Starting phenix.real_space_refine on Fri Mar 1 19:59:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssl_25409/03_2024/7ssl_25409_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssl_25409/03_2024/7ssl_25409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssl_25409/03_2024/7ssl_25409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssl_25409/03_2024/7ssl_25409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssl_25409/03_2024/7ssl_25409_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssl_25409/03_2024/7ssl_25409_updated.pdb" } resolution = 3.8 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= 0.116 sd= 0.863 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: 5 Type Number sf(0) Gaussians P 4733 5.49 5 S 178 5.16 5 C 77732 2.51 5 N 28483 2.21 5 O 42222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "8 GLU 58": "OE1" <-> "OE2" Residue "8 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 80": "OE1" <-> "OE2" Residue "8 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 176": "OE1" <-> "OE2" Residue "8 GLU 177": "OE1" <-> "OE2" Residue "8 PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 184": "OD1" <-> "OD2" Residue "8 ASP 197": "OD1" <-> "OD2" Residue "8 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 205": "OE1" <-> "OE2" Residue "8 ASP 210": "OD1" <-> "OD2" Residue "8 GLU 224": "OE1" <-> "OE2" Residue "8 TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 300": "OD1" <-> "OD2" Residue "8 ASP 304": "OD1" <-> "OD2" Residue "8 ASP 313": "OD1" <-> "OD2" Residue "8 PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 347": "OD1" <-> "OD2" Residue "8 ARG 359": "NH1" <-> "NH2" Residue "8 PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 362": "NH1" <-> "NH2" Residue "8 GLU 376": "OE1" <-> "OE2" Residue "8 ASP 381": "OD1" <-> "OD2" Residue "8 ASP 390": "OD1" <-> "OD2" Residue "8 ASP 395": "OD1" <-> "OD2" Residue "8 GLU 410": "OE1" <-> "OE2" Residue "8 GLU 413": "OE1" <-> "OE2" Residue "8 GLU 463": "OE1" <-> "OE2" Residue "8 ASP 471": "OD1" <-> "OD2" Residue "8 GLU 480": "OE1" <-> "OE2" Residue "8 ASP 500": "OD1" <-> "OD2" Residue "8 TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 535": "OE1" <-> "OE2" Residue "8 GLU 548": "OE1" <-> "OE2" Residue "8 ASP 554": "OD1" <-> "OD2" Residue "8 ASP 587": "OD1" <-> "OD2" Residue "8 ASP 630": "OD1" <-> "OD2" Residue "8 GLU 662": "OE1" <-> "OE2" Residue "8 TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 34": "OE1" <-> "OE2" Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 113": "OD1" <-> "OD2" Residue "b TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 179": "OE1" <-> "OE2" Residue "b PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "c ASP 200": "OD1" <-> "OD2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 144": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e GLU 31": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ASP 112": "OD1" <-> "OD2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f GLU 166": "OE1" <-> "OE2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g GLU 127": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 95": "OD1" <-> "OD2" Residue "i GLU 122": "OE1" <-> "OE2" Residue "i GLU 140": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 73": "OD1" <-> "OD2" Residue "k PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 80": "OD1" <-> "OD2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "l GLU 10": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ASP 81": "OD1" <-> "OD2" Residue "l GLU 86": "OE1" <-> "OE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ASP 25": "OD1" <-> "OD2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 55": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ASP 89": "OD1" <-> "OD2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 67": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 46": "OE1" <-> "OE2" Residue "r ASP 55": "OD1" <-> "OD2" Residue "r GLU 62": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s ASP 68": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 42": "OE1" <-> "OE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t ASP 79": "OD1" <-> "OD2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 8": "OD1" <-> "OD2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v GLU 41": "OE1" <-> "OE2" Residue "w ASP 11": "OD1" <-> "OD2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 66": "OE1" <-> "OE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ASP 39": "OD1" <-> "OD2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z GLU 57": "OE1" <-> "OE2" Residue "z GLU 58": "OE1" <-> "OE2" Residue "A ASP 31": "OD1" <-> "OD2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "K ASP 13": "OD1" <-> "OD2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 67": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 19": "OE1" <-> "OE2" Residue "X PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153348 Number of models: 1 Model: "" Number of chains: 59 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 100, 'rna2p_pyr': 58, 'rna3p_pur': 774, 'rna3p_pyr': 607} Link IDs: {'rna2p': 158, 'rna3p': 1380} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 233, 'rna2p_pyr': 113, 'rna3p_pur': 1441, 'rna3p_pyr': 1116} Link IDs: {'rna2p': 346, 'rna3p': 2556} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 60, 'rna3p_pyr': 52} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 30, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "8" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5400 Classifications: {'peptide': 697} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 663} Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "a" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "i" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 355 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 413 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "8" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 58.45, per 1000 atoms: 0.38 Number of scatterers: 153348 At special positions: 0 Unit cell: (268.808, 249.784, 242.