Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:19:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/02_2023/6s91_10126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/02_2023/6s91_10126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/02_2023/6s91_10126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/02_2023/6s91_10126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/02_2023/6s91_10126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/02_2023/6s91_10126_updated.pdb" } resolution = 2.68 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= -0.000 sd= 0.688 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 Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "C TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "F PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 217": "OD1" <-> "OD2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 230": "OE1" <-> "OE2" Residue "G PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 68": "OD1" <-> "OD2" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 191": "OD1" <-> "OD2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J ASP 125": "OD1" <-> "OD2" Residue "J ASP 149": "OD1" <-> "OD2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 215": "OD1" <-> "OD2" Residue "J ARG 246": "NH1" <-> "NH2" Residue "J ASP 259": "OD1" <-> "OD2" Residue "J TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 332": "OE1" <-> "OE2" Residue "J ARG 335": "NH1" <-> "NH2" Residue "J ASP 338": "OD1" <-> "OD2" Residue "J PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 433": "NH1" <-> "NH2" Residue "J TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K ASP 179": "OD1" <-> "OD2" Residue "K TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 206": "OD1" <-> "OD2" Residue "K ARG 218": "NH1" <-> "NH2" Residue "K TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 281": "OE1" <-> "OE2" Residue "K PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 294": "OD1" <-> "OD2" Residue "K TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 355": "NH1" <-> "NH2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "K TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 479": "OE1" <-> "OE2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K ARG 549": "NH1" <-> "NH2" Residue "K PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 723": "OE1" <-> "OE2" Residue "K ARG 736": "NH1" <-> "NH2" Residue "K ARG 763": "NH1" <-> "NH2" Residue "K ASP 803": "OD1" <-> "OD2" Residue "K ARG 821": "NH1" <-> "NH2" Residue "K PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 891": "NH1" <-> "NH2" Residue "K PHE 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 923": "NH1" <-> "NH2" Residue "K GLU 951": "OE1" <-> "OE2" Residue "K ARG 953": "NH1" <-> "NH2" Residue "K TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 984": "OD1" <-> "OD2" Residue "K ARG 988": "NH1" <-> "NH2" Residue "K ARG 992": "NH1" <-> "NH2" Residue "K ASP 1000": "OD1" <-> "OD2" Residue "K TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ASP 130": "OD1" <-> "OD2" Residue "L ASP 162": "OD1" <-> "OD2" Residue "L PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 28": "OD1" <-> "OD2" Residue "M ASP 34": "OD1" <-> "OD2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ASP 28": "OD1" <-> "OD2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N GLU 152": "OE1" <-> "OE2" Residue "N PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 64": "OD1" <-> "OD2" Residue "P ARG 118": "NH1" <-> "NH2" Residue "P TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 34": "OD1" <-> "OD2" Residue "Q ARG 118": "NH1" <-> "NH2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "Q TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 61": "OD1" <-> "OD2" Residue "S ASP 104": "OD1" <-> "OD2" Residue "S ASP 116": "OD1" <-> "OD2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S ASP 130": "OD1" <-> "OD2" Residue "S ASP 131": "OD1" <-> "OD2" Residue "S PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 143": "OD1" <-> "OD2" Residue "S TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T ASP 104": "OD1" <-> "OD2" Residue "T ARG 118": "NH1" <-> "NH2" Residue "T TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 118": "NH1" <-> "NH2" Residue "W PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 157": "OE1" <-> "OE2" Residue "X TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 35": "OE1" <-> "OE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X ASP 143": "OD1" <-> "OD2" Residue "X GLU 157": "OE1" <-> "OE2" Residue "X GLU 161": "OE1" <-> "OE2" Residue "X TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 51": "OE1" <-> "OE2" Residue "l TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 105": "OD1" <-> "OD2" Residue "l TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 118": "NH1" <-> "NH2" Residue "l ASP 130": "OD1" <-> "OD2" Residue "m ASP 105": "OD1" <-> "OD2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "m ASP 130": "OD1" <-> "OD2" Residue "m TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 161": "OE1" <-> "OE2" Residue "n PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 34": "OD1" <-> "OD2" Residue "n TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 143": "OD1" <-> "OD2" Residue "n PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 61": "OD1" <-> "OD2" Residue "o TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 104": "OD1" <-> "OD2" Residue "o ASP 105": "OD1" <-> "OD2" Residue "o TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 118": "NH1" <-> "NH2" Residue "o ASP 130": "OD1" <-> "OD2" Residue "o PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 6": "OE1" <-> "OE2" Residue "p ARG 118": "NH1" <-> "NH2" Residue "p PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 118": "NH1" <-> "NH2" Residue "q ASP 130": "OD1" <-> "OD2" Residue "q GLU 140": "OE1" <-> "OE2" Residue "q PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 82": "OD1" <-> "OD2" Residue "r TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 118": "NH1" <-> "NH2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 105": "OD1" <-> "OD2" Residue "s ARG 118": "NH1" <-> "NH2" Residue "s ASP 130": "OD1" <-> "OD2" Residue "s TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 118": "NH1" <-> "NH2" Residue "t ASP 131": "OD1" <-> "OD2" Residue "t PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 162": "OD1" <-> "OD2" Residue "w PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w ASP 104": "OD1" <-> "OD2" Residue "w ARG 118": "NH1" <-> "NH2" Residue "w GLU 173": "OE1" <-> "OE2" Residue "x GLU 51": "OE1" <-> "OE2" Residue "x TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 118": "NH1" <-> "NH2" Residue "x TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "R ASP 130": "OD1" <-> "OD2" Residue "R ASP 131": "OD1" <-> "OD2" Residue "R TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 62045 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1253 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "B" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "D" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "E" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "F" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "G" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2258 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2528 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2282 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain: "J" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3833 Classifications: {'peptide': 467} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 461} Chain breaks: 1 Chain: "K" Number of atoms: 8408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8408 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 987} Chain breaks: 1 Chain: "U" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 758 Inner-chain residues flagged as termini: ['pdbres=" U U 36 "'] Classifications: {'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 18} Link IDs: {'rna2p': 5, 'rna3p': 30} Chain: "V" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1025 Classifications: {'RNA': 48} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 8, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 27} Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "N" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "O" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "l" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "m" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "n" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "o" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "p" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "r" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "s" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "t" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "w" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "x" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MN': 3, ' ZN': 1, 'ANP': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25242 SG CYS K 464 67.083 104.612 42.720 1.00 47.65 S ATOM 25609 SG CYS K 512 66.052 102.876 39.613 1.00 51.91 S ATOM 25636 SG CYS K 515 64.040 102.059 42.575 1.00 48.62 S Time building chain proxies: 25.51, per 1000 atoms: 0.41 Number of scatterers: 62045 At special positions: 0 Unit cell: (153.088, 170.56, 251.