Starting phenix.real_space_refine on Tue Mar 12 04:52:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/03_2024/6s91_10126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/03_2024/6s91_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_10126/03_2024/6s91_10126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/03_2024/6s91_10126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/03_2024/6s91_10126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s91_10126/03_2024/6s91_10126_updated.pdb" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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. 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-5265/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: 28.09, per 1000 atoms: 0.45 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: 18.73 Conformation dependent library (CDL) restraints added in 8.0 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: 20.28 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: 23.82 Time building geometry restraints manager: 20.65 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: 38065 35.34 - 70.68: 831 70.68 - 106.02: 89 106.02 - 141.35: 3 141.35 - 176.69: 4 Dihedral angle restraints: 38992 sinusoidal: 16876 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 38989 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 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: 6.460 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: 0.050 Extract box with map and model: 27.050 Check model and map are aligned: 0.700 Set scattering table: 0.420 Process input model: 151.510 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 15.520 176.692 24677 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 % Allowed : 7.40 % Favored : 92.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 281 HIS 0.008 0.001 HIS Q 29 PHE 0.029 0.002 PHE B 14 TYR 0.031 0.002 TYR x 7 ARG 0.011 0.001 ARG C 101 *********************** 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 : 5.327 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: J 105 LEU cc_start: 0.7713 (pp) cc_final: 0.7452 (pp) REVERT: J 264 ASP cc_start: 0.6414 (t70) cc_final: 0.6194 (t70) REVERT: K 494 ASP cc_start: 0.5236 (p0) cc_final: 0.4766 (m-30) REVERT: K 496 LYS cc_start: 0.8431 (tmmt) cc_final: 0.7804 (tptt) REVERT: K 734 MET cc_start: 0.5722 (mmp) cc_final: 0.5458 (ttt) REVERT: P 7 TYR cc_start: 0.7945 (t80) cc_final: 0.7701 (t80) REVERT: P 65 TYR cc_start: 0.8148 (p90) cc_final: 0.7861 (p90) REVERT: Q 14 ASN cc_start: 0.4651 (m110) cc_final: 0.4391 (m110) REVERT: S 34 ASP cc_start: 0.6689 (t70) cc_final: 0.6438 (t70) REVERT: S 39 HIS cc_start: 0.6990 (m-70) cc_final: 0.6759 (m90) REVERT: S 153 LYS cc_start: 0.4645 (tttt) cc_final: 0.4408 (tttt) REVERT: X 155 LYS cc_start: 0.6933 (mmtt) cc_final: 0.6713 (tppt) REVERT: m 20 VAL cc_start: 0.5417 (p) cc_final: 0.5149 (m) REVERT: p 52 LYS cc_start: 0.6145 (mptt) cc_final: 0.5899 (pptt) REVERT: q 99 LYS cc_start: 0.5986 (mmmt) cc_final: 0.4962 (mmmt) REVERT: w 154 VAL cc_start: 0.7578 (m) cc_final: 0.7311 (t) outliers start: 6 outliers final: 6 residues processed: 1519 average time/residue: 1.2905 time to fit residues: 2579.9140 Evaluate side-chains 1016 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1010 time to evaluate : 5.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain Q residue 135 ASN Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain n residue 69 ILE Chi-restraints excluded: chain r residue 95 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 629 optimal weight: 5.9990 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 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 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 195 ASN 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 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 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 r 14 ASN r 76 GLN r 79 GLN t 150 GLN w 40 ASN w 135 ASN x 4 GLN ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1689 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= 0.299 Angle : 0.744 18.102 86040 Z= 0.389 Chirality : 0.049 0.329 10054 Planarity : 0.005 0.073 10538 Dihedral : 12.201 177.619 9513 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 12.31 % Favored : 87.68 % Rotamer: Outliers : 3.90 % Allowed : 17.45 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.03 (0.08), residues: 7418 helix: -1.94 (0.10), residues: 2040 sheet: -1.97 (0.13), residues: 1241 loop : -3.43 (0.08), residues: 4137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 281 HIS 0.005 0.001 HIS Q 29 PHE 0.037 0.002 PHE B 14 TYR 0.039 0.002 TYR x 7 ARG 0.011 0.001 ARG L 118 *********************** 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 1415 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1149 time to evaluate : 5.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.5229 (t80) REVERT: D 178 ASN cc_start: 0.7551 (m110) cc_final: 0.7133 (t0) REVERT: G 150 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: H 113 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7195 (mmm160) REVERT: I 53 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7753 (pt) REVERT: J 105 LEU cc_start: 0.7657 (pp) cc_final: 0.7359 (pp) REVERT: K 583 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: K 734 MET cc_start: 0.5737 (mmp) cc_final: 0.5479 (ttt) REVERT: K 765 ILE cc_start: 0.7799 (mm) cc_final: 0.7586 (mm) REVERT: K 893 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6102 (pp-130) REVERT: K 1001 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: P 4 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7196 (mm-40) REVERT: P 87 LYS cc_start: 0.5233 (mtpt) cc_final: 0.4944 (mtpp) REVERT: P 156 ILE cc_start: 0.5715 (OUTLIER) cc_final: 0.5262 (tt) REVERT: Q 14 ASN cc_start: 0.4782 (m110) cc_final: 0.4548 (m110) REVERT: Q 112 TYR cc_start: 0.5303 (t80) cc_final: 0.4994 (t80) REVERT: S 34 ASP cc_start: 0.6526 (t70) cc_final: 0.6280 (t70) REVERT: S 39 HIS cc_start: 0.7120 (m-70) cc_final: 0.6878 (m90) REVERT: S 61 ASP cc_start: 0.7314 (m-30) cc_final: 0.6835 (m-30) REVERT: S 105 ASP cc_start: 0.4932 (t0) cc_final: 0.4005 (m-30) REVERT: S 153 LYS cc_start: 0.4502 (tttt) cc_final: 0.4186 (tttt) REVERT: X 110 ILE cc_start: 0.5755 (mp) cc_final: 0.5457 (mt) REVERT: X 155 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6773 (tppt) REVERT: m 20 VAL cc_start: 0.5255 (p) cc_final: 0.4888 (m) REVERT: m 36 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6920 (ttm170) REVERT: n 143 ASP cc_start: 0.5783 (OUTLIER) cc_final: 0.4681 (p0) REVERT: n 146 TYR cc_start: 0.4433 (m-80) cc_final: 0.3579 (m-80) REVERT: p 52 LYS cc_start: 0.6139 (mptt) cc_final: 0.5913 (pptt) REVERT: q 64 ASP cc_start: 0.5929 (m-30) cc_final: 0.5049 (m-30) REVERT: r 156 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7182 (mm) REVERT: w 154 VAL cc_start: 0.7655 (m) cc_final: 0.7443 (t) outliers start: 266 outliers final: 110 residues processed: 1288 average time/residue: 1.1546 time to fit residues: 2011.3702 Evaluate side-chains 1110 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 988 time to evaluate : 5.