P 92 " --> pdb=" O GLN P 65 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN P 65 " --> pdb=" O TYR P 92 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP P 98 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR P 59 " --> pdb=" O ASP P 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 71 through 77 removed outlier: 4.225A pdb=" N SER P 82 " --> pdb=" O LYS P 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 3 through 7 removed outlier: 5.643A pdb=" N SER Q 106 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL Q 71 " --> pdb=" O SER Q 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AD6, first strand: chain 'R' and resid 7 through 10 removed outlier: 3.620A pdb=" N VAL R 29 " --> pdb=" O ARG R 76 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER R 52 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AD8, first strand: chain 'S' and resid 63 through 64 removed outlier: 4.169A pdb=" N ALA S 25 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY S 21 " --> pdb=" O VAL S 9 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL S 9 " --> pdb=" O GLY S 21 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 40 through 42 removed outlier: 3.832A pdb=" N THR S 59 " --> pdb=" O MET S 41 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 82 through 86 removed outlier: 3.752A pdb=" N ILE S 93 " --> pdb=" O GLY S 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 7 through 8 removed outlier: 5.478A pdb=" N LYS T 37 " --> pdb=" O GLY T 33 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY T 33 " --> pdb=" O LYS T 37 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N LYS T 26 " --> pdb=" O THR T 87 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ILE T 89 " --> pdb=" O LYS T 26 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE T 91 " --> pdb=" O PRO T 28 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL T 30 " --> pdb=" O PHE T 91 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA T 93 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR T 32 " --> pdb=" O ALA T 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE T 86 " --> pdb=" O PHE T 79 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE T 79 " --> pdb=" O ILE T 86 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS T 88 " --> pdb=" O TYR T 77 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR T 77 " --> pdb=" O HIS T 88 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP T 90 " --> pdb=" O ALA T 75 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE T 70 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE T 61 " --> pdb=" O VAL T 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 30 through 31 removed outlier: 6.713A pdb=" N LEU U 67 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 54 through 57 Processing sheet with id=AE5, first strand: chain 'V' and resid 15 through 17 Processing sheet with id=AE6, first strand: chain 'V' and resid 33 through 37 Processing sheet with id=AE7, first strand: chain 'X' and resid 34 through 38 Processing sheet with id=AE8, first strand: chain 'Y' and resid 10 through 12 removed outlier: 3.609A pdb=" N HIS Y 10 " --> pdb=" O GLY Y 26 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY Y 26 " --> pdb=" O HIS Y 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '1' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain '1' and resid 31 through 36 removed outlier: 3.572A pdb=" N CYS 1 36 " --> pdb=" O LYS 1 41 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS 1 41 " --> pdb=" O CYS 1 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '3' and resid 14 through 16 Processing sheet with id=AF3, first strand: chain '4' and resid 18 through 19 Processing sheet with id=AF4, first strand: chain 'b' and resid 31 through 35 removed outlier: 6.392A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU b 34 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE b 38 " --> pdb=" O GLU b 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 183 through 185 removed outlier: 7.582A pdb=" N ILE b 183 " --> pdb=" O ASP b 197 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL b 199 " --> pdb=" O ILE b 183 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY b 185 " --> pdb=" O VAL b 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'e' and resid 14 through 17 removed outlier: 6.729A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'e' and resid 20 through 21 Processing sheet with id=AF8, first strand: chain 'e' and resid 85 through 89 removed outlier: 3.862A pdb=" N GLY e 87 " --> pdb=" O VAL e 94 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL e 94 " --> pdb=" O GLY e 87 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'f' and resid 42 through 46 removed outlier: 5.011A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR f 60 " --> pdb=" O GLY f 44 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 73 through 74 removed outlier: 3.709A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL g 89 " --> pdb=" O GLU g 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'h' and