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 178 16.00 P 4733 15.00 O 42222 8.00 N 28483 7.00 C 77732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 14 " distance=2.02 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 Atom "ATOM 78553 O4' G 12121 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 58.96 Conformation dependent library (CDL) restraints added in 7.0 seconds 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12174 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 187 helices and 75 sheets defined 36.0% alpha, 15.7% beta 978 base pairs and 2505 stacking pairs defined. Time for finding SS restraints: 75.36 Creating SS restraints... Processing helix chain '8' and resid 22 through 35 removed outlier: 4.201A pdb=" N THR 8 26 " --> pdb=" O GLY 8 22 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR 8 27 " --> pdb=" O LYS 8 23 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE 8 30 " --> pdb=" O THR 8 26 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU 8 31 " --> pdb=" O THR 8 27 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY 8 35 " --> pdb=" O LEU 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 106 removed outlier: 3.811A pdb=" N VAL 8 99 " --> pdb=" O PHE 8 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET 8 103 " --> pdb=" O VAL 8 99 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG 8 104 " --> pdb=" O GLU 8 100 " (cutoff:3.500A) Processing helix chain '8' and resid 120 through 134 removed outlier: 4.136A pdb=" N GLU 8 124 " --> pdb=" O GLN 8 120 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL 8 126 " --> pdb=" O GLN 8 122 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 8 128 " --> pdb=" O GLU 8 124 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN 8 129 " --> pdb=" O THR 8 125 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA 8 130 " --> pdb=" O VAL 8 126 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN 8 131 " --> pdb=" O TRP 8 127 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR 8 133 " --> pdb=" O GLN 8 129 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 161 removed outlier: 3.621A pdb=" N VAL 8 154 " --> pdb=" O ASN 8 150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS 8 159 " --> pdb=" O VAL 8 155 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR 8 160 " --> pdb=" O ASN 8 156 " (cutoff:3.500A) Processing helix chain '8' and resid 211 through 231 removed outlier: 3.669A pdb=" N ALA 8 215 " --> pdb=" O MET 8 211 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN 8 216 " --> pdb=" O VAL 8 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN 8 220 " --> pdb=" O ASN 8 216 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN 8 221 " --> pdb=" O GLU 8 217 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER 8 225 " --> pdb=" O ASN 8 221 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA 8 226 " --> pdb=" O LEU 8 222 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA 8 227 " --> pdb=" O ILE 8 223 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU 8 228 " --> pdb=" O GLU 8 224 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA 8 229 " --> pdb=" O SER 8 225 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU 8 231 " --> pdb=" O ALA 8 227 " (cutoff:3.500A) Processing helix chain '8' and resid 232 through 240 removed outlier: 4.538A pdb=" N LYS 8 236 " --> pdb=" O GLU 8 232 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU 8 238 " --> pdb=" O MET 8 234 " (cutoff:3.500A) Processing helix chain '8' and resid 244 through 259 removed outlier: 3.686A pdb=" N ILE 8 248 " --> pdb=" O THR 8 244 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS 8 249 " --> pdb=" O GLU 8 245 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY 8 250 " --> pdb=" O ALA 8 246 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA 8 251 " --> pdb=" O GLU 8 247 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN 8 254 " --> pdb=" O GLY 8 250 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL 8 256 " --> pdb=" O LEU 8 252 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU 8 257 " --> pdb=" O ARG 8 253 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN 8 258 " --> pdb=" O GLN 8 254 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN 8 259 " --> pdb=" O ARG 8 255 " (cutoff:3.500A) Processing helix chain '8' and resid 274 through 285 removed outlier: 3.897A pdb=" N LEU 8 279 " --> pdb=" O VAL 8 275 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP 8 280 " --> pdb=" O GLN 8 276 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA 8 281 " --> pdb=" O ALA 8 277 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL 8 282 " --> pdb=" O MET 8 278 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE 8 283 " --> pdb=" O LEU 8 279 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP 8 284 " --> pdb=" O ASP 8 280 " (cutoff:3.500A) Processing helix chain '8' and resid 288 through 293 Proline residue: 8 293 - end of helix Processing helix chain '8' and resid 424 through 443 removed outlier: 3.757A pdb=" N GLN 8 428 " --> pdb=" O THR 8 424 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU 8 429 " --> pdb=" O LYS 8 425 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS 8 430 " --> pdb=" O ALA 8 426 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU 8 433 " --> pdb=" O GLU 8 429 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA 8 434 " --> pdb=" O LYS 8 430 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU 8 435 " --> pdb=" O MET 8 431 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY 8 436 " --> pdb=" O GLY 8 432 