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain J residue 454 SER Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 504 MET Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 633 ARG Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 893 MET Chi-restraints excluded: chain K residue 1001 GLU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 118 ARG Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 14 ASN Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 61 ASP Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 163 ILE Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 119 ASN Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 53 ASN Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 61 ASP Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 74 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 134 VAL Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 106 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain x residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 375 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 563 optimal weight: 0.3980 chunk 460 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 677 optimal weight: 30.0000 chunk 732 optimal weight: 20.0000 chunk 603 optimal weight: 10.0000 chunk 672 optimal weight: 30.0000 chunk 231 optimal weight: 0.8980 chunk 543 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 203 ASN G 185 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN 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 285 ASN ** 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 ** 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 101 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** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN n 174 GLN p 135 ASN ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 63308 Z= 0.282 Angle : 0.710 18.326 86040 Z= 0.371 Chirality : 0.048 0.305 10054 Planarity : 0.005 0.082 10538 Dihedral : 11.825 177.842 9501 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.73 % Favored : 88.24 % Rotamer: Outliers : 5.05 % Allowed : 19.56 % Favored : 75.39 % 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: -3.57 (0.09), residues: 7418 helix: -1.51 (0.11), residues: 2018 sheet: -1.71 (0.13), residues: 1331 loop : -3.18 (0.08), residues: 4069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 770 HIS 0.007 0.001 HIS J 23 PHE 0.036 0.002 PHE H 229 TYR 0.038 0.002 TYR x 7 ARG 0.007 0.000 ARG J 117 *********************** 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 1440 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1096 time to evaluate : 5.490 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: A 79 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6404 (mtp180) REVERT: B 24 TYR cc_start: 0.4339 (OUTLIER) cc_final: 0.3857 (t80) REVERT: B 87 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.5329 (t80) REVERT: D 178 ASN cc_start: 0.7483 (m110) cc_final: 0.7156 (t0) REVERT: G 150 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: H 113 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7251 (mmm160) REVERT: I 53 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7661 (pt) REVERT: J 105 LEU cc_start: 0.7643 (pp) cc_final: 0.7295 (pp) REVERT: K 250 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8093 (mm) REVERT: K 583 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5777 (tm-30) REVERT: K 734 MET cc_start: 0.5690 (mmp) cc_final: 0.5406 (ttt) REVERT: K 1001 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: P 4 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7224 (mm-40) REVERT: P 156 ILE cc_start: 0.5737 (OUTLIER) cc_final: 0.5184 (tt) REVERT: S 34 ASP cc_start: 0.6511 (t70) cc_final: 0.6238 (t70) REVERT: S 105 ASP cc_start: 0.5007 (t0) cc_final: 0.4201 (m-30) REVERT: S 153 LYS cc_start: 0.4423 (tttt) cc_final: 0.4053 (tttt) REVERT: W 86 LEU cc_start: 0.6242 (tp) cc_final: 0.6013 (tp) REVERT: W 156 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7537 (tt) REVERT: m 20 VAL cc_start: 0.5177 (p) cc_final: 0.4782 (m) REVERT: n 143 ASP cc_start: 0.5910 (OUTLIER) cc_final: 0.4780 (p0) REVERT: n 146 TYR cc_start: 0.4219 (OUTLIER) cc_final: 0.3382 (m-80) REVERT: r 156 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7193 (mm) REVERT: s 124 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7015 (mmmt) REVERT: w 154 VAL cc_start: 0.7538 (m) cc_final: 0.7337 (t) outliers start: 344 outliers final: 155 residues processed: 1293 average time/residue: 1.1405 time to fit residues: 2002.9879 Evaluate side-chains 1135 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 964 time to evaluate : 5.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 588 GLU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 633 ARG Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 1001 GLU Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain K residue 1011 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 118 ARG Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 14 ASN Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 126 VAL Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 163 ILE Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 61 ASP Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 74 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain p residue 168 SER Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 64 ASP Chi-restraints excluded: chain s residue 124 LYS Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 110 ILE Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 16 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 669 optimal weight: 7.9990 chunk 509 optimal weight: 0.0870 chunk 351 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 680 optimal weight: 6.9990 chunk 720 optimal weight: 9.9990 chunk 355 optimal weight: 2.9990 chunk 644 optimal weight: 0.2980 chunk 194 optimal weight: 5.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- 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 77 ASN ** 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 46 ASN ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN J 220 HIS J 285 ASN 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 ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 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** ** 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** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 174 GLN n 4 GLN ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN q 40 ASN ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 63308 Z= 0.248 Angle : 0.690 22.055 86040 Z= 0.359 Chirality : 0.048 0.313 10054 Planarity : 0.005 0.079 10538 Dihedral : 11.609 177.623 9501 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.45 % Favored : 88.53 % Rotamer: Outliers : 5.66 % Allowed : 20.68 % Favored : 73.66 % 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: -3.29 (0.09), residues: 7418 helix: -1.24 (0.11), residues: 2012 sheet: -1.55 (0.14), residues: 1289 loop : -3.01 (0.08), residues: 4117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 411 HIS 0.004 0.001 HIS w 29 PHE 0.035 0.002 PHE H 229 TYR 0.031 0.002 TYR m 112 ARG 0.014 0.000 ARG L 118 *********************** 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 1481 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1095 time to evaluate : 5.914 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: A 79 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6392 (mtp180) REVERT: B 52 TYR cc_start: 0.6969 (t80) cc_final: 0.6079 (t80) REVERT: B 87 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.5321 (t80) REVERT: D 178 ASN cc_start: 0.7444 (m110) cc_final: 0.7162 (t0) REVERT: H 113 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7279 (mmm160) REVERT: I 53 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7613 (pt) REVERT: K 250 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8082 (mm) REVERT: K 583 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5825 (tm-30) REVERT: K 734 MET cc_start: 0.5733 (mmp) cc_final: 0.5427 (ttt) REVERT: K 893 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6475 (pp-130) REVERT: K 947 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7650 (ptpp) REVERT: O 109 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: P 4 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7145 (mm-40) REVERT: S 34 ASP cc_start: 0.6461 (t70) cc_final: 0.6198 (t70) REVERT: S 153 LYS cc_start: 0.4351 (tttt) cc_final: 0.3875 (tttt) REVERT: T 55 ARG cc_start: 0.4833 (mtt-85) cc_final: 0.4425 (mpp-170) REVERT: T 106 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5607 (tt) REVERT: W 156 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7519 (tt) REVERT: l 124 LYS cc_start: 0.8258 (ptmt) cc_final: 0.7892 (ptmt) REVERT: m 20 VAL cc_start: 0.4985 (p) cc_final: 0.4556 (m) REVERT: n 143 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.4629 (p0) REVERT: n 146 TYR cc_start: 0.4064 (OUTLIER) cc_final: 0.3325 (m-80) REVERT: q 99 LYS cc_start: 0.5961 (tptm) cc_final: 0.5252 (mmtt) REVERT: q 159 VAL cc_start: 0.2419 (OUTLIER) cc_final: 0.2205 (t) REVERT: r 156 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7211 (mm) REVERT: s 93 LEU cc_start: 0.6093 (pt) cc_final: 0.5689 (pp) REVERT: s 121 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6784 (mmt) REVERT: t 163 ILE cc_start: 0.7627 (mp) cc_final: 0.7405 (mm) REVERT: w 76 GLN cc_start: 0.3211 (OUTLIER) cc_final: 0.2062 (pt0) outliers start: 386 outliers final: 188 residues processed: 1333 average time/residue: 1.1120 time to fit residues: 2020.4961 Evaluate side-chains 1188 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 982 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 199 TYR Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 700 SER Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 893 MET Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 947 LYS Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain K residue 1011 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 118 ARG Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 14 ASN Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain l residue 136 ASN Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 106 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 162 ASP Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 18 ILE Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 112 TYR Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 61 ASP Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 74 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 114 SER Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 64 ASP Chi-restraints excluded: chain s residue 121 MET Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 76 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 599 optimal weight: 30.0000 chunk 408 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 536 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 614 optimal weight: 6.9990 chunk 497 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 chunk 646 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** B 28 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 133 ASN F 178 ASN H 97 GLN 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 J 337 ASN ** 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** M 4 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** T 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 63308 Z= 0.430 Angle : 0.761 20.591 86040 Z= 0.396 Chirality : 0.050 0.246 10054 Planarity : 0.005 0.087 10538 Dihedral : 11.655 176.513 9501 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.63 % Favored : 87.34 % Rotamer: Outliers : 6.33 % Allowed : 21.94 % Favored : 71.73 % 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: -3.33 (0.09), residues: 7418 helix: -1.31 (0.11), residues: 2007 sheet: -1.54 (0.14), residues: 1317 loop : -3.03 (0.08), residues: 4094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 281 HIS 0.007 0.001 HIS K 994 PHE 0.037 0.002 PHE H 229 TYR 0.031 0.002 TYR J 20 ARG 0.008 0.001 ARG E 262 *********************** 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 1425 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 431 poor density : 994 time to evaluate : 5.455 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: A 79 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.5803 (mtp180) REVERT: B 87 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.5411 (t80) REVERT: D 178 ASN cc_start: 0.7598 (m110) cc_final: 0.7179 (t0) REVERT: H 113 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7319 (mmm160) REVERT: I 53 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7732 (pt) REVERT: J 105 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7376 (pp) REVERT: K 250 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8101 (mm) REVERT: K 633 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5765 (mmm160) REVERT: K 734 MET cc_start: 0.5685 (mmp) cc_final: 0.5411 (ttt) REVERT: K 1001 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: O 109 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: P 4 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7237 (mm-40) REVERT: Q 112 TYR cc_start: 0.5203 (t80) cc_final: 0.4754 (t80) REVERT: S 34 ASP cc_start: 0.6596 (t70) cc_final: 0.6319 (t70) REVERT: S 153 LYS cc_start: 0.4397 (tttt) cc_final: 0.3931 (tttt) REVERT: W 156 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7542 (tt) REVERT: m 20 VAL cc_start: 0.5131 (p) cc_final: 0.4658 (m) REVERT: n 143 ASP cc_start: 0.5888 (OUTLIER) cc_final: 0.4811 (p0) REVERT: n 146 TYR cc_start: 0.4207 (OUTLIER) cc_final: 0.3508 (m-80) REVERT: o 19 ASP cc_start: 0.4449 (OUTLIER) cc_final: 0.4013 (p0) REVERT: p 119 ASN cc_start: 0.6612 (OUTLIER) cc_final: 0.6334 (m-40) REVERT: q 84 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6427 (pp) REVERT: q 99 LYS cc_start: 0.5892 (tptm) cc_final: 0.5258 (mmtt) REVERT: r 156 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7220 (mm) REVERT: s 93 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5612 (pp) REVERT: t 16 ILE cc_start: 0.5066 (OUTLIER) cc_final: 0.4440 (tp) REVERT: t 163 ILE cc_start: 0.7735 (mp) cc_final: 0.7466 (mm) REVERT: w 8 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.7156 (t) REVERT: w 76 GLN cc_start: 0.3435 (OUTLIER) cc_final: 0.2228 (pt0) REVERT: w 160 LYS cc_start: 0.7974 (ptpp) cc_final: 0.7661 (mppt) outliers start: 431 outliers final: 232 residues processed: 1268 average time/residue: 1.1101 time to fit residues: 1920.4356 Evaluate side-chains 1181 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 928 time to evaluate : 5.