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 3 24.99 S 103 16.00 P 88 15.00 O 12077 8.00 N 10223 7.00 C 39550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS Q 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS S 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 256 " - pdb=" SG CYS l 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 256 " - pdb=" SG CYS m 63 " distance=2.03 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS N 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 304 " - pdb=" SG CYS x 63 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS p 63 " distance=2.04 Simple disulfide: pdb=" SG CYS J 111 " - pdb=" SG CYS t 63 " distance=2.03 Simple disulfide: pdb=" SG CYS J 262 " - pdb=" SG CYS J 268 " distance=2.02 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 474 " distance=2.03 Simple disulfide: pdb=" SG CYS J 396 " - pdb=" SG CYS J 399 " distance=2.03 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS w 63 " distance=2.03 Simple disulfide: pdb=" SG CYS K 578 " - pdb=" SG CYS K 587 " distance=2.03 Simple disulfide: pdb=" SG CYS K 711 " - pdb=" SG CYS K 721 " 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: 22.40 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1101 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 512 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 515 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 464 " 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 103 sheets defined 25.2% alpha, 13.1% beta 26 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 16.49 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 removed outlier: 3.503A pdb=" N PHE A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 17 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 removed outlier: 4.126A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 62 through 72 removed outlier: 3.799A pdb=" N SER A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.638A pdb=" N SER A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 130 through 151 removed outlier: 3.820A pdb=" N ALA A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 removed outlier: 4.221A pdb=" N LEU B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.680A pdb=" N ARG B 35 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 36 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 42 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 43 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 62 through 65 No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 85 through 100 removed outlier: 4.802A pdb=" N TYR B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.668A pdb=" N GLN B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.740A pdb=" N ASN B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 150 removed outlier: 3.564A pdb=" N ARG B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 144 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 Processing helix chain 'C' and resid 24 through 44 removed outlier: 3.620A pdb=" N ASP C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.895A pdb=" N PHE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.641A pdb=" N SER C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 116 through 128 removed outlier: 4.354A pdb=" N LEU C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'D' and resid 46 through 60 Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.605A pdb=" N ARG D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP D 66 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 71 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU D 72 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 137 through 149 removed outlier: 4.212A pdb=" N LYS D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 removed outlier: 4.845A pdb=" N GLU D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'E' and resid 46 through 60 removed outlier: 3.631A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 115 through 130 Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.905A pdb=" N LYS E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.820A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 Processing helix chain 'E' and resid 282 through 285 No H-bonds generated for 'chain 'E' and resid 282 through 285' Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.951A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 115 through 130 removed outlier: 3.698A pdb=" N GLN F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 149 removed outlier: 4.021A pdb=" N LYS F 149 " --> pdb=" O THR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.829A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 253 No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 282 through 285 No H-bonds generated for 'chain 'F' and resid 282 through 285' Processing helix chain 'G' and resid 46 through 60 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 115 through 126 Processing helix chain 'G' and resid 137 through 149 removed outlier: 4.235A pdb=" N LYS G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 205 Processing helix chain 'G' and resid 248 through 256 Processing helix chain 'G' and resid 258 through 260 No H-bonds generated for 'chain 'G' and resid 258 through 260' Processing helix chain 'H' and resid 39 through 50 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 98 through 106 removed outlier: 4.740A pdb=" N ASN H 102 " --> pdb=" O HIS H 99 " (cutoff:3.500A) Proline residue: H 104 - end of helix Processing helix chain 'H' and resid 111 through 121 Processing helix chain 'H' and resid 128 through 130 No H-bonds generated for 'chain 'H' and resid 128 through 130' Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'H' and resid 233 through 235 No H-bonds generated for 'chain 'H' and resid 233 through 235' Processing helix chain 'H' and resid 271 through 280 removed outlier: 4.135A pdb=" N ASP H 275 " --> pdb=" O SER H 272 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN H 279 " --> pdb=" O PHE H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 295 removed outlier: 3.706A pdb=" N ARG H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS H 291 " --> pdb=" O TYR H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 9 through 15 Processing helix chain 'I' and resid 22 through 34 removed outlier: 3.796A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 39 No H-bonds generated for 'chain 'I' and resid 36 through 39' Processing helix chain 'I' and resid 54 through 57 No H-bonds generated for 'chain 'I' and resid 54 through 57' Processing helix chain 'I' and resid 65 through 87 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 154 through 177 removed outlier: 6.885A pdb=" N GLU I 171 " --> pdb=" O GLY I 167 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N GLN I 172 " --> pdb=" O LYS I 168 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA I 174 " --> pdb=" O GLY I 170 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 260 Proline residue: I 250 - end of helix removed outlier: 3.992A pdb=" N ASP I 253 " --> pdb=" O PRO I 250 " (cutoff:3.500A) Proline residue: I 256 - end of helix removed outlier: 3.813A pdb=" N LEU I 259 " --> pdb=" O PRO I 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE I 260 " --> pdb=" O ILE I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 35 through 56 Processing helix chain 'J' and resid 64 through 75 removed outlier: 5.476A pdb=" N ASP J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 112 removed outlier: 3.661A pdb=" N ASP J 110 " --> pdb=" O ASP J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 158 Processing helix chain 'J' and resid 162 through 165 No H-bonds generated for 'chain 'J' and resid 162 through 165' Processing helix chain 'J' and resid 182 through 200 removed outlier: 3.573A pdb=" N GLU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR J 199 " --> pdb=" O ASN J 195 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE J 200 " --> pdb=" O TYR J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 241 Processing helix chain 'J' and resid 248 through 250 No H-bonds generated for 'chain 'J' and resid 248 through 250' Processing helix chain 'J' and resid 265 through 