resid 26 through 28 Processing sheet with id=AG3, first strand: chain 'k' and resid 20 through 24 removed outlier: 3.680A pdb=" N ILE k 31 " --> pdb=" O ARG k 24 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'k' and resid 84 through 86 removed outlier: 6.811A pdb=" N VAL k 84 " --> pdb=" O ARG k 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'p' and resid 5 through 7 removed outlier: 3.589A pdb=" N VAL p 21 " --> pdb=" O ARG p 6 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'q' and resid 11 through 13 Processing sheet with id=AG7, first strand: chain 'q' and resid 25 through 31 Processing sheet with id=AG8, first strand: chain 's' and resid 50 through 52 Processing sheet with id=AG9, first strand: chain 'v' and resid 44 through 46 Processing sheet with id=AH1, first strand: chain 'v' and resid 172 through 173 removed outlier: 4.156A pdb=" N ILE v 185 " --> pdb=" O ILE v 173 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3164 hydrogen bonds 5018 hydrogen bond angles 0 basepair planarities 1273 basepair parallelities 1941 stacking parallelities Total time for adding SS restraints: 196.67 Time building geometry restraints manager: 156.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.58: 236943 1.58 - 2.36: 9278 2.36 - 3.14: 7 3.14 - 3.92: 2 3.92 - 4.69: 3 Bond restraints: 246233 Sorted by residual: bond pdb=" CD LYS l 134 " pdb=" CE LYS l 134 " ideal model delta sigma weight residual 1.520 4.508 -2.988 3.00e-02 1.11e+03 9.92e+03 bond pdb=" CB TYR n 16 " pdb=" CG TYR n 16 " ideal model delta sigma weight residual 1.512 3.622 -2.110 2.20e-02 2.07e+03 9.19e+03 bond pdb=" CG LEU K 2 " pdb=" CD1 LEU K 2 " ideal model delta sigma weight residual 1.521 4.434 -2.913 3.30e-02 9.18e+02 7.79e+03 bond pdb=" CG1 ILE b 107 " pdb=" CD1 ILE b 107 " ideal model delta sigma weight residual 1.513 4.695 -3.182 3.90e-02 6.57e+02 6.66e+03 bond pdb=" C1' G A 393 " pdb=" N9 G A 393 " ideal model delta sigma weight residual 1.475 2.487 -1.012 1.50e-02 4.44e+03 4.55e+03 ... (remaining 246228 not shown) Histogram of bond angle deviations from ideal: 65.68 - 84.87: 11 84.87 - 104.07: 16943 104.07 - 123.27: 393389 123.27 - 142.46: 32176 142.46 - 161.66: 8 Bond angle restraints: 442527 Sorted by residual: angle pdb=" C3' G a 36 " pdb=" O3' G a 36 " pdb=" P C a 37 " ideal model delta sigma weight residual 120.20 161.66 -41.46 1.50e+00 4.44e-01 7.64e+02 angle pdb=" O LYS h 90 " pdb=" C LYS h 90 " pdb=" N ALA h 91 " ideal model delta sigma weight residual 123.31 98.22 25.09 1.17e+00 7.31e-01 4.60e+02 angle pdb=" C ALA h 89 " pdb=" N LYS h 90 " pdb=" CA LYS h 90 " ideal model delta sigma weight residual 122.74 154.80 -32.06 1.54e+00 4.22e-01 4.33e+02 angle pdb=" N ARG s 36 " pdb=" CA ARG s 36 " pdb=" CB ARG s 36 " ideal model delta sigma weight residual 110.80 84.61 26.19 1.49e+00 4.50e-01 3.09e+02 angle pdb=" N LYS h 90 " pdb=" CA LYS h 90 " pdb=" C LYS h 90 " ideal model delta sigma weight residual 108.76 135.21 -26.45 1.69e+00 3.50e-01 2.45e+02 ... (remaining 442522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 85637 35.96 - 71.93: 10099 71.93 - 107.89: 1482 107.89 - 143.86: 95 143.86 - 179.82: 62 Dihedral angle restraints: 97375 sinusoidal: 79608 harmonic: 17767 Sorted by residual: dihedral pdb=" CA THR q 22 " pdb=" C THR q 22 " pdb=" N ILE q 23 " pdb=" CA ILE q 23 " ideal model delta harmonic sigma weight residual 180.00 97.55 82.45 0 5.00e+00 4.00e-02 2.72e+02 dihedral pdb=" CA HIS k 118 " pdb=" C HIS k 118 " pdb=" N ASN k 119 " pdb=" CA ASN k 119 " ideal model delta harmonic sigma weight residual 180.00 117.76 62.24 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA PRO k 123 " pdb=" C PRO k 123 " pdb=" N PRO k 124 " pdb=" CA PRO k 124 " ideal model delta harmonic sigma weight residual 180.00 119.41 60.59 0 5.00e+00 4.00e-02 1.47e+02 ... (remaining 97372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 29455 0.346 - 0.692: 12 0.692 - 1.037: 1 1.037 - 1.383: 0 1.383 - 1.729: 1 Chirality restraints: 29469 Sorted by residual: chirality pdb=" P G A1229 " pdb=" OP1 G A1229 " pdb=" OP2 G A1229 " pdb=" O5' G A1229 " both_signs ideal model delta sigma weight residual True 2.41 0.68 1.73 2.00e-01 2.50e+01 7.47e+01 chirality pdb=" P C a 37 " pdb=" OP1 C a 37 " pdb=" OP2 C a 37 " pdb=" O5' C a 37 " both_signs ideal model delta sigma weight residual True 2.41 -3.16 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" P C a 697 " pdb=" OP1 C a 697 " pdb=" OP2 C a 697 " pdb=" O5' C a 697 " both_signs ideal model delta sigma weight residual True 2.41 1.74 0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 29466 not shown) Planarity restraints: 20993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U a 606 " 0.153 2.00e-02 2.50e+03 8.60e-02 2.22e+02 pdb=" N1 U a 606 " -0.065 2.00e-02 2.50e+03 pdb=" C2 U a 606 " 0.010 2.00e-02 2.50e+03 pdb=" O2 U a 606 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U a 606 " -0.087 2.00e-02 2.50e+03 pdb=" C4 U a 606 " 0.070 2.00e-02 2.50e+03 pdb=" O4 U a 606 " 0.015 