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 18 CYS Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain J residue 20 TYR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 337 ASN Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain J residue 454 SER Chi-restraints excluded: chain J residue 461 ILE Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 633 ARG Chi-restraints excluded: chain K residue 700 SER Chi-restraints excluded: chain K residue 773 SER Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 1001 GLU Chi-restraints excluded: chain K residue 1004 TYR Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain K residue 1011 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 118 ARG Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 GLU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 130 ASP Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 172 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 126 VAL Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain l residue 166 LEU Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 136 ASN Chi-restraints excluded: chain m residue 141 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 18 ILE Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 112 TYR Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 19 ASP Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 61 ASP Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 74 THR Chi-restraints excluded: chain o residue 149 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 84 LEU Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 114 SER Chi-restraints excluded: chain q residue 121 MET Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 141 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 64 ASP Chi-restraints excluded: chain s residue 74 THR Chi-restraints excluded: chain s residue 93 LEU Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 28 ASP Chi-restraints excluded: chain t residue 45 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 66 VAL Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 170 TYR Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 76 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 132 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 242 optimal weight: 3.9990 chunk 648 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 422 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 720 optimal weight: 8.9990 chunk 598 optimal weight: 9.9990 chunk 333 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 238 optimal weight: 0.8980 chunk 378 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 185 ASN ** 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 J 337 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 101 ASN ** 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 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** l 174 GLN m 101 ASN ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 63308 Z= 0.289 Angle : 0.711 19.837 86040 Z= 0.369 Chirality : 0.048 0.251 10054 Planarity : 0.005 0.086 10538 Dihedral : 11.562 177.290 9501 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.50 % Favored : 88.49 % Rotamer: Outliers : 5.78 % Allowed : 23.55 % Favored : 70.66 % 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: -3.16 (0.09), residues: 7418 helix: -1.11 (0.11), residues: 1992 sheet: -1.43 (0.13), residues: 1391 loop : -2.97 (0.09), residues: 4035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 411 HIS 0.008 0.001 HIS K 994 PHE 0.037 0.002 PHE B 14 TYR 0.027 0.002 TYR J 20 ARG 0.016 0.000 ARG L 118 *********************** 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 1398 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 394 poor density : 1004 time to evaluate : 5.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5842 (mtp180) REVERT: B 87 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.5633 (t80) REVERT: D 178 ASN cc_start: 0.7504 (m110) cc_final: 0.7234 (t0) REVERT: H 113 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7298 (mmm160) REVERT: I 53 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7662 (pt) REVERT: K 104 ILE cc_start: 0.8419 (mp) cc_final: 0.8202 (mp) REVERT: K 205 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8475 (mm) REVERT: K 250 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8041 (mm) REVERT: K 734 MET cc_start: 0.5735 (mmp) cc_final: 0.5459 (ttt) REVERT: K 893 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6443 (pp-130) REVERT: N 36 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6657 (mtm-85) REVERT: O 109 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: P 4 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7125 (mm-40) REVERT: P 16 ILE cc_start: 0.3187 (pp) cc_final: 0.2772 (pp) REVERT: Q 112 TYR cc_start: 0.5416 (t80) cc_final: 0.4941 (t80) REVERT: S 34 ASP cc_start: 0.6518 (t70) cc_final: 0.6242 (t70) REVERT: S 153 LYS cc_start: 0.4282 (tttt) cc_final: 0.3794 (tttt) REVERT: T 55 ARG cc_start: 0.4886 (mtt-85) cc_final: 0.4421 (mtm-85) REVERT: W 156 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7552 (tt) REVERT: X 139 LYS cc_start: 0.5627 (mmtt) cc_final: 0.5280 (tmmm) REVERT: l 27 SER cc_start: 0.6319 (m) cc_final: 0.5736 (m) REVERT: n 143 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.4559 (p0) REVERT: n 146 TYR cc_start: 0.3982 (OUTLIER) cc_final: 0.3390 (m-80) REVERT: o 19 ASP cc_start: 0.4218 (OUTLIER) cc_final: 0.3850 (p0) REVERT: o 99 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6853 (tttm) REVERT: q 64 ASP cc_start: 0.6156 (m-30) cc_final: 0.5845 (p0) REVERT: q 99 LYS cc_start: 0.5898 (tptm) cc_final: 0.5170 (mmpt) REVERT: r 156 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7208 (mm) REVERT: s 121 MET cc_start: 0.7005 (mmt) cc_final: 0.6750 (mmt) REVERT: s 124 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7406 (mtmt) REVERT: t 16 ILE cc_start: 0.5029 (OUTLIER) cc_final: 0.4423 (tp) REVERT: w 76 GLN cc_start: 0.3160 (OUTLIER) cc_final: 0.2139 (pt0) outliers start: 394 outliers final: 226 residues processed: 1271 average time/residue: 1.1262 time to fit residues: 1955.7015 Evaluate side-chains 1166 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 921 time to evaluate : 5.