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG 8 437 " --> pdb=" O LEU 8 433 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU 8 438 " --> pdb=" O ALA 8 434 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS 8 440 " --> pdb=" O GLY 8 436 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU 8 441 " --> pdb=" O ARG 8 437 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP 8 442 " --> pdb=" O LEU 8 438 " (cutoff:3.500A) Proline residue: 8 443 - end of helix Processing helix chain '8' and resid 462 through 476 removed outlier: 3.695A pdb=" N ILE 8 468 " --> pdb=" O LEU 8 464 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL 8 470 " --> pdb=" O LEU 8 466 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG 8 475 " --> pdb=" O ASP 8 471 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU 8 476 " --> pdb=" O ARG 8 472 " (cutoff:3.500A) Processing helix chain '8' and resid 546 through 564 removed outlier: 3.697A pdb=" N ILE 8 550 " --> pdb=" O PRO 8 546 " (cutoff:3.500A) Proline residue: 8 551 - end of helix removed outlier: 3.573A pdb=" N ASP 8 554 " --> pdb=" O ILE 8 550 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE 8 557 " --> pdb=" O VAL 8 553 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN 8 560 " --> pdb=" O GLY 8 556 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS 8 562 " --> pdb=" O GLN 8 558 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA 8 563 " --> pdb=" O GLU 8 559 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY 8 564 " --> pdb=" O GLN 8 560 " (cutoff:3.500A) Processing helix chain '8' and resid 589 through 609 removed outlier: 4.116A pdb=" N ILE 8 599 " --> pdb=" O LEU 8 595 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA 8 600 " --> pdb=" O ALA 8 596 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE 8 601 " --> pdb=" O ALA 8 597 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS 8 602 " --> pdb=" O SER 8 598 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE 8 605 " --> pdb=" O PHE 8 601 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS 8 606 " --> pdb=" O LYS 8 602 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS 8 607 " --> pdb=" O GLU 8 603 " (cutoff:3.500A) Processing helix chain '8' and resid 627 through 639 removed outlier: 3.952A pdb=" N VAL 8 631 " --> pdb=" O ASN 8 627 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG 8 638 " --> pdb=" O ASP 8 634 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG 8 639 " --> pdb=" O LEU 8 635 " (cutoff:3.500A) Processing helix chain '8' and resid 659 through 664 removed outlier: 4.868A pdb=" N PHE 8 664 " --> pdb=" O LEU 8 660 " (cutoff:3.500A) Processing helix chain '8' and resid 665 through 675 removed outlier: 3.509A pdb=" N LYS 8 675 " --> pdb=" O ARG 8 671 " (cutoff:3.500A) Processing helix chain '8' and resid 693 through 698 Processing helix chain 'b' and resid 9 through 15 removed outlier: 5.655A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 removed outlier: 3.793A pdb=" N ILE b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) Proline residue: b 135 - end of helix No H-bonds generated for 'chain 'b' and resid 130 through 135' Processing helix chain 'b' and resid 206 through 214 removed outlier: 3.848A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.714A pdb=" N LYS c 70 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 97 through 104 removed outlier: 4.253A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA c 102 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 removed outlier: 3.905A pdb=" N PHE d 19 " --> pdb=" O SER d 15 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY d 20 " --> pdb=" O GLU d 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 15 through 20' Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.753A pdb=" N HIS d 29 " --> pdb=" O GLU d 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL d 33 " --> pdb=" O HIS d 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY d 38 " --> pdb=" O ALA d 34 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA d 39 " --> pdb=" O TYR d 35 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.882A pdb=" N GLY d 103 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER d 107 " --> pdb=" O GLY d 103 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU d 109 " --> pdb=" O LEU d 105 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER d 110 " --> pdb=" O LYS d 106 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU d 112 " --> pdb=" O ILE d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.608A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN d 136 " --> pdb=" O LYS d 132 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS d 137 " --> pdb=" O LEU d 133 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA d 142 " --> pdb=" O LEU d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 162 removed outlier: 4.150A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 3.843A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.912A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU d 197 " --> pdb=" O VAL d 193 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 10 removed outlier: 3.952A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS e 8 " --> pdb=" O HIS e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 20 removed outlier: 4.882A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 60 removed outlier: 4.880A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP e 50 " --> pdb=" O LYS e 46 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA e 58 " --> pdb=" O ALA e 54 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.026A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU e 100 " --> pdb=" O TRP e 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU e 102 " --> pdb=" O PHE e 98 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 