2.00e-02 2.50e+03 pdb=" C5 U a 606 " 0.101 2.00e-02 2.50e+03 pdb=" C6 U a 606 " -0.195 2.00e-02 2.50e+03 pdb=" H5 U a 606 " 0.002 2.00e-02 2.50e+03 pdb=" H3 U a 606 " 0.001 2.00e-02 2.50e+03 pdb=" H6 U a 606 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a 605 " -0.001 2.00e-02 2.50e+03 5.55e-02 1.08e+02 pdb=" N9 G a 605 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G a 605 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G a 605 " -0.010 2.00e-02 2.50e+03 pdb=" C5 G a 605 " 0.125 2.00e-02 2.50e+03 pdb=" C6 G a 605 " -0.054 2.00e-02 2.50e+03 pdb=" O6 G a 605 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G a 605 " -0.080 2.00e-02 2.50e+03 pdb=" C2 G a 605 " 0.065 2.00e-02 2.50e+03 pdb=" N2 G a 605 " 0.052 2.00e-02 2.50e+03 pdb=" N3 G a 605 " -0.105 2.00e-02 2.50e+03 pdb=" C4 G a 605 " 0.012 2.00e-02 2.50e+03 pdb=" H8 G a 605 " 0.000 2.00e-02 2.50e+03 pdb=" H1 G a 605 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE s 74 " -0.011 2.00e-02 2.50e+03 4.00e-02 4.81e+01 pdb=" CG PHE s 74 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE s 74 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE s 74 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE s 74 " -0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE s 74 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE s 74 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE s 74 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE s 74 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE s 74 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE s 74 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE s 74 " 0.000 2.00e-02 2.50e+03 ... (remaining 20990 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 9619 2.11 - 2.73: 362076 2.73 - 3.35: 680932 3.35 - 3.98: 957704 3.98 - 4.60: 1370928 Nonbonded interactions: 3381259 Sorted by model distance: nonbonded pdb=" N7 A A2379 " pdb=" H21 G A2392 " model vdw 1.487 2.000 nonbonded pdb=" H ARG C 177 " pdb=" O GLY C 273 " model vdw 1.552 1.850 nonbonded pdb=" O5' U A1823 " pdb=" H LYS C 257 " model vdw 1.563 1.850 nonbonded pdb=" O THR d 64 " pdb=" H PHE d 68 " model vdw 1.571 1.850 nonbonded pdb=" O LEU g 104 " pdb=" H LYS g 136 " model vdw 1.573 1.850 ... (remaining 3381254 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4558 5.49 5 S 106 5.16 5 C 70620 2.51 5 N 25987 2.21 5 O 39468 1.98 5 H 93218 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 2.140 Extract box with map and model: 25.780 Check model and map are aligned: 2.330 Convert atoms to be neutral: 1.300 Process input model: 710.590 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 752.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2828 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 : 0.023 3.182 153015 Z= 1.462 Angle : 1.273 41.460 229187 Z= 0.634 Chirality : 0.060 1.729 29469 Planarity : 0.008 0.099 12090 Dihedral : 22.264 179.822 71380 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 20.52 % Favored : 79.39 % Rotamer Outliers : 21.29 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.14 % Twisted General : 1.51 % 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: -5.98 (0.08), residues: 5503 helix: -3.76 (0.09), residues: 1228 sheet: -4.03 (0.16), residues: 551 loop : -4.35 (0.08), residues: 3724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11006 Ramachandran restraints generated. 5503 Oldfield, 0 Emsley, 5503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11006 Ramachandran restraints generated. 5503 Oldfield, 0 Emsley, 5503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 1632 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 947 poor density : 685 time to evaluate : 7.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 947 outliers final: 356 residues processed: 1481 average time/residue: 2.5436 time to fit residues: 6064.7042 Evaluate side-chains 807 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 451 time to evaluate : 7.234 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 356 outliers final: 100 residues processed: 356 average time/residue: 2.4025 time to fit residues: 1420.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 837 optimal weight: 0.8980 chunk 751 optimal weight: 20.0000 chunk 417 optimal weight: 0.8980 chunk 256 optimal weight: 6.9990 chunk 507 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 777 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 472 optimal weight: 4.9990 chunk 578 optimal weight: 0.8980 chunk 900 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN D 66 ASN D 167 GLN G 23 HIS H 68 ASN H 136 GLN ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 106 GLN ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 HIS ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN S 44 HIS ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 ASN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 3 GLN 3 21 GLN 3 40 GLN 3 43 GLN 4 34 GLN ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS d 82 HIS e 145 GLN h 22 HIS h 122 ASN i 70 HIS j 56 HIS k 40 ASN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 125 GLN ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 46 ASN ** t 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN v 62 ASN ** v 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3078 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 2.122 153015 Z= 0.812 Angle : 0.895 31.190 229187 Z= 0.448 Chirality : 0.044 1.890 29469 Planarity : 0.006 0.095 12090 Dihedral : 21.936 179.855 60818 Min Nonbonded Distance : 1.224 Molprobity Statistics. All-atom Clashscore : 30.