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 14 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain J residue 20 TYR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 199 TYR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 337 ASN Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 205 ILE Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 270 ARG Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 700 SER Chi-restraints excluded: chain K residue 773 SER Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 893 MET Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 1004 TYR Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain K residue 1011 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 118 ARG Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 14 ASN Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 131 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain l residue 166 LEU Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 55 ARG Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 136 ASN Chi-restraints excluded: chain m residue 141 VAL Chi-restraints excluded: chain m residue 163 ILE Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 18 ILE Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 112 TYR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 19 ASP Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 61 ASP Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 74 THR Chi-restraints excluded: chain o residue 99 LYS Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain p residue 168 SER Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 114 SER Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 141 VAL Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 64 ASP Chi-restraints excluded: chain s residue 74 THR Chi-restraints excluded: chain s residue 124 LYS Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 45 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 134 VAL Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 66 VAL Chi-restraints excluded: chain w residue 76 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 694 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 410 optimal weight: 5.9990 chunk 526 optimal weight: 0.0000 chunk 407 optimal weight: 4.9990 chunk 606 optimal weight: 0.9990 chunk 402 optimal weight: 0.3980 chunk 718 optimal weight: 4.9990 chunk 449 optimal weight: 20.0000 chunk 437 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 133 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 285 ASN J 310 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 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN ** 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 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 174 GLN m 101 ASN n 4 GLN ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN o 150 GLN ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 79 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3080 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= 0.219 Angle : 0.694 19.788 86040 Z= 0.358 Chirality : 0.048 0.386 10054 Planarity : 0.005 0.085 10538 Dihedral : 11.405 177.507 9501 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.05 % Favored : 88.92 % Rotamer: Outliers : 5.21 % Allowed : 24.71 % Favored : 70.08 % 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: -2.94 (0.09), residues: 7418 helix: -0.88 (0.12), residues: 1973 sheet: -1.26 (0.14), residues: 1386 loop : -2.87 (0.09), residues: 4059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 411 HIS 0.008 0.001 HIS K 994 PHE 0.034 0.001 PHE B 14 TYR 0.029 0.002 TYR t 109 ARG 0.017 0.000 ARG B 31 *********************** 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 1386 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1031 time to evaluate : 5.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5843 (mtp180) REVERT: B 87 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5577 (t80) REVERT: D 178 ASN cc_start: 0.7412 (m110) cc_final: 0.7147 (t0) REVERT: H 113 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7258 (mmm160) REVERT: I 53 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7598 (pt) REVERT: K 104 ILE cc_start: 0.8382 (mp) cc_final: 0.8150 (mp) REVERT: K 250 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8001 (mm) REVERT: K 734 MET cc_start: 0.5750 (mmp) cc_final: 0.5443 (ttt) REVERT: K 1001 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: L 160 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6863 (pptt) REVERT: N 36 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6720 (mtm-85) REVERT: O 109 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: P 4 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7039 (mm-40) REVERT: P 65 TYR cc_start: 0.8158 (p90) cc_final: 0.7735 (p90) REVERT: Q 112 TYR cc_start: 0.5065 (t80) cc_final: 0.4836 (t80) REVERT: S 34 ASP cc_start: 0.6344 (t70) cc_final: 0.6105 (t70) REVERT: W 156 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7536 (tt) REVERT: m 134 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7824 (p) REVERT: n 143 ASP cc_start: 0.5584 (OUTLIER) cc_final: 0.4484 (p0) REVERT: n 146 TYR cc_start: 0.3951 (OUTLIER) cc_final: 0.3196 (m-80) REVERT: o 19 ASP cc_start: 0.4013 (OUTLIER) cc_final: 0.3363 (p0) REVERT: o 55 ARG cc_start: 0.6354 (mmp-170) cc_final: 0.6038 (mpp80) REVERT: o 99 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6779 (tttm) REVERT: q 56 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.5090 (mm) REVERT: q 64 ASP cc_start: 0.6076 (m-30) cc_final: 0.5828 (p0) REVERT: q 99 LYS cc_start: 0.5880 (tptm) cc_final: 0.5178 (mmtt) REVERT: q 114 SER cc_start: 0.6556 (OUTLIER) cc_final: 0.6259 (m) REVERT: r 151 LYS cc_start: 0.4715 (OUTLIER) cc_final: 0.4245 (pmtt) REVERT: r 156 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7179 (mm) REVERT: s 63 CYS cc_start: 0.7640 (m) cc_final: 0.7248 (m) REVERT: s 93 LEU cc_start: 0.5903 (pt) cc_final: 0.5494 (pp) REVERT: s 106 LEU cc_start: 0.5310 (mp) cc_final: 0.5107 (mt) REVERT: s 121 MET cc_start: 0.6898 (mmt) cc_final: 0.6667 (mmt) REVERT: t 10 ILE cc_start: 0.7443 (tp) cc_final: 0.7094 (tp) REVERT: t 16 ILE cc_start: 0.5099 (OUTLIER) cc_final: 0.4567 (tp) REVERT: w 76 GLN cc_start: 0.3001 (OUTLIER) cc_final: 0.1992 (pt0) REVERT: w 160 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7488 (mppt) outliers start: 355 outliers final: 188 residues processed: 1276 average time/residue: 1.1212 time to fit residues: 1956.9134 Evaluate side-chains 1157 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 947 time to evaluate : 5.