278 removed outlier: 7.777A pdb=" N LYS J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE J 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE J 278 " --> pdb=" O LEU J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 297 Processing helix chain 'J' and resid 339 through 350 removed outlier: 4.080A pdb=" N TYR J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 373 Processing helix chain 'J' and resid 392 through 394 No H-bonds generated for 'chain 'J' and resid 392 through 394' Processing helix chain 'J' and resid 417 through 423 Processing helix chain 'J' and resid 461 through 474 Processing helix chain 'K' and resid 15 through 18 No H-bonds generated for 'chain 'K' and resid 15 through 18' Processing helix chain 'K' and resid 25 through 28 No H-bonds generated for 'chain 'K' and resid 25 through 28' Processing helix chain 'K' and resid 35 through 38 No H-bonds generated for 'chain 'K' and resid 35 through 38' Processing helix chain 'K' and resid 51 through 55 Processing helix chain 'K' and resid 73 through 76 No H-bonds generated for 'chain 'K' and resid 73 through 76' Processing helix chain 'K' and resid 78 through 83 Processing helix chain 'K' and resid 85 through 90 Processing helix chain 'K' and resid 125 through 135 removed outlier: 3.914A pdb=" N GLU K 130 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU K 135 " --> pdb=" O TYR K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 160 removed outlier: 4.386A pdb=" N TYR K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 153 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 194 removed outlier: 3.996A pdb=" N THR K 184 " --> pdb=" O HIS K 180 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA K 185 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA K 186 " --> pdb=" O TYR K 182 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET K 187 " --> pdb=" O ALA K 183 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 215 Processing helix chain 'K' and resid 220 through 244 removed outlier: 3.983A pdb=" N VAL K 237 " --> pdb=" O LEU K 233 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE K 238 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP K 240 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 270 Processing helix chain 'K' and resid 279 through 288 removed outlier: 4.166A pdb=" N LEU K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 299 No H-bonds generated for 'chain 'K' and resid 296 through 299' Processing helix chain 'K' and resid 334 through 359 Processing helix chain 'K' and resid 366 through 374 Processing helix chain 'K' and resid 378 through 381 No H-bonds generated for 'chain 'K' and resid 378 through 381' Processing helix chain 'K' and resid 397 through 399 No H-bonds generated for 'chain 'K' and resid 397 through 399' Processing helix chain 'K' and resid 413 through 430 removed outlier: 3.785A pdb=" N ARG K 419 " --> pdb=" O ASP K 415 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU K 430 " --> pdb=" O LYS K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 442 through 446 Processing helix chain 'K' and resid 483 through 486 No H-bonds generated for 'chain 'K' and resid 483 through 486' Processing helix chain 'K' and resid 496 through 504 removed outlier: 4.003A pdb=" N SER K 500 " --> pdb=" O LYS K 496 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET K 504 " --> pdb=" O SER K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 523 Processing helix chain 'K' and resid 527 through 532 removed outlier: 3.800A pdb=" N LEU K 532 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 548 Processing helix chain 'K' and resid 558 through 562 Processing helix chain 'K' and resid 564 through 573 removed outlier: 3.581A pdb=" N GLU K 572 " --> pdb=" O GLU K 568 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS K 573 " --> pdb=" O GLU K 569 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 581 No H-bonds generated for 'chain 'K' and resid 578 through 581' Processing helix chain 'K' and resid 599 through 603 Processing helix chain 'K' and resid 615 through 618 No H-bonds generated for 'chain 'K' and resid 615 through 618' Processing helix chain 'K' and resid 626 through 635 removed outlier: 3.657A pdb=" N HIS K 635 " --> pdb=" O VAL K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 658 Processing helix chain 'K' and resid 673 through 675 No H-bonds generated for 'chain 'K' and resid 673 through 675' Processing helix chain 'K' and resid 682 through 696 Processing helix chain 'K' and resid 700 through 715 removed outlier: 5.976A pdb=" N GLU K 714 " --> pdb=" O CYS K 711 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN K 715 " --> pdb=" O ILE K 712 " (cutoff:3.500A) Processing helix chain 'K' and resid 726 through 733 removed outlier: 4.078A pdb=" N ALA K 731 " --> pdb=" O SER K 727 " (cutoff:3.500A) Processing helix chain 'K' and resid 744 through 761 removed outlier: 3.774A pdb=" N LYS K 749 " --> pdb=" O GLU K 745 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE K 755 " --> pdb=" O SER K 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 768 through 792 removed outlier: 3.770A pdb=" N GLU K 787 " --> pdb=" O LEU K 783 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS K 792 " --> pdb=" O LEU K 788 " (cutoff:3.500A) Processing helix chain 'K' and resid 813 through 825 removed outlier: 3.831A pdb=" N ALA K 825 " --> pdb=" O ARG K 821 " (cutoff:3.500A) Processing helix chain 'K' and resid 870 through 887 removed outlier: 4.317A pdb=" N LYS K 885 " --> pdb=" O LEU K 881 " (cutoff:3.500A) Processing helix chain 'K' and resid 930 through 932 No H-bonds generated for 'chain 'K' and resid 930 through 932' Processing helix chain 'K' and resid 937 through 950 removed outlier: 3.523A pdb=" N VAL K 941 " --> pdb=" O SER K 937 " (cutoff:3.500A) Processing helix chain 'K' and resid 956 through 960 Processing helix chain 'K' and resid 962 through 971 removed outlier: 3.628A pdb=" N HIS K 967 " --> pdb=" O GLU K 963 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU K 968 " --> pdb=" O LYS K 964 " (cutoff:3.500A) Processing helix chain 'K' and resid 975 through 988 Processing helix chain 'K' and resid 1021 through 1035 removed outlier: 3.513A pdb=" N GLY K1035 " --> pdb=" O ILE K1031 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 145 removed outlier: 4.166A pdb=" N ASP L 143 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 166 No H-bonds generated for 'chain 'L' and resid 163 through 166' Processing helix chain 'M' and resid 131 through 144 removed outlier: 3.719A pdb=" N ASP M 143 " --> pdb=" O LYS M 139 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS M 144 " --> pdb=" O GLU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 166 removed outlier: 4.491A pdb=" N ILE M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS M 164 " --> pdb=" O LYS M 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 135 Processing helix chain 'N' and resid 137 through 140 No H-bonds generated for 'chain 'N' and resid 137 through 140' Processing helix chain 'N' and resid 157 through 166 removed outlier: 4.506A pdb=" N ASP N 162 " --> pdb=" O LYS N 158 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS N 164 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'O' and resid 156 through 166 removed outlier: 4.308A pdb=" N ASP O 162 " --> pdb=" O LYS O 158 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 138 Processing helix chain 'P' and resid 155 through 166 removed outlier: 4.024A pdb=" N LYS P 160 " --> pdb=" O GLU P 157 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU P 161 " --> pdb=" O LYS P 158 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU P 165 " --> pdb=" O ASP P 162 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU P 166 " --> pdb=" O ILE P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 140 removed outlier: 4.550A pdb=" N ASN Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE Q 137 " --> pdb=" O ILE Q 133 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE Q 138 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS Q 139 " --> pdb=" O ASN Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 145 No H-bonds generated for 'chain 'Q' and resid 142 through 145' Processing helix chain 'Q' and resid 157 through 166 removed outlier: 3.809A pdb=" N ILE Q 163 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 138 removed outlier: 4.546A pdb=" N ILE S 137 " --> pdb=" O ILE S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 145 Processing helix chain 'S' and resid 156 through 160 Processing helix chain 'S' and resid 163 through 166 No H-bonds generated for 'chain 'S' and resid 163 through 166' Processing helix chain 'T' and resid 131 through 141 removed outlier: 4.859A pdb=" N ASN T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE T 138 " --> pdb=" O VAL T 134 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS T 139 " --> pdb=" O ASN T 135 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 160 No H-bonds generated for 'chain 'T' and resid 157 through 160' Processing helix chain 'T' and resid 163 through 166 No H-bonds generated for 'chain 'T' and resid 163 through 166' Processing helix chain 'W' and resid 131 through 141 Processing helix chain 'W' and resid 158 through 166 Processing helix chain 'X' and resid 131 through 135 Processing helix chain 'X' and resid 138 through 141 No H-bonds generated for 'chain 'X' and resid 138 through 141' Processing helix chain 'X' and resid 158 through 161 No H-bonds generated for 'chain 'X' and resid 158 through 161' Processing helix chain 'X' and resid 163 through 166 No H-bonds generated for 'chain 'X' and resid 163 through 166' Processing helix chain 'l' and resid 76 through 78 No H-bonds generated for 'chain 'l' and resid 76 through 78' Processing helix chain 'l' and resid 131 through 140 removed outlier: 4.043A pdb=" N ASN l 136 " --> pdb=" O THR l 132 " (cutoff:3.500A) Processing helix chain 'l' and resid 142 through 145 No H-bonds generated for 'chain 'l' and resid 142 through 145' Processing helix chain 'l' and resid 148 through 151 No H-bonds generated for 'chain 'l' and resid 148 through 151' Processing helix chain 'l' and resid 157 through 166 removed outlier: 3.918A pdb=" N ASP l 162 " --> pdb=" O LYS l 158 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS l 164 " --> pdb=" O LYS l 160 " (cutoff:3.500A) Processing helix chain 'm' and resid 131 through 140 removed outlier: 4.036A pdb=" N ASN m 136 " --> pdb=" O THR m 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 156 through 164 Processing helix chain 'n' and resid 132 through 140 Processing helix chain 'n' and resid 156 through 166 Processing helix chain 'o' and resid 131 through 138 removed outlier: 4.451A pdb=" N ASN o 136 " --> pdb=" O THR o 132 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE o 137 " --> pdb=" O ILE o 133 " (cutoff:3.500A) Processing helix chain 'o' and resid 157 through 164 Processing helix chain 'p' and resid 131 through 140 removed outlier: 3.931A pdb=" N ILE p 137 " --> pdb=" O ILE p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 145 No H-bonds generated for 'chain 'p' and resid 142 through 145' Processing helix chain 'p' and resid 157 through 166 removed outlier: 3.820A pdb=" N LYS p 164 " --> pdb=" O LYS p 160 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU p 165 " --> pdb=" O GLU p 161 " (cutoff:3.500A) Processing helix chain 'q' and resid 131 through 140 removed outlier: 3.948A pdb=" N LYS q 139 " --> pdb=" O ASN q 135 " (cutoff:3.500A) Processing helix chain 'q' and resid 157 through 162 removed outlier: 4.970A pdb=" N ASP q 162 " --> pdb=" O LYS q 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 140 removed outlier: 4.445A pdb=" N ASN r 136 " --> pdb=" O ILE r 133 " (cutoff:3.500A) Processing helix chain 'r' and resid 156 through 165 Processing helix chain 's' and resid 131 through 141 removed outlier: 4.652A pdb=" N ASN s 136 " --> pdb=" O THR s 132 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE s 137 " --> pdb=" O ILE s 133 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS s 139 " --> pdb=" O ASN s 135 " (cutoff:3.500A) Processing helix chain 's' and resid 156 through 161 removed outlier: 3.873A pdb=" N LYS s 160 " --> pdb=" O ILE s 156 " (cutoff:3.500A) Processing helix chain 't' and resid 131 through 139 removed outlier: 3.702A pdb=" N ILE t 138 " --> pdb=" O VAL t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 142 through 145 No H-bonds generated for 'chain 't' and resid 142 through 145' Processing helix chain 't' and resid 158 through 166 removed outlier: 5.263A pdb=" N ILE t 163 " --> pdb=" O VAL t 159 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS t 164 " --> pdb=" O LYS t 160 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLU t 165 " --> pdb=" O GLU t 161 " (cutoff:3.500A) Processing helix chain 'w' and resid 132 through 140 removed outlier: 4.448A pdb=" N LYS w 139 " --> pdb=" O ASN w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 142 through 145 No H-bonds generated for 'chain 'w' and resid 142 through 145' Processing helix chain 'w' and resid 156 through 161 Processing helix chain 'w' and resid 163 through 166 No H-bonds generated for 'chain 'w' and resid 163 through 166' Processing helix chain 'x' and resid 131 through 140 Processing helix chain 'x' and resid 163 through 166 No H-bonds generated for 'chain 'x' and resid 163 through 166' Processing helix chain 'R' and resid 132 through 140 removed outlier: 4.411A pdb=" N ILE R 137 " --> pdb=" O ILE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 145 No H-bonds generated for 'chain 'R' and resid 142 through 145' Processing helix chain 'R' and resid 156 through 166 removed outlier: 3.663A pdb=" N LYS R 164 " --> pdb=" O LYS R 160 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU R 165 " --> pdb=" O GLU R 161 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 263 through 265 removed outlier: 6.808A pdb=" N GLY D 244 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA D 7 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 242 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER D 240 " --> pdb=" O PRO D 9 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE D 11 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE D 238 " --> pdb=" O PHE D 11 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 94 through 97 Processing sheet with id= C, first strand: chain 'D' and resid 162 through 165 Processing sheet with id= D, first strand: chain 'D' and resid 207 through 212 Processing sheet with id= E, first strand: chain 'D' and resid 90 through 93 removed outlier: 6.776A pdb=" N ILE D 237 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 263 through 265 Processing sheet with id= G, first strand: chain 'E' and resid 94 through 97 Processing sheet with id= H, first strand: chain 'E' and resid 163 through 165 Processing sheet with id= I, first strand: chain 'E' and resid 90 through 93 removed outlier: 6.806A pdb=" N ILE E 237 " --> pdb=" O PHE E 92 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 263 through 265 Processing sheet with id= K, first strand: chain 'F' and resid 94 through 97 Processing sheet with id= L, first strand: chain 'F' and resid 98 through 100 Processing sheet with id= M, first strand: chain 'F' and resid 207 through 212 Processing sheet with id= N, first strand: chain 'F' and resid 90 through 93 removed outlier: 6.659A pdb=" N ILE F 237 " --> pdb=" O PHE F 92 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 263 through 265 removed outlier: 3.540A pdb=" N PHE G 6 " --> pdb=" O GLY G 244 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 94 through 97 removed outlier: 3.808A pdb=" N LEU G 190 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 98 through 100 Processing sheet with id= R, first strand: chain 'G' and resid 207 through 212 Processing sheet with id= S, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.843A pdb=" N ILE G 237 " --> pdb=" O PHE G 92 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 184 through 186 removed outlier: 3.634A pdb=" N LYS H 184 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 83 through 87 Processing sheet with id= V, first strand: chain 'H' and resid 132 through 140 Processing sheet with id= W, first strand: chain 'H' and resid 212 through 214 Processing sheet with id= X, first strand: chain 'H' and resid 242 through 246 Processing sheet with id= Y, first strand: chain 'I' and resid 274 through 278 removed outlier: 6.476A pdb=" N GLU I 117 " --> pdb=" O ARG I 277 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG I 196 " --> pdb=" O THR I 235 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG I 237 " --> pdb=" O PRO I 194 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 202 through 209 Processing sheet with id= AA, first strand: chain 'J' and resid 84 through 86 removed outlier: 3.525A pdb=" N MET J 6 " --> pdb=" O ILE J 212 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU J 214 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU J 4 " --> pdb=" O LEU J 214 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS J 11 " --> pdb=" O ILE J 257 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE J 257 " --> pdb=" O LYS J 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU J 13 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU J 255 " --> pdb=" O LEU J 13 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 171 through 175 Processing sheet with id= AC, first strand: chain 'J' and resid 333 through 335 removed outlier: 3.503A pdb=" N ILE J 437 " --> pdb=" O