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.15 % Favored : 83.80 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.09 % Twisted General : 0.99 % 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: -5.18 (0.09), residues: 5505 helix: -2.75 (0.12), residues: 1240 sheet: -3.39 (0.18), residues: 593 loop : -3.99 (0.08), residues: 3672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 784 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 509 time to evaluate : 7.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 275 outliers final: 163 residues processed: 740 average time/residue: 2.5227 time to fit residues: 3060.9489 Evaluate side-chains 586 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 423 time to evaluate : 7.215 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 75 residues processed: 163 average time/residue: 2.2880 time to fit residues: 641.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 500 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 749 optimal weight: 30.0000 chunk 613 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 902 optimal weight: 0.0170 chunk 974 optimal weight: 0.0070 chunk 803 optimal weight: 5.9990 chunk 894 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 723 optimal weight: 30.0000 overall best weight: 2.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS D 50 GLN ** D 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 119 GLN H 48 HIS H 131 HIS ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN J 68 ASN ** K 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 79 GLN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 GLN ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 101 ASN ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS d 149 ASN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 109 HIS ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3716 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 2.104 153015 Z= 0.831 Angle : 1.024 44.655 229187 Z= 0.509 Chirality : 0.049 1.959 29469 Planarity : 0.008 0.130 12090 Dihedral : 22.022 179.301 60818 Min Nonbonded Distance : 1.288 Molprobity Statistics. All-atom Clashscore : 37.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 18.55 % Favored : 81.34 % Rotamer Outliers : 7.13 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.66 % Twisted General : 0.84 % 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: -4.88 (0.09), residues: 5505 helix: -2.40 (0.12), residues: 1245 sheet: -2.94 (0.19), residues: 581 loop : -3.88 (0.08), residues: 3679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 787 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 470 time to evaluate : 7.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 317 outliers final: 171 residues processed: 732 average time/residue: 2.4316 time to fit residues: 2967.0719 Evaluate side-chains 558 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 387 time to evaluate : 7.194 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 71 residues processed: 171 average time/residue: 2.3050 time to fit residues: 672.2572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 891 optimal weight: 9.9990 chunk 678 optimal weight: 20.0000 chunk 468 optimal weight: 0.0370 chunk 99 optimal weight: 5.9990 chunk 430 optimal weight: 0.8980 chunk 605 optimal weight: 30.0000 chunk 905 optimal weight: 0.4980 chunk 958 optimal weight: 7.9990 chunk 473 optimal weight: 10.0000 chunk 858 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 overall best weight: 3.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN K 12 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 79 GLN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 GLN P 88 HIS P 101 ASN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 2 HIS U 48 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 3 GLN ** 2 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 57 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4091 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 2.075 153015 Z= 0.792 Angle : 0.938 38.626 229187 Z= 0.465 Chirality : 0.047 1.921 29469 Planarity : 0.007 0.126 12090 Dihedral : 22.013 179.016 60818 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 35.