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 14 PHE Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 266 ARG Chi-restraints excluded: chain J residue 20 TYR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 700 SER Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 1001 GLU Chi-restraints excluded: chain K residue 1004 TYR Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain K residue 1011 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 118 ARG Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 131 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain l residue 166 LEU Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 106 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 134 VAL Chi-restraints excluded: chain m residue 136 ASN Chi-restraints excluded: chain m residue 141 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 112 TYR Chi-restraints excluded: chain n residue 123 THR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 19 ASP Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 61 ASP Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 74 THR Chi-restraints excluded: chain o residue 99 LYS Chi-restraints excluded: chain o residue 119 ASN Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 114 SER Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 151 LYS Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 56 LEU Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 45 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 66 VAL Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 134 VAL Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 66 VAL Chi-restraints excluded: chain w residue 76 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 444 optimal weight: 0.0470 chunk 286 optimal weight: 3.9990 chunk 428 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 456 optimal weight: 8.9990 chunk 489 optimal weight: 8.9990 chunk 355 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 564 optimal weight: 6.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- 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** 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 ** K 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN N 4 GLN ** N 29 HIS ** 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 ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** T 76 GLN ** 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 ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 63308 Z= 0.212 Angle : 0.702 19.169 86040 Z= 0.360 Chirality : 0.047 0.235 10054 Planarity : 0.005 0.087 10538 Dihedral : 11.254 177.920 9501 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.47 % Favored : 89.51 % Rotamer: Outliers : 4.36 % Allowed : 26.39 % Favored : 69.25 % 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: -2.79 (0.09), residues: 7418 helix: -0.78 (0.12), residues: 1996 sheet: -1.11 (0.14), residues: 1393 loop : -2.79 (0.09), residues: 4029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP K 411 HIS 0.007 0.001 HIS K 994 PHE 0.033 0.001 PHE H 229 TYR 0.035 0.001 TYR B 96 ARG 0.013 0.000 ARG L 118 *********************** 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 1329 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1032 time to evaluate : 5.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.5843 (mtp180) REVERT: B 27 LYS cc_start: 0.4060 (tmtt) cc_final: 0.3822 (tptt) REVERT: B 87 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.5531 (t80) REVERT: H 113 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7281 (mmm160) REVERT: K 104 ILE cc_start: 0.8462 (mp) cc_final: 0.8262 (mp) REVERT: K 250 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7992 (mm) REVERT: K 734 MET cc_start: 0.5715 (mmp) cc_final: 0.5393 (ttt) REVERT: K 1001 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: L 160 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6875 (pptt) REVERT: O 109 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: P 4 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7040 (mm-40) REVERT: P 156 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5223 (tt) REVERT: S 34 ASP cc_start: 0.6319 (t70) cc_final: 0.6082 (t70) REVERT: W 156 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7556 (tt) REVERT: l 44 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7891 (mm) REVERT: n 60 LEU cc_start: 0.8051 (mp) cc_final: 0.7804 (pt) REVERT: n 143 ASP cc_start: 0.5577 (OUTLIER) cc_final: 0.4463 (p0) REVERT: n 146 TYR cc_start: 0.4011 (OUTLIER) cc_final: 0.3217 (m-80) REVERT: n 169 TYR cc_start: 0.6365 (p90) cc_final: 0.5974 (p90) REVERT: o 55 ARG cc_start: 0.6377 (mmp-170) cc_final: 0.6059 (mpp80) REVERT: o 99 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6811 (tttm) REVERT: r 151 LYS cc_start: 0.4617 (OUTLIER) cc_final: 0.4312 (pmtt) REVERT: r 156 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7195 (mm) REVERT: s 63 CYS cc_start: 0.7532 (m) cc_final: 0.7136 (m) REVERT: s 93 LEU cc_start: 0.5959 (pt) cc_final: 0.5545 (pp) REVERT: s 106 LEU cc_start: 0.5236 (mp) cc_final: 0.5003 (mt) REVERT: s 124 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7494 (mmmt) REVERT: t 10 ILE cc_start: 0.7482 (tp) cc_final: 0.6638 (tp) REVERT: t 16 ILE cc_start: 0.4978 (OUTLIER) cc_final: 0.4445 (tp) REVERT: t 167 PHE cc_start: 0.5939 (m-80) cc_final: 0.5620 (m-10) REVERT: w 76 GLN cc_start: 0.2957 (OUTLIER) cc_final: 0.1941 (pt0) outliers start: 297 outliers final: 179 residues processed: 1237 average time/residue: 1.1246 time to fit residues: 1904.6639 Evaluate side-chains 1132 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 934 time to evaluate : 5.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 14 PHE Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain J residue 20 TYR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 700 SER Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 1001 GLU Chi-restraints excluded: chain K residue 1004 TYR Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 131 ASP Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 130 ASP Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 44 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain l residue 166 LEU Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 136 ASN Chi-restraints excluded: chain m residue 141 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 99 LYS Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 12 ILE Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 151 LYS Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 64 ASP Chi-restraints excluded: chain s residue 74 THR Chi-restraints excluded: chain s residue 124 LYS Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 45 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 66 VAL Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 134 VAL Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 66 VAL Chi-restraints excluded: chain w residue 76 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 84 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 653 optimal weight: 5.9990 chunk 687 optimal weight: 20.0000 chunk 627 optimal weight: 4.9990 chunk 669 optimal weight: 0.0170 chunk 402 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 525 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 604 optimal weight: 3.9990 chunk 632 optimal weight: 8.9990 chunk 666 optimal weight: 4.