133 through 138 removed outlier: 4.787A pdb=" N PHE e 137 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Proline residue: e 138 - end of helix No H-bonds generated for 'chain 'e' and resid 133 through 138' Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.632A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA e 170 " --> pdb=" O ARG e 166 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 7 Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 78 removed outlier: 3.971A pdb=" N ALA f 67 " --> pdb=" O GLN f 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN f 72 " --> pdb=" O ARG f 68 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.669A pdb=" N GLY f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL f 143 " --> pdb=" O VAL f 139 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU f 147 " --> pdb=" O VAL f 143 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 4.215A pdb=" N ASN g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.841A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU g 48 " --> pdb=" O ILE g 44 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 72 removed outlier: 5.333A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU g 70 " --> pdb=" O ASN g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 106 removed outlier: 3.818A pdb=" N ALA g 100 " --> pdb=" O THR g 96 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP g 101 " --> pdb=" O ARG g 97 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL g 103 " --> pdb=" O ILE g 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 15 removed outlier: 4.419A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG a 12 " --> pdb=" O MET a 8 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 27 removed outlier: 3.517A pdb=" N ALA a 26 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 22 through 27' Processing helix chain 'a' and resid 182 through 200 removed outlier: 3.675A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA a 199 " --> pdb=" O ALA a 195 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 30 Proline residue: i 25 - end of helix removed outlier: 5.859A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 49 removed outlier: 3.881A pdb=" N PHE i 37 " --> pdb=" O ASN i 33 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE i 41 " --> pdb=" O PHE i 37 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN i 42 " --> pdb=" O CYS i 38 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU i 49 " --> pdb=" O THR i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.854A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY i 84 " --> pdb=" O LYS i 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 116 removed outlier: 3.784A pdb=" N LEU i 105 " --> pdb=" O SER i 101 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP i 115 " --> pdb=" O THR i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 122 through 136 removed outlier: 4.496A pdb=" N ARG i 126 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA i 132 " --> pdb=" O ILE i 128 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER i 134 " --> pdb=" O GLY i 130 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET i 135 " --> pdb=" O THR i 131 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.574A pdb=" N THR j 30 " --> pdb=" O GLY j 26 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG j 35 " --> pdb=" O GLU j 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.684A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY j 107 " --> pdb=" O ILE j 103 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.673A pdb=" N ALA j 117 " --> pdb=" O PRO j 113 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 119 removed outlier: 4.463A pdb=" N SER k 117 " --> pdb=" O MET k 113 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU k 118 " --> pdb=" O LYS k 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 removed outlier: 4.083A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 75 removed outlier: 3.562A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 78 through 83 removed outlier: 4.642A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 94 through 99 removed outlier: 4.262A pdb=" N ALA l 98 " --> pdb=" O THR l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.684A pdb=" N ALA l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.714A pdb=" N ILE m 46 " --> pdb=" O THR m 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR m 54 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.729A pdb=" N ALA m 113 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.591A pdb=" N ALA n 19 " --> pdb=" O SER n 15 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER n 27 " --> pdb=" O ASN n 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL n 29 " --> pdb=" O ALA n 25 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS n 31 " --> pdb=" O SER n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 58 removed outlier: 3.661A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.898A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 70 removed outlier: 4.088A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 4.501A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.724A pdb=" N ALA o 6 " --> pdb=" O ASP o 2 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA o 11 " --> pdb=" O ARG o 7 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 3.936A pdb=" N ALA o 59 " --> pdb=" O GLU o 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU o 60 " --> pdb=" O LYS o 56 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 55 through 63' Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.653A pdb=" N ALA o 71 " --> pdb=" O ASN o 67 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA o 73 " --> pdb=" O ASP o 69 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL o 74 " --> pdb=" O ALA o 