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.97 % Favored : 84.92 % Rotamer Outliers : 4.41 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.62 % Twisted General : 0.75 % 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: -4.66 (0.09), residues: 5505 helix: -2.10 (0.13), residues: 1227 sheet: -2.81 (0.20), residues: 575 loop : -3.77 (0.08), residues: 3703 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 673 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 477 time to evaluate : 8.062 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 TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 128 residues processed: 637 average time/residue: 2.4273 time to fit residues: 2594.8635 Evaluate side-chains 538 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 410 time to evaluate : 7.313 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 63 residues processed: 128 average time/residue: 2.2562 time to fit residues: 503.5617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 798 optimal weight: 10.0000 chunk 544 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 713 optimal weight: 30.0000 chunk 395 optimal weight: 20.0000 chunk 818 optimal weight: 10.0000 chunk 662 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 489 optimal weight: 3.9990 chunk 860 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 134 HIS ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 GLN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 ASN ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 166 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 74 ASN m 76 ASN n 52 GLN ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4980 moved from start: 1.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 2.080 153015 Z= 0.931 Angle : 1.409 54.764 229187 Z= 0.690 Chirality : 0.065 2.191 29469 Planarity : 0.011 0.218 12090 Dihedral : 23.177 179.799 60818 Min Nonbonded Distance : 1.305 Molprobity Statistics. All-atom Clashscore : 60.76 Ramachandran Plot: Outliers : 0.54 % Allowed : 22.13 % Favored : 77.33 % Rotamer Outliers : 7.01 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.09 % Twisted General : 1.01 % 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: -5.37 (0.09), residues: 5505 helix: -3.17 (0.11), residues: 1216 sheet: -3.01 (0.20), residues: 539 loop : -4.10 (0.08), residues: 3750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 894 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 582 time to evaluate : 7.234 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 TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 312 outliers final: 189 residues processed: 825 average time/residue: 2.5009 time to fit residues: 3431.5623 Evaluate side-chains 659 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 470 time to evaluate : 7.289 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 64 residues processed: 189 average time/residue: 2.3185 time to fit residues: 754.7363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 322 optimal weight: 0.6980 chunk 863 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 562 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 959 optimal weight: 10.0000 chunk 796 optimal weight: 9.9990 chunk 444 optimal weight: 0.3980 chunk 79 optimal weight: 8.9990 chunk 317 optimal weight: 4.9990 chunk 503 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 119 GLN H 136 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 ASN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 moved from start: 1.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 2.070 153015 Z= 0.776 Angle : 0.889 31.565 229187 Z= 0.450 Chirality : 0.046 2.092 29469 Planarity : 0.007 0.155 12090 Dihedral : 22.369 179.608 60818 Min Nonbonded Distance : 1.269 Molprobity Statistics. All-atom Clashscore : 33.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.60 % Favored : 84.34 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.63 % 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: -4.81 (0.09), residues: 5505 helix: -2.43 (0.13), residues: 1203 sheet: -2.75 (0.20), residues: 589 loop : -3.82 (0.08), residues: 3713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 651 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 517 time to evaluate : 7.315 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 TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 97 residues processed: 612 average time/residue: 2.6231 time to fit residues: 2685.2598 Evaluate side-chains 546 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 449 time to evaluate : 8.122 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 56 residues processed: 97 average time/residue: 2.4035 time to fit residues: 402.6846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 925 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 546 optimal weight: 0.0870 chunk 700 optimal weight: 30.0000 chunk 543 optimal weight: 9.9990 chunk 807 optimal weight: 0.9990 chunk 535 optimal weight: 8.9990 chunk 956 optimal weight: 3.9990 chunk 598 optimal weight: 10.0000 chunk 582 optimal weight: 6.9990 chunk 441 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** Y 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS d 137 GLN e 131 ASN g 67 ASN l 42 GLN ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5164 moved from start: 1.