TYR J 445 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.657A pdb=" N LYS J 143 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL J 103 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER J 141 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 311 through 317 removed outlier: 3.583A pdb=" N TYR K 201 " --> pdb=" O LEU K 316 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 795 through 798 removed outlier: 6.677A pdb=" N LEU K 805 " --> pdb=" O ILE K 797 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP K 650 " --> pdb=" O SER K 858 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 836 through 838 Processing sheet with id= AH, first strand: chain 'K' and resid 888 through 890 Processing sheet with id= AI, first strand: chain 'L' and resid 84 through 86 removed outlier: 7.065A pdb=" N ARG L 5 " --> pdb=" O TYR L 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE L 69 " --> pdb=" O VAL L 8 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 47 through 49 Processing sheet with id= AK, first strand: chain 'L' and resid 124 through 126 Processing sheet with id= AL, first strand: chain 'M' and resid 42 through 45 removed outlier: 5.403A pdb=" N LYS M 107 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR M 7 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR M 109 " --> pdb=" O TYR M 7 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N PHE M 9 " --> pdb=" O TYR M 109 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 47 through 49 Processing sheet with id= AN, first strand: chain 'M' and resid 124 through 126 removed outlier: 3.546A pdb=" N TYR M 169 " --> pdb=" O VAL M 126 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 42 through 45 removed outlier: 6.383A pdb=" N LYS N 107 " --> pdb=" O ARG N 5 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR N 7 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR N 109 " --> pdb=" O TYR N 7 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N PHE N 9 " --> pdb=" O TYR N 109 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 47 through 50 Processing sheet with id= AQ, first strand: chain 'N' and resid 124 through 127 Processing sheet with id= AR, first strand: chain 'O' and resid 6 through 8 Processing sheet with id= AS, first strand: chain 'O' and resid 42 through 45 removed outlier: 3.541A pdb=" N LEU O 42 " --> pdb=" O GLY O 68 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'O' and resid 86 through 88 Processing sheet with id= AU, first strand: chain 'O' and resid 124 through 127 Processing sheet with id= AV, first strand: chain 'P' and resid 5 through 7 Processing sheet with id= AW, first strand: chain 'P' and resid 42 through 45 Processing sheet with id= AX, first strand: chain 'P' and resid 124 through 126 removed outlier: 3.682A pdb=" N TYR P 169 " --> pdb=" O VAL P 126 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 6 through 9 removed outlier: 3.690A pdb=" N VAL Q 71 " --> pdb=" O GLU Q 6 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Q' and resid 43 through 45 Processing sheet with id= BA, first strand: chain 'Q' and resid 47 through 50 removed outlier: 3.823A pdb=" N ARG Q 55 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Q' and resid 84 through 86 Processing sheet with id= BC, first strand: chain 'Q' and resid 124 through 126 removed outlier: 3.871A pdb=" N ALA Q 171 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'S' and resid 69 through 72 removed outlier: 5.887A pdb=" N LYS S 107 " --> pdb=" O ARG S 5 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR S 7 " --> pdb=" O LYS S 107 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR S 109 " --> pdb=" O TYR S 7 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE S 110 " --> pdb=" O LEU S 84 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'S' and resid 43 through 45 Processing sheet with id= BF, first strand: chain 'S' and resid 47 through 50 removed outlier: 4.397A pdb=" N ASP S 50 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG S 55 " --> pdb=" O ASP S 50 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'T' and resid 107 through 110 removed outlier: 3.704A pdb=" N TYR T 109 " --> pdb=" O ARG T 5 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU T 42 " --> pdb=" O GLY T 68 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'T' and resid 124 through 127 Processing sheet with id= BI, first strand: chain 'W' and resid 6 through 8 Processing sheet with id= BJ, first strand: chain 'W' and resid 43 through 45 Processing sheet with id= BK, first strand: chain 'W' and resid 83 through 86 removed outlier: 3.608A pdb=" N LEU W 86 " --> pdb=" O ILE W 108 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'W' and resid 124 through 127 Processing sheet with id= BM, first strand: chain 'X' and resid 69 through 71 removed outlier: 3.569A pdb=" N LEU X 86 " --> pdb=" O ILE X 108 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'X' and resid 42 through 45 Processing sheet with id= BO, first strand: chain 'l' and resid 83 through 88 removed outlier: 7.062A pdb=" N ARG l 5 " --> pdb=" O TYR l 109 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N TYR l 7 " --> pdb=" O PRO l 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL l 71 " --> pdb=" O GLU l 6 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'l' and resid 124 through 127 Processing sheet with id= BQ, first strand: chain 'm' and resid 86 through 88 removed outlier: 7.636A pdb=" N ARG m 5 " --> pdb=" O TYR m 109 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'm' and resid 47 through 49 Processing sheet with id= BS, first strand: chain 'm' and resid 124 through 126 Processing sheet with id= BT, first strand: chain 'n' and resid 5 through 7 Processing sheet with id= BU, first strand: chain 'n' and resid 42 through 45 Processing sheet with id= BV, first strand: chain 'n' and resid 124 through 126 Processing sheet with id= BW, first strand: chain 'o' and resid 5 through 9 removed outlier: 3.700A pdb=" N GLY o 68 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU o 42 " --> pdb=" O GLY o 68 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'o' and resid 47 through 49 Processing sheet with id= BY, first strand: chain 'o' and resid 84 through 86 Processing sheet with id= BZ, first strand: chain 'o' and resid 124 through 127 removed outlier: 4.045A pdb=" N TYR o 169 " --> pdb=" O VAL o 126 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'p' and resid 42 through 45 removed outlier: 6.326A pdb=" N LYS p 107 " --> pdb=" O ARG p 5 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR p 7 " --> pdb=" O LYS p 107 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR p 109 " --> pdb=" O TYR p 7 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE p 9 " --> pdb=" O TYR p 109 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'p' and resid 47 through 49 Processing sheet with id= CC, first strand: chain 'p' and resid 124 through 127 Processing sheet with id= CD, first strand: chain 'q' and resid 6 through 9 Processing sheet with id= CE, first strand: chain 'q' and resid 84 through 88 removed outlier: 4.270A pdb=" N LEU q 84 " --> pdb=" O ILE q 110 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE q 110 " --> pdb=" O LEU q 84 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'q' and resid 124 through 127 Processing sheet with id= CG, first strand: chain 'r' and resid 6 through 8 Processing sheet with id= CH, first strand: chain 'r' and resid 42 through 45 removed outlier: 3.516A pdb=" N LEU r 42 " --> pdb=" O GLY r 68 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'r' and resid 47 through 50 removed outlier: 3.716A pdb=" N ASP r 50 " --> pdb=" O ARG r 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG r 55 " --> pdb=" O ASP r 50 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'r' and resid 124 through 126 Processing sheet with id= CK, first strand: chain 's' and resid 42 through 45 Processing sheet with id= CL, first strand: chain 's' and resid 48 through 50 removed outlier: 3.708A pdb=" N ASP s 50 " --> pdb=" O ARG s 55 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG s 55 " --> pdb=" O ASP s 50 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 's' and resid 84 through 86 removed outlier: 4.189A pdb=" N LEU s 84 " --> pdb=" O ILE s 110 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE s 110 " --> pdb=" O LEU s 84 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 's' and resid 124 through 126 Processing sheet with id= CO, first strand: chain 't' and resid 42 through 45 removed outlier: 6.088A pdb=" N LYS t 107 " --> pdb=" O ARG t 5 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR t 7 " --> pdb=" O LYS t 107 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR t 109 " --> pdb=" O TYR t 7 