70 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY o 75 " --> pdb=" O ALA o 71 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS o 76 " --> pdb=" O ALA o 72 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.569A pdb=" N GLU o 112 " --> pdb=" O ASP o 108 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 12 removed outlier: 3.676A pdb=" N LYS p 5 " --> pdb=" O SER p 1 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU p 8 " --> pdb=" O ILE p 4 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN p 9 " --> pdb=" O LYS p 5 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 98 through 103 removed outlier: 3.694A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 98 through 103' Processing helix chain 'q' and resid 5 through 21 removed outlier: 3.665A pdb=" N ARG q 10 " --> pdb=" O GLY q 6 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.454A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 72 removed outlier: 3.976A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE q 61 " --> pdb=" O ARG q 57 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA q 62 " --> pdb=" O GLN q 58 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG q 69 " --> pdb=" O ASN q 65 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN q 70 " --> pdb=" O ALA q 66 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN q 71 " --> pdb=" O ALA q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 4.062A pdb=" N PHE q 78 " --> pdb=" O SER q 74 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE q 79 " --> pdb=" O TYR q 75 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN q 80 " --> pdb=" O SER q 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS q 84 " --> pdb=" O ASN q 80 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA q 85 " --> pdb=" O GLY q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.782A pdb=" N ALA q 95 " --> pdb=" O ARG q 91 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL q 99 " --> pdb=" O ALA q 95 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP q 101 " --> pdb=" O ILE q 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.912A pdb=" N ALA q 107 " --> pdb=" O VAL q 103 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU q 108 " --> pdb=" O ALA q 104 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL q 109 " --> pdb=" O PHE q 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA q 114 " --> pdb=" O GLU q 110 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU q 116 " --> pdb=" O ALA q 112 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 22 removed outlier: 3.600A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 4.205A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR s 39 " --> pdb=" O ILE s 35 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 4.421A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU s 52 " --> pdb=" O LYS s 48 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER s 53 " --> pdb=" O LYS s 49 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE s 55 " --> pdb=" O LEU s 51 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN s 61 " --> pdb=" O ASN s 57 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 12 removed outlier: 4.319A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG t 12 " --> pdb=" O LEU t 8 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 removed outlier: 3.698A pdb=" N THR t 22 " --> pdb=" O GLU t 18 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS t 26 " --> pdb=" O THR t 22 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 50 removed outlier: 3.525A pdb=" N ILE t 43 " --> pdb=" O THR t 39 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.529A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 65 through 70' Processing helix chain 'v' and resid 13 through 24 removed outlier: 3.683A pdb=" N SER v 17 " --> pdb=" O GLY v 13 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU v 20 " --> pdb=" O ALA v 16 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 52 removed outlier: 4.115A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET v 48 " --> pdb=" O HIS v 44 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET v 50 " --> pdb=" O LYS v 46 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 4.875A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL x 57 " --> pdb=" O LYS x 53 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS x 61 " --> pdb=" O VAL x 57 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 removed outlier: 3.613A pdb=" N LEU x 67 " --> pdb=" O ILE x 63 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 7 removed outlier: 4.454A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 2 through 7' Processing helix chain 'y' and resid 9 through 22 removed outlier: 3.514A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU y 19 " --> pdb=" O ASN y 15 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 35 removed outlier: 4.637A pdb=" N LEU y 28 " --> pdb=" O GLU y 24 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN y 31 " --> pdb=" O ASN y 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA y 32 " --> pdb=" O LEU y 28 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 4.377A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN y 45 " --> pdb=" O HIS y 41 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR y 55 " --> pdb=" O ALA y 51 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 16 removed outlier: 5.958A pdb=" N ARG z 15 " --> pdb=" O SER z 11 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU z 16 " --> pdb=" O ALA z 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 11 through 16' Processing helix chain 'z' and resid 17 through 27 removed outlier: 3.729A pdb=" N LEU z 23 " --> pdb=" O HIS z 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY z 25 " --> pdb=" O ALA z 21 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 