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 2.067 153015 Z= 0.826 Angle : 0.982 87.468 229187 Z= 0.491 Chirality : 0.049 2.003 29469 Planarity : 0.008 0.219 12090 Dihedral : 22.213 179.776 60818 Min Nonbonded Distance : 1.294 Molprobity Statistics. All-atom Clashscore : 39.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 19.80 % Favored : 79.98 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.58 % 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: -4.68 (0.09), residues: 5505 helix: -2.30 (0.13), residues: 1215 sheet: -2.59 (0.21), residues: 535 loop : -3.75 (0.08), residues: 3755 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 632 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 497 time to evaluate : 8.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 93 residues processed: 597 average time/residue: 2.4118 time to fit residues: 2400.4636 Evaluate side-chains 519 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 426 time to evaluate : 7.264 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 49 residues processed: 93 average time/residue: 2.2329 time to fit residues: 363.1648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 591 optimal weight: 1.9990 chunk 381 optimal weight: 10.0000 chunk 571 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 607 optimal weight: 40.0000 chunk 651 optimal weight: 30.0000 chunk 472 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 751 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN O 38 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 ASN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 171 ASN c 166 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 1.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 2.064 153015 Z= 0.906 Angle : 1.108 88.975 229187 Z= 0.535 Chirality : 0.053 1.986 29469 Planarity : 0.008 0.154 12090 Dihedral : 22.219 179.883 60818 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 41.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 20.27 % Favored : 79.71 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.09 % Twisted General : 0.60 % 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: -4.72 (0.09), residues: 5505 helix: -2.34 (0.13), residues: 1220 sheet: -2.70 (0.21), residues: 525 loop : -3.76 (0.08), residues: 3760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 563 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 447 time to evaluate : 7.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 90 residues processed: 526 average time/residue: 2.2789 time to fit residues: 1997.4320 Evaluate side-chains 518 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 428 time to evaluate : 7.283 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 49 residues processed: 90 average time/residue: 2.0387 time to fit residues: 324.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 869 optimal weight: 10.0000 chunk 915 optimal weight: 7.9990 chunk 835 optimal weight: 20.0000 chunk 890 optimal weight: 0.3980 chunk 536 optimal weight: 3.9990 chunk 388 optimal weight: 40.0000 chunk 699 optimal weight: 40.0000 chunk 273 optimal weight: 4.9990 chunk 805 optimal weight: 7.9990 chunk 842 optimal weight: 10.0000 chunk 887 optimal weight: 1.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 1.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 2.064 153015 Z= 0.937 Angle : 1.126 88.975 229187 Z= 0.551 Chirality : 0.053 1.986 29469 Planarity : 0.008 0.211 12090 Dihedral : 22.219 179.883 60818 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 42.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 20.27 % Favored : 79.71 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.09 % Twisted General : 0.60 % 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: -4.72 (0.09), residues: 5505 helix: -2.34 (0.13), residues: 1220 sheet: -2.70 (0.21), residues: 525 loop : -3.76 (0.08), residues: 3760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 482 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 433 time to evaluate : 7.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 49 residues processed: 472 average time/residue: 2.3442 time to fit residues: 1848.9680 Evaluate side-chains 478 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 429 time to evaluate : 7.329 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 49 residues processed: 49 average time/residue: 2.3034 time to fit residues: 194.6719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 585 optimal weight: 0.9980 chunk 942 optimal weight: 5.9990 chunk 575 optimal weight: 50.0000 chunk 446 optimal weight: 3.9990 chunk 654 optimal weight: 6.9990 chunk 988 optimal weight: 9.9990 chunk 909 optimal weight: 6.9990 chunk 786 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 607 optimal weight: 40.0000 chunk 482 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 1.