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N PHE t 9 " --> pdb=" O TYR t 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU t 106 " --> pdb=" O LEU t 88 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 't' and resid 47 through 50 Processing sheet with id= CQ, first strand: chain 'w' and resid 5 through 9 Processing sheet with id= CR, first strand: chain 'w' and resid 83 through 87 Processing sheet with id= CS, first strand: chain 'w' and resid 124 through 127 removed outlier: 3.564A pdb=" N ALA w 171 " --> pdb=" O LYS w 124 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'x' and resid 69 through 72 removed outlier: 3.939A pdb=" N VAL x 8 " --> pdb=" O ILE x 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR x 7 " --> pdb=" O TYR x 109 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'x' and resid 94 through 96 removed outlier: 4.310A pdb=" N TYR x 94 " --> pdb=" O VAL x 43 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'x' and resid 124 through 127 Processing sheet with id= CW, first strand: chain 'R' and resid 5 through 7 Processing sheet with id= CX, first strand: chain 'R' and resid 47 through 49 Processing sheet with id= CY, first strand: chain 'R' and resid 124 through 127 removed outlier: 3.678A pdb=" N TYR R 169 " --> pdb=" O VAL R 126 " (cutoff:3.500A) 1571 hydrogen bonds defined for protein. 4170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 23.50 Time building geometry restraints manager: 24.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14644 1.33 - 1.45: 13058 1.45 - 1.58: 35285 1.58 - 1.70: 171 1.70 - 1.82: 150 Bond restraints: 63308 Sorted by residual: bond pdb=" O3A ANP K1102 " pdb=" PB ANP K1102 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" O3A ANP K1103 " pdb=" PB ANP K1103 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N3B ANP K1103 " pdb=" PG ANP K1103 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" N3B ANP K1102 " pdb=" PG ANP K1102 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O5' ANP K1103 " pdb=" PA ANP K1103 " ideal model delta sigma weight residual 1.655 1.571 0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 63303 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.51: 1816 106.51 - 113.78: 36911 113.78 - 121.06: 29347 121.06 - 128.34: 17627 128.34 - 135.61: 339 Bond angle restraints: 86040 Sorted by residual: angle pdb=" N ILE s 148 " pdb=" CA ILE s 148 " pdb=" C ILE s 148 " ideal model delta sigma weight residual 113.53 105.19 8.34 9.80e-01 1.04e+00 7.25e+01 angle pdb=" N VAL l 154 " pdb=" CA VAL l 154 " pdb=" C VAL l 154 " ideal model delta sigma weight residual 113.53 106.20 7.33 9.80e-01 1.04e+00 5.59e+01 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 114.75 106.07 8.68 1.26e+00 6.30e-01 4.75e+01 angle pdb=" N SER K 990 " pdb=" CA SER K 990 " pdb=" C SER K 990 " ideal model delta sigma weight residual 110.80 124.57 -13.77 2.13e+00 2.20e-01 4.18e+01 angle pdb=" N GLY S 54 " pdb=" CA GLY S 54 " pdb=" C GLY S 54 " ideal model delta sigma weight residual 111.03 119.81 -8.78 1.40e+00 5.10e-01 3.93e+01 ... (remaining 86035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 37916 35.34 - 70.68: 688 70.68 - 106.02: 57 106.02 - 141.35: 3 141.35 - 176.69: 4 Dihedral angle restraints: 38668 sinusoidal: 16552 harmonic: 22116 Sorted by residual: dihedral pdb=" CB CYS J 111 " pdb=" SG CYS J 111 " pdb=" SG CYS t 63 " pdb=" CB CYS t 63 " ideal model delta sinusoidal sigma weight residual -86.00 -174.70 88.70 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS J 356 " pdb=" SG CYS J 356 " pdb=" SG CYS J 474 " pdb=" CB CYS J 474 " ideal model delta sinusoidal sigma weight residual -86.00 -171.10 85.10 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" O4' U V 3 " pdb=" C1' U V 3 " pdb=" N1 U V 3 " pdb=" C2 U V 3 " ideal model delta sinusoidal sigma weight residual 200.00 28.25 171.75 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 38665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 8252 0.068 - 0.135: 1700 0.135 - 0.203: 92 0.203 - 0.270: 8 0.270 - 0.338: 2 Chirality restraints: 10054 Sorted by residual: chirality pdb=" C3' ANP K1103 " pdb=" C2' ANP K1103 " pdb=" C4' ANP K1103 " pdb=" O3' ANP K1103 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C3' ANP K1102 " pdb=" C2' ANP K1102 " pdb=" C4' ANP K1102 " pdb=" O3' ANP K1102 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL D 232 " pdb=" CA VAL D 232 " pdb=" CG1 VAL D 232 " pdb=" CG2 VAL D 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 10051 not shown) Planarity restraints: 10538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 19 " 0.044 2.00e-02 2.50e+03 2.04e-02 1.14e+01 pdb=" N9 A V 19 " -0.048 2.00e-02 2.50e+03 pdb=" C8 A V 19 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A V 19 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A V 19 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A V 19 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A V 19 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A V 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A V 19 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A V 19 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A V 19 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 13 " -0.044 2.00e-02 2.50e+03 1.92e-02 1.01e+01 pdb=" N9 A V 13 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A V 13 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A V 13 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A V 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A V 13 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A V 13 " -0.012 2.00e-02 2.50e+03 pdb=" N1 A V 13 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A V 13 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A V 13 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A V 13 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U 12 " 0.037 2.00e-02 2.50e+03 1.74e-02 9.10e+00 pdb=" N9 G U 12 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G U 12 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G U 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G U 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G U 12 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G U 12 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G U 12 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G U 12 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G U 12 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G U 12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G U 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 10535 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 241 2.34 - 2.98: 33275 2.98 - 3.62: 94399 3.62 - 4.26: 154436 4.26 - 4.90: 247649 Nonbonded interactions: 530000 Sorted by model distance: nonbonded pdb=" O1A ANP K1102 " pdb="MN MN K1106 " model vdw 1.696 2.320 nonbonded pdb=" O3G ANP K1102 " pdb="MN MN K1106 " model vdw 1.711 2.320 nonbonded pdb=" O THR K 207 " pdb="MN MN K1106 " model vdw 1.736 2.320 nonbonded pdb=" O2B ANP K1103 " pdb="MN MN K1104 " model vdw 1.762 2.320 nonbonded pdb=" O1A ANP K1103 " pdb="MN MN K1105 " model vdw 1.889 2.320 ... (remaining 529995 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 152) selection = (chain 'B' and resid 3 through 152) selection = (chain 'C' and resid 3 through 152) } ncs_group { reference = (chain 'D' and resid 2 through 284) selection = (chain 'E' and resid 2 through 284) selection = (chain 'F' and resid 2 through 284) selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } 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: 7 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 1 6.06 5 P 88 5.49 5 S 103 5.16 5 C 39550 2.51 5 N 10223 2.21 5 O 12077 1.98 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 30.470 Check model and map are aligned: 0.680 Process input model: 148.220 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Set scattering table: 0.450 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.157 63308 Z= 0.393 Angle : 0.796 18.380 86040 Z= 0.442 Chirality : 0.051 0.338 10054 Planarity : 0.005 0.068 10538 Dihedral : 14.750 176.692 24353 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.55 % Favored : 86.29 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.91 (0.07), residues: 7418 helix: -2.95 (0.08), residues: 2045 sheet: -2.37 (0.13), residues: 1197 loop : -3.87 (0.07), residues: 4176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1513 time to evaluate : 5.752 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 outliers start: 6 outliers final: 6 residues processed: 1519 average time/residue: 1.3091 time to fit residues: 2624.6149 Evaluate side-chains 1012 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1006 time to evaluate : 5.634 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 