51 Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.582A pdb=" N ARG B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Proline residue: C 30 - end of helix No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'D' and resid 8 through 16 removed outlier: 4.476A pdb=" N ARG D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 24 through 38 removed outlier: 4.488A pdb=" N VAL D 30 " --> pdb=" O ASN D 26 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.556A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 5.309A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.038A pdb=" N LEU E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 26 through 31 removed outlier: 3.566A pdb=" N ILE G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 26 through 31' Processing helix chain 'G' and resid 41 through 63 removed outlier: 4.097A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.896A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.592A pdb=" N ALA G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 121 removed outlier: 5.402A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 110 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 129 removed outlier: 6.519A pdb=" N LYS G 127 " --> pdb=" O GLY G 123 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 123 through 129' Processing helix chain 'G' and resid 130 through 148 removed outlier: 3.996A pdb=" N LEU G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.181A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS G 169 " --> pdb=" O ALA G 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 164 through 169' Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.656A pdb=" N ASN G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 4.560A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU G 222 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.758A pdb=" N ILE H 9 " --> pdb=" O HIS H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 46 removed outlier: 4.523A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP H 35 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU H 45 " --> pdb=" O TYR H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.792A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.792A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.516A pdb=" N VAL H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 4.441A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.876A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.555A pdb=" N GLN I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS I 59 " --> pdb=" O ARG I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 5.903A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 6.350A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 removed outlier: 3.786A pdb=" N VAL I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.785A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 3.736A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 5.505A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 204 removed outlier: 4.566A pdb=" N VAL I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER I 204 " --> pdb=" O VAL I 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 196 through 204' Processing helix chain 'J' and resid 54 through 70 removed outlier: 4.126A pdb=" N ALA J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 7.255A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 3.909A pdb=" N VAL J 135 " --> pdb=" O ASN J 131 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN J 145 " --> pdb=" O ASP J 141 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.197A pdb=" N ARG J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 4.048A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 3.825A pdb=" N VAL K 18 " --> pdb=" O GLN K 14 " (cutoff:3.500A) Proline residue: K 19 - end of helix removed outlier: 3.929A pdb=" N GLU K 23 " --> pdb=" O PRO K 19 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.600A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 31 removed outlier: 3.888A pdb=" N ALA L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL L 31 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.614A pdb=" N ALA L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN L 51 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 4.147A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG L 69 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 3.667A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L 98 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG L 108 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.540A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA L 126 " --> pdb=" O GLU L 122 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA L 127 " --> pdb=" O LEU L 123 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.920A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU L 138 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 4.279A pdb=" N ARG M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN M 15 " --> pdb=" O THR M 11 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY M 16 " --> pdb=" O ARG M 12 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN M 17 " --> pdb=" O ILE M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.718A pdb=" N VAL M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA M 34 " --> pdb=" O LYS M 30 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.506A pdb=" N GLY M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 49 removed outlier: 4.489A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.615A pdb=" N ILE N 78 " --> pdb=" O GLN N 74 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE N 82 " --> pdb=" O ILE N 78 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG N 84 " --> pdb=" O HIS