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN O 40 ASN ** 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** 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 ** o 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 135 ASN o 150 GLN ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3366 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= 0.297 Angle : 0.734 19.884 86040 Z= 0.376 Chirality : 0.049 0.307 10054 Planarity : 0.005 0.094 10538 Dihedral : 11.262 178.230 9501 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.00 % Favored : 88.99 % Rotamer: Outliers : 4.29 % Allowed : 27.18 % Favored : 68.54 % 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: -2.79 (0.09), residues: 7418 helix: -0.81 (0.12), residues: 1995 sheet: -1.13 (0.14), residues: 1418 loop : -2.78 (0.09), residues: 4005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 281 HIS 0.008 0.001 HIS J 23 PHE 0.042 0.002 PHE r 9 TYR 0.051 0.002 TYR I 271 ARG 0.011 0.000 ARG B 31 *********************** 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 1253 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 961 time to evaluate : 5.429 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: A 79 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.5848 (mtp180) REVERT: B 87 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.5736 (t80) REVERT: C 5 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6750 (pt0) REVERT: G 150 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: H 113 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7331 (mmm160) REVERT: K 104 ILE cc_start: 0.8433 (mp) cc_final: 0.8203 (mp) REVERT: K 250 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7996 (mm) REVERT: K 734 MET cc_start: 0.5893 (mmp) cc_final: 0.5552 (ttt) REVERT: K 1001 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: L 53 ASN cc_start: 0.7182 (p0) cc_final: 0.6924 (m110) REVERT: O 55 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6657 (mmm160) REVERT: O 109 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: P 4 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.6890 (mm-40) REVERT: P 156 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5177 (tt) REVERT: S 34 ASP cc_start: 0.6329 (t70) cc_final: 0.6099 (t70) REVERT: W 156 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7560 (tt) REVERT: X 155 LYS cc_start: 0.5454 (tppt) cc_final: 0.4734 (mtmt) REVERT: l 44 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7886 (mm) REVERT: n 60 LEU cc_start: 0.8057 (mp) cc_final: 0.7840 (pt) REVERT: n 143 ASP cc_start: 0.5612 (OUTLIER) cc_final: 0.4510 (p0) REVERT: n 146 TYR cc_start: 0.3946 (OUTLIER) cc_final: 0.3431 (m-80) REVERT: n 169 TYR cc_start: 0.6248 (p90) cc_final: 0.5897 (p90) REVERT: n 170 TYR cc_start: 0.7952 (m-80) cc_final: 0.7562 (m-10) REVERT: o 55 ARG cc_start: 0.6503 (mmp-170) cc_final: 0.6069 (mpp80) REVERT: o 85 THR cc_start: 0.6344 (p) cc_final: 0.6117 (p) REVERT: o 99 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6836 (tttm) REVERT: r 156 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7214 (mm) REVERT: s 63 CYS cc_start: 0.7623 (m) cc_final: 0.7272 (m) REVERT: s 106 LEU cc_start: 0.5303 (mp) cc_final: 0.5076 (mt) REVERT: s 124 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7496 (mtmt) REVERT: t 10 ILE cc_start: 0.7527 (tp) cc_final: 0.6643 (tp) REVERT: t 16 ILE cc_start: 0.5059 (OUTLIER) cc_final: 0.4496 (tp) REVERT: t 167 PHE cc_start: 0.5906 (m-80) cc_final: 0.5652 (m-10) REVERT: w 76 GLN cc_start: 0.2800 (OUTLIER) cc_final: 0.1820 (pt0) REVERT: w 160 LYS cc_start: 0.7618 (mttp) cc_final: 0.7296 (mppt) outliers start: 292 outliers final: 199 residues processed: 1171 average time/residue: 1.1499 time to fit residues: 1862.7725 Evaluate side-chains 1146 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 927 time to evaluate : 5.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 14 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 271 TYR Chi-restraints excluded: chain J residue 20 TYR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 372 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 597 MET Chi-restraints excluded: chain K residue 700 SER Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 887 ILE Chi-restraints excluded: chain K residue 1001 GLU Chi-restraints excluded: chain K residue 1004 TYR Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 131 ASP Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 130 ASP Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 44 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain l residue 166 LEU Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 55 ARG Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 136 ASN Chi-restraints excluded: chain m residue 141 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 18 ILE Chi-restraints excluded: chain n residue 112 TYR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 99 LYS Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain p residue 168 SER Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 12 ILE Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 69 ILE Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 64 ASP Chi-restraints excluded: chain s residue 74 THR Chi-restraints excluded: chain s residue 124 LYS Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 45 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 66 VAL Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 134 VAL Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 66 VAL Chi-restraints excluded: chain w residue 76 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 95 LEU 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: 0.9990 chunk 431 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 491 optimal weight: 9.9990 chunk 742 optimal weight: 20.0000 chunk 683 optimal weight: 5.9990 chunk 591 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 456 optimal weight: 5.9990 chunk 362 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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** H 97 GLN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN H 279 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 ** K 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN O 101 ASN ** 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** 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 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 135 ASN o 150 GLN ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 63308 Z= 0.359 Angle : 0.763 19.734 86040 Z= 0.391 Chirality : 0.050 0.271 10054 Planarity : 0.005 0.099 10538 Dihedral : 11.338 177.545 9501 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.59 % Favored : 88.39 % Rotamer: Outliers : 3.95 % Allowed : 27.80 % Favored : 68.26 % 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: -2.86 (0.09), residues: 7418 helix: -0.92 (0.11), residues: 1999 sheet: -1.15 (0.14), residues: 1408 loop : -2.79 (0.09), residues: 4011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 281 HIS 0.007 0.001 HIS K 994 PHE 0.037 0.002 PHE H 229 TYR 0.039 0.002 TYR Q 112 ARG 0.015 0.001 ARG P 5 ********************** 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 1210 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 941 time to evaluate : 5.333 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: A 79 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.5837 (mtp180) REVERT: B 87 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.5824 (t80) REVERT: C 5 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6776 (pt0) REVERT: G 150 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: H 113 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7380 (mmm160) REVERT: J 105 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7444 (pp) REVERT: K 104 ILE cc_start: 0.8463 (mp) cc_final: 0.8225 (mp) REVERT: K 250 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8023 (mm) REVERT: K 734 MET cc_start: 0.5945 (mmp) cc_final: 0.5605 (ttt) REVERT: K 1001 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: O 55 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6717 (mmm160) REVERT: O 109 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: P 156 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5165 (tt) REVERT: S 34 ASP cc_start: 0.6338 (t70) cc_final: 0.6104 (t70) REVERT: S 166 LEU cc_start: 0.6768 (tt) cc_final: 0.6534 (tt) REVERT: W 156 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7607 (tt) REVERT: X 155 LYS cc_start: 0.5451 (tppt) cc_final: 0.4885 (mtmt) REVERT: l 44 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7912 (mm) REVERT: n 60 LEU cc_start: 0.8068 (mp) cc_final: 0.7864 (pt) REVERT: n 143 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.4571 (p0) REVERT: n 146 TYR cc_start: 0.4013 (OUTLIER) cc_final: 0.3470 (m-80) REVERT: n 169 TYR cc_start: 0.6262 (p90) cc_final: 0.5921 (p90) REVERT: n 170 TYR cc_start: 0.7935 (m-80) cc_final: 0.7527 (m-10) REVERT: o 55 ARG cc_start: 0.6397 (mmp-170) cc_final: 0.5983 (mpp80) REVERT: o 99 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6893 (tttm) REVERT: q 122 LYS cc_start: 0.6418 (mmtt) cc_final: 0.6099 (mmmt) REVERT: r 156 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7160 (mm) REVERT: s 124 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7504 (mtmt) REVERT: t 10 ILE cc_start: 0.7523 (tp) cc_final: 0.6683 (tp) REVERT: t 16 ILE cc_start: 0.5101 (OUTLIER) cc_final: 0.4552 (tp) REVERT: t 167 PHE cc_start: 0.5923 (m-80) cc_final: 0.5646 (m-10) REVERT: w 76 GLN cc_start: 0.2863 (OUTLIER) cc_final: 0.1868 (pt0) REVERT: w 160 LYS cc_start: 0.7642 (mttp) cc_final: 0.7291 (mppt) outliers start: 269 outliers final: 201 residues processed: 1135 average time/residue: 1.1152 time to fit residues: 1743.6947 Evaluate side-chains 1121 residues out of total 6814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 900 time to evaluate : 5.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain B residue 14 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 ASP Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 227 ASP Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 183 ARG Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 246 ASP Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain J residue 20 TYR Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 453 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 597 MET Chi-restraints excluded: chain K residue 700 SER Chi-restraints excluded: chain K residue 733 VAL Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 820 SER Chi-restraints excluded: chain K residue 1001 GLU Chi-restraints excluded: chain K residue 1004 TYR Chi-restraints excluded: chain K residue 1009 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 161 GLU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 131 ASP Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 130 ASP Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 44 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain m residue 141 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 18 ILE Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain n residue 112 TYR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 143 ASP Chi-restraints excluded: chain n residue 146 TYR Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 64 ASP Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain o residue 99 LYS Chi-restraints excluded: chain o residue 150 GLN Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 156 ILE Chi-restraints excluded: chain p residue 168 SER Chi-restraints excluded: chain q residue 32 ASN Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 94 TYR Chi-restraints excluded: chain q residue 99 LYS Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain q residue 159 VAL Chi-restraints excluded: chain r residue 12 ILE Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 156 ILE Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 64 ASP Chi-restraints excluded: chain s residue 74 THR Chi-restraints excluded: chain s residue 124 LYS Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 16 ILE Chi-restraints excluded: chain t residue 45 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 59 THR Chi-restraints excluded: chain t residue 66 VAL Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 130 ASP Chi-restraints excluded: chain t residue 134 VAL Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 172 LEU Chi-restraints excluded: chain w residue 17 THR Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 66 VAL Chi-restraints excluded: chain w residue 76 GLN Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 126 VAL Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 745 random chunks: chunk 469 optimal weight: 20.0000 chunk 629 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 544 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 591 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 607 optimal weight: 0.0170 chunk 74 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3024 ------------------------------------------------------------------------------- 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 148 GLN K 834 ASN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN O 101 ASN ** 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** 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 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 135 ASN ** r 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.192997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.131131 restraints weight = 91421.332| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.29 r_work: 0.3436 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 63308 Z= 0.236 Angle : 0.731 18.854 86040 Z= 0.374 Chirality : 0.048 0.271 10054 Planarity : 0.005 0.080 10538 Dihedral : 11.293 178.178 9501 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.72 % Favored : 89.27 % Rotamer: Outliers : 3.57 % Allowed : 28.19 % Favored : 68.24 % 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: -2.78 (0.09), residues: 7418 helix: -0.81 (0.12), residues: 1997 sheet: -1.09 (0.14), residues: 1396 loop : -2.77 (0.09), residues: 4025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 411 HIS 0.008 0.001 HIS K 994 PHE 0.040 0.002 PHE r 9 TYR 0.050 0.002 TYR B 96 ARG 0.019 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27582.08 seconds wall clock time: 478 minutes 24.39 seconds (28704.39 seconds total)