2 average time/residue: 0.5575 time to fit residues: 9.7556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 629 optimal weight: 6.9990 chunk 564 optimal weight: 0.9990 chunk 313 optimal weight: 0.0050 chunk 192 optimal weight: 10.0000 chunk 380 optimal weight: 4.9990 chunk 301 optimal weight: 8.9990 chunk 583 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 434 optimal weight: 6.9990 chunk 676 optimal weight: 10.0000 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS C 106 GLN D 138 ASN D 178 ASN D 185 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 17 HIS F 77 ASN F 130 GLN F 177 ASN F 260 ASN G 13 HIS G 77 ASN G 185 ASN H 28 HIS H 52 ASN H 66 ASN H 91 HIS ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN I 21 ASN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 195 ASN J 220 HIS J 345 ASN J 406 ASN J 440 ASN ** K 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 165 ASN K 189 ASN K 330 GLN K 728 ASN K 989 ASN K1024 ASN M 4 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN N 4 GLN N 40 ASN N 79 GLN O 91 ASN O 135 ASN P 39 HIS P 53 ASN ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 76 GLN S 91 ASN ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 135 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN X 77 GLN l 147 ASN l 174 GLN m 4 GLN m 14 ASN m 53 ASN m 135 ASN ** n 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN n 119 ASN n 135 ASN n 174 GLN p 91 ASN p 174 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 ASN r 76 GLN r 79 GLN t 150 GLN w 40 ASN w 135 ASN x 4 GLN x 40 ASN x 53 ASN x 77 GLN x 135 ASN x 174 GLN R 39 HIS R 76 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 63308 Z= 0.301 Angle : 0.744 17.790 86040 Z= 0.390 Chirality : 0.049 0.286 10054 Planarity : 0.005 0.073 10538 Dihedral : 9.737 177.329 9177 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 12.28 % Favored : 87.71 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.04 (0.08), residues: 7418 helix: -1.95 (0.10), residues: 2040 sheet: -1.98 (0.13), residues: 1240 loop : -3.44 (0.08), residues: 4138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1143 time to evaluate : 5.559 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 outliers start: 268 outliers final: 108 residues processed: 1281 average time/residue: 1.1938 time to fit residues: 2087.1869 Evaluate side-chains 1096 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 988 time to evaluate : 5.634 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 59 residues processed: 52 average time/residue: 0.6607 time to fit residues: 64.3335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 375 optimal weight: 0.8980 chunk 209 optimal weight: 0.0170 chunk 563 optimal weight: 0.8980 chunk 460 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 677 optimal weight: 30.0000 chunk 732 optimal weight: 20.0000 chunk 603 optimal weight: 6.9990 chunk 672 optimal weight: 30.0000 chunk 231 optimal weight: 0.8980 chunk 543 optimal weight: 10.0000 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN G 185 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN H 228 ASN I 87 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 ASN O 135 ASN ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** n 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN o 135 ASN p 135 ASN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 40 ASN q 136 ASN r 150 GLN ** r 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 63308 Z= 0.210 Angle : 0.690 17.914 86040 Z= 0.360 Chirality : 0.048 0.275 10054 Planarity : 0.005 0.069 10538 Dihedral : 9.410 178.048 9177 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.20 % Favored : 88.78 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.49 (0.09), residues: 7418 helix: -1.43 (0.11), residues: 2017 sheet: -1.66 (0.13), residues: 1320 loop : -3.14 (0.08), residues: 4081 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1145 time to evaluate : 5.651 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 outliers start: 326 outliers final: 138 residues processed: 1343 average time/residue: 1.1545 time to fit residues: 2126.6191 Evaluate side-chains 1108 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 970 time to evaluate : 5.623 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 97 residues processed: 44 average time/residue: 0.5484 time to fit residues: 50.4757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 669 optimal weight: 9.9990 chunk 509 optimal weight: 0.9980 chunk 351 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 323 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 680 optimal weight: 0.3980 chunk 720 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 644 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 166 ASN H 97 GLN H 228 ASN I 64 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN J 220 HIS J 310 ASN J 337 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN M 4 GLN ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN o 135 ASN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 63308 Z= 0.201 Angle : 0.669 21.335 86040 Z= 0.348 Chirality : 0.047 0.277 10054 Planarity : 0.004 0.072 10538 Dihedral : 9.127 177.628 9177 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.89 % Favored : 89.09 % Rotamer Outliers : 5.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -3.19 (0.09), residues: 7418 helix: -1.11 (0.11), residues: 2000 sheet: -1.50 (0.14), residues: 1302 loop : -2.96 (0.08), residues: 4116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1104 time to evaluate : 5.827 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 outliers start: 368 outliers final: 166 residues processed: 1340 average time/residue: 1.1507 time to fit residues: 2121.8826 Evaluate side-chains 1141 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 975 time to evaluate : 5.668 Switching outliers to nearest non-outliers outliers start: 166 outliers final: 121 residues processed: 48 average time/residue: 0.6256 time to fit residues: 58.2547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 599 optimal weight: 0.9990 chunk 408 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 536 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 614 optimal weight: 0.6980 chunk 497 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 367 optimal weight: 7.9990 chunk 646 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 87 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 310 ASN J 337 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN M 4 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 135 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN n 4 GLN ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN n 174 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 63308 Z= 0.303 Angle : 0.705 20.706 86040 Z= 0.366 Chirality : 0.048 0.268 10054 Planarity : 0.005 0.077 10538 Dihedral : 9.109 177.189 9177 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.31 % Favored : 88.68 % Rotamer Outliers : 5.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -3.10 (0.09), residues: 7418 helix: -1.05 (0.11), residues: 1983 sheet: -1.46 (0.14), residues: 1327 loop : -2.89 (0.09), residues: 4108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 999 time to evaluate : 5.710 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 outliers start: 396 outliers final: 212 residues processed: 1266 average time/residue: 1.1746 time to fit residues: 2042.9689 Evaluate side-chains 1123 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 911 time to evaluate : 5.702 Switching outliers to nearest non-outliers outliers start: 212 outliers final: 152 residues processed: 63 average time/residue: 0.6314 time to fit residues: 74.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 242 optimal weight: 7.9990 chunk 648 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 422 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 720 optimal weight: 10.0000 chunk 598 optimal weight: 9.9990 chunk 333 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 378 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 133 ASN F 178 ASN H 97 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 310 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 32 ASN ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 174 GLN m 101 ASN ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN n 119 ASN n 174 GLN ** o 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 150 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 63308 Z= 0.394 Angle : 0.742 19.962 86040 Z= 0.385 Chirality : 0.050 0.294 10054 Planarity : 0.005 0.086 10538 Dihedral : 9.206 176.807 9177 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.89 % Favored : 88.10 % Rotamer Outliers : 6.