N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 101 removed outlier: 4.993A pdb=" N SER N 95 " --> pdb=" O GLU N 91 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 33 removed outlier: 3.569A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 87 removed outlier: 3.877A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.381A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 45 through 50' Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.970A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 59 through 75 removed outlier: 3.781A pdb=" N GLN P 63 " --> pdb=" O PRO P 59 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL P 64 " --> pdb=" O PHE P 60 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 103 removed outlier: 4.462A pdb=" N SER P 94 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN P 100 " --> pdb=" O ILE P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 removed outlier: 4.259A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.882A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.662A pdb=" N LEU R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 37 removed outlier: 3.952A pdb=" N LYS R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 4.902A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 60 removed outlier: 3.539A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.579A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU R 71 " --> pdb=" O ASP R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.933A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG R 91 " --> pdb=" O GLY R 87 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY R 93 " --> pdb=" O ARG R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 removed outlier: 3.551A pdb=" N LYS R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 20 removed outlier: 3.569A pdb=" N GLU S 9 " --> pdb=" O MET S 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 28 removed outlier: 5.132A pdb=" N LYS S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 removed outlier: 4.266A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 79 through 90 removed outlier: 4.572A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 14 removed outlier: 3.711A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 24 removed outlier: 5.046A pdb=" N GLY T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER T 23 " --> pdb=" O ASN T 19 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR T 24 " --> pdb=" O ASP T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 43 removed outlier: 3.883A pdb=" N ALA T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 4.829A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU T 55 " --> pdb=" O SER T 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU T 56 " --> pdb=" O ARG T 52 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG T 57 " --> pdb=" O ARG T 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET T 58 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP T 67 " --> pdb=" O ARG T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 84 removed outlier: 4.188A pdb=" N LEU T 80 " --> pdb=" O ARG T 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.739A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.580A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 17 removed outlier: 5.691A pdb=" N GLU W 15 " --> pdb=" O ARG W 11 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL W 17 " --> pdb=" O THR W 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 11 through 17' Processing helix chain 'W' and resid 24 through 32 removed outlier: 3.573A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.528A pdb=" N GLY W 45 " --> pdb=" O SER W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 65 removed outlier: 3.721A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG W 60 " --> pdb=" O ARG W 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 24 removed outlier: 4.140A pdb=" N VAL X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL X 22 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.648A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) Proline residue: X 75 - end of helix Processing helix chain 'Y' and resid 14 through 41 removed outlier: 4.035A pdb=" N ARG Y 23 " --> pdb=" O HIS Y 19 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG Y 28 " --> pdb=" O ARG Y 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA Y 37 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE Y 38 " --> pdb=" O VAL Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 removed outlier: 3.552A pdb=" N LYS Y 48 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.908A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA Y 62 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 5.311A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Y 75 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN Y 81 " --> pdb=" O ASN Y 77 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA Y 86 " --> pdb=" O ILE Y 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 21 removed outlier: 5.003A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER Z 21 " --> pdb=" O ARG Z 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 16 through 21' Processing helix chain 'Z' and resid 25 through 31 removed outlier: 4.063A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 4.361A pdb=" N ARG Z 46 " --> pdb=" O THR Z 42 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA Z 51 " --> pdb=" O ALA Z 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG Z 54 " --> pdb=" O SER Z 50 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG Z 61 " --> pdb=" O LYS Z 57 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '8' and resid 65 through 73 removed outlier: 4.160A pdb=" N TRP 8 72 " --> pdb=" O HIS 8 82 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY 8 108 " --> pdb=" O ASN 8 12 