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 2.064 153015 Z= 0.937 Angle : 1.126 88.975 229187 Z= 0.551 Chirality : 0.053 1.986 29469 Planarity : 0.008 0.211 12090 Dihedral : 22.219 179.883 60818 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 42.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 20.27 % Favored : 79.71 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.09 % Twisted General : 0.60 % 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: -4.72 (0.09), residues: 5505 helix: -2.34 (0.13), residues: 1220 sheet: -2.70 (0.21), residues: 525 loop : -3.76 (0.08), residues: 3760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11010 Ramachandran restraints generated. 5505 Oldfield, 0 Emsley, 5505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLY E 207 " (corrupted residue). Skipping it. Residue LYS 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue THR 18 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY H 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. Residue ILE 63 is missing expected H atoms. Skipping. Residue THR 65 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ALA P 102 " (corrupted residue). Skipping it. Residue LYS 16 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLU Q 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. Residue THR 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ALA U 93 " (corrupted residue). Skipping it. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. Residue LYS 66 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue SER 27 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue MET 34 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue ILE 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "GLY 4 37 " (corrupted residue). Skipping it. Residue ILE 14 is missing expected H atoms. Skipping. Residue ILE 15 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 47 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue VAL 98 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG d 200 " (corrupted residue). Skipping it. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP f 95 " (corrupted residue). Skipping it. Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue TYR 85 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "TRP h 132 " (corrupted residue). Skipping it. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 106 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. Residue ILE 16 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 48 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue MET 81 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ARG o 89 " (corrupted residue). Skipping it. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue MET 19 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ILE 4 is missing expected H atoms. Skipping. Residue MET 28 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Evaluate side-chains 478 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 429 time to evaluate : 7.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 49 residues processed: 468 average time/residue: 2.3016 time to fit residues: 1790.6999 Evaluate side-chains 478 residues out of total 4768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 429 time to evaluate : 7.268 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG c 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 102 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 49 residues processed: 49 average time/residue: 2.2959 time to fit residues: 192.8545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 992 random chunks: chunk 625 optimal weight: 20.0000 chunk 838 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 725 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 218 optimal weight: 30.0000 chunk 788 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 809 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.214930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.206785 restraints weight = 842825.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.204863 restraints weight = 614707.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.203159 restraints weight = 611044.736| |-----------------------------------------------------------------------------| r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4952 moved from start: 1.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 2.064 153015 Z= 0.937 Angle : 1.126 88.975 229187 Z= 0.551 Chirality : 0.053 1.986 29469 Planarity : 0.008 0.211 12090 Dihedral : 22.219 179.883 60818 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 42.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 20.27 % Favored : 79.71 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.09 % Twisted General : 0.60 % 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: -4.72 (0.09), residues: 5505 helix: -2.34 (0.13), residues: 1220 sheet: -2.70 (0.21), residues: 525 loop : -3.76 (0.08), residues: 3760 =============================================================================== Job complete usr+sys time: 70052.97 seconds wall clock time: 1204 minutes 37.87 seconds (72277.87 seconds total)