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -3.13 (0.09), residues: 7418 helix: -1.11 (0.11), residues: 1981 sheet: -1.40 (0.14), residues: 1347 loop : -2.93 (0.09), residues: 4090 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 426 poor density : 954 time to evaluate : 5.645 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 outliers start: 426 outliers final: 246 residues processed: 1249 average time/residue: 1.1491 time to fit residues: 1980.0517 Evaluate side-chains 1131 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 885 time to evaluate : 5.726 Switching outliers to nearest non-outliers outliers start: 246 outliers final: 179 residues processed: 69 average time/residue: 0.7014 time to fit residues: 85.8356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 694 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 410 optimal weight: 4.9990 chunk 526 optimal weight: 0.0170 chunk 407 optimal weight: 0.6980 chunk 606 optimal weight: 0.0980 chunk 402 optimal weight: 4.9990 chunk 718 optimal weight: 0.2980 chunk 449 optimal weight: 1.9990 chunk 437 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN E 77 ASN E 203 ASN F 133 ASN F 185 ASN H 97 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN I 64 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 310 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN O 101 ASN ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 119 ASN S 174 GLN ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN n 174 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 79 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 63308 Z= 0.181 Angle : 0.692 18.157 86040 Z= 0.355 Chirality : 0.047 0.277 10054 Planarity : 0.005 0.075 10538 Dihedral : 8.946 178.545 9177 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.16 % Favored : 89.82 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.09), residues: 7418 helix: -0.83 (0.12), residues: 1972 sheet: -1.14 (0.14), residues: 1347 loop : -2.80 (0.09), residues: 4099 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1073 time to evaluate : 5.698 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 outliers start: 326 outliers final: 175 residues processed: 1314 average time/residue: 1.1585 time to fit residues: 2114.5122 Evaluate side-chains 1123 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 948 time to evaluate : 6.631 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 147 residues processed: 29 average time/residue: 0.6048 time to fit residues: 39.1642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 444 optimal weight: 0.5980 chunk 286 optimal weight: 7.9990 chunk 428 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 141 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 456 optimal weight: 1.9990 chunk 489 optimal weight: 3.9990 chunk 355 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 564 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN H 97 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 310 ASN J 337 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 GLN ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN o 135 ASN o 150 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 63308 Z= 0.196 Angle : 0.692 17.145 86040 Z= 0.356 Chirality : 0.047 0.353 10054 Planarity : 0.005 0.094 10538 Dihedral : 8.774 178.226 9177 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.16 % Favored : 89.82 % Rotamer Outliers : 3.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.09), residues: 7418 helix: -0.74 (0.12), residues: 2003 sheet: -1.06 (0.14), residues: 1352 loop : -2.73 (0.09), residues: 4063 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1017 time to evaluate : 5.661 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 outliers start: 267 outliers final: 175 residues processed: 1221 average time/residue: 1.1516 time to fit residues: 1955.6483 Evaluate side-chains 1120 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 945 time to evaluate : 5.639 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 148 residues processed: 29 average time/residue: 0.6731 time to fit residues: 40.0752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 653 optimal weight: 4.9990 chunk 687 optimal weight: 20.0000 chunk 627 optimal weight: 8.9990 chunk 669 optimal weight: 7.9990 chunk 402 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 525 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 604 optimal weight: 3.9990 chunk 632 optimal weight: 0.0170 chunk 666 optimal weight: 4.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN F 133 ASN H 97 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 310 ASN J 337 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 79 GLN ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN o 150 GLN q 39 HIS ** r 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 63308 Z= 0.295 Angle : 0.726 18.038 86040 Z= 0.373 Chirality : 0.049 0.267 10054 Planarity : 0.005 0.097 10538 Dihedral : 8.789 177.259 9177 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.87 % Favored : 89.12 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.75 (0.09), residues: 7418 helix: -0.82 (0.12), residues: 2011 sheet: -1.11 (0.14), residues: 1349 loop : -2.70 (0.09), residues: 4058 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 960 time to evaluate : 5.701 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 outliers start: 259 outliers final: 187 residues processed: 1161 average time/residue: 1.1882 time to fit residues: 1906.6441 Evaluate side-chains 1106 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 919 time to evaluate : 5.646 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 159 residues processed: 31 average time/residue: 0.6587 time to fit residues: 41.8912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 439 optimal weight: 9.9990 chunk 707 optimal weight: 5.9990 chunk 431 optimal weight: 8.9990 chunk 335 optimal weight: 5.9990 chunk 491 optimal weight: 3.9990 chunk 742 optimal weight: 20.0000 chunk 683 optimal weight: 0.9990 chunk 591 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 456 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 ASN H 97 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 310 ASN J 337 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN o 150 GLN ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 63308 Z= 0.386 Angle : 0.777 17.202 86040 Z= 0.398 Chirality : 0.050 0.270 10054 Planarity : 0.005 0.109 10538 Dihedral : 8.945 176.750 9177 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.39 % Favored : 88.60 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.83 (0.09), residues: 7418 helix: -0.93 (0.11), residues: 1989 sheet: -1.13 (0.14), residues: 1404 loop : -2.75 (0.09), residues: 4025 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14836 Ramachandran restraints generated. 7418 Oldfield, 0 Emsley, 7418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 927 time to evaluate : 5.618 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 outliers start: 228 outliers final: 179 residues processed: 1121 average time/residue: 1.1736 time to fit residues: 1823.0965 Evaluate side-chains 1078 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 899 time to evaluate : 5.594 Switching outliers to nearest non-outliers outliers start: 179 outliers final: 160 residues processed: 23 average time/residue: 0.6494 time to fit residues: 33.4081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 469 optimal weight: 8.9990 chunk 629 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 544 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 591 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 607 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 310 ASN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 ASN ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN n 4 GLN ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN ** o 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.194966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133021 restraints weight = 91521.722| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.45 r_work: 0.3465 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 63308 Z= 0.203 Angle : 0.718 15.039 86040 Z= 0.367 Chirality : 0.047 0.320 10054 Planarity : 0.005 0.085 10538 Dihedral : 8.740 178.401 9177 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.16 % Favored : 89.82 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.65 (0.09), residues: 7418 helix: -0.74 (0.12), residues: 2015 sheet: -0.98 (0.14), residues: 1365 loop : -2.68 (0.09), residues: 4038 =============================================================================== Job complete usr+sys time: 28056.50 seconds wall clock time: 486 minutes 16.84 seconds (29176.84 seconds total)