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY 8 14 " --> pdb=" O GLY 8 108 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU 8 263 " --> pdb=" O ARG 8 137 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '8' and resid 181 through 185 removed outlier: 4.138A pdb=" N VAL 8 182 " --> pdb=" O ILE 8 191 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE 8 191 " --> pdb=" O VAL 8 182 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU 8 203 " --> pdb=" O ASN 8 192 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '8' and resid 295 through 298 removed outlier: 4.694A pdb=" N ILE 8 295 " --> pdb=" O ARG 8 309 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY 8 297 " --> pdb=" O ALA 8 307 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '8' and resid 317 through 321 removed outlier: 7.913A pdb=" N PHE 8 317 " --> pdb=" O CYS 8 398 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N CYS 8 398 " --> pdb=" O PHE 8 317 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA 8 319 " --> pdb=" O THR 8 396 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR 8 396 " --> pdb=" O ALA 8 319 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA 8 321 " --> pdb=" O GLY 8 394 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '8' and resid 323 through 327 removed outlier: 4.549A pdb=" N LYS 8 323 " --> pdb=" O PHE 8 335 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '8' and resid 348 through 352 removed outlier: 3.623A pdb=" N GLU 8 358 " --> pdb=" O VAL 8 349 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN 8 351 " --> pdb=" O ALA 8 356 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA 8 356 " --> pdb=" O ASN 8 351 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '8' and resid 363 through 366 removed outlier: 4.047A pdb=" N ILE 8 363 " --> pdb=" O ILE 8 374 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '8' and resid 445 through 449 removed outlier: 4.380A pdb=" N ILE 8 457 " --> pdb=" O TRP 8 448 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR 8 456 " --> pdb=" O VAL 8 420 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA 8 419 " --> pdb=" O GLY 8 484 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLU 8 480 " --> pdb=" O LYS 8 423 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '8' and resid 491 through 494 removed outlier: 4.149A pdb=" N ARG 8 491 " --> pdb=" O LEU 8 613 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY 8 651 " --> pdb=" O GLU 8 648 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '8' and resid 502 through 506 removed outlier: 3.610A pdb=" N GLY 8 503 " --> pdb=" O VAL 8 518 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL 8 518 " --> pdb=" O GLY 8 503 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL 8 519 " --> pdb=" O HIS 8 579 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY 8 575 " --> pdb=" O TYR 8 523 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU 8 535 " --> pdb=" O MET 8 574 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 8 576 " --> pdb=" O GLU 8 535 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE 8 537 " --> pdb=" O ILE 8 576 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU 8 578 " --> pdb=" O ILE 8 537 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '8' and resid 617 through 623 removed outlier: 3.520A pdb=" N GLU 8 620 " --> pdb=" O THR 8 681 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR 8 681 " --> pdb=" O GLU 8 620 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU 8 622 " --> pdb=" O SER 8 679 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER 8 679 " --> pdb=" O GLU 8 622 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '8' and resid 612 through 615 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'b' and resid 1 through 4 removed outlier: 4.253A pdb=" N VAL b 19 " --> pdb=" O ALA b 1 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL b 3 " --> pdb=" O LYS b 17 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'b' and resid 32 through 35 removed outlier: 7.383A pdb=" N LEU b 32 " --> pdb=" O ILE b 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE b 63 " --> pdb=" O LEU b 32 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'b' and resid 74 through 77 removed outlier: 4.719A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'b' and resid 79 through 82 removed outlier: 3.709A pdb=" N ARG b 79 " --> pdb=" O LEU b 92 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'b' and resid 169 through 175 removed outlier: 8.627A pdb=" N ALA b 169 " --> pdb=" O ALA b 185 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG b 181 " --> pdb=" O LEU b 173 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'c' and resid 3 through 7 removed outlier: 6.866A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE c 202 " --> pdb=" O THR c 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY c 111 " --> pdb=" O VAL c 170 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL c 170 " --> pdb=" O GLY c 111 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'c' and resid 11 through 15 removed outlier: 3.539A pdb=" N ILE c 27 " --> pdb=" O LEU c 187 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU c 186 " --> pdb=" O ASP c 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'c' and resid 32 through 35 removed outlier: 6.709A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR c 45 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU c 40 " --> pdb=" O TYR c 45 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN c 36 " --> pdb=" O GLN c 49 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'c' and resid 46 through 49 removed outlier: 5.255A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'c' and resid 105 through 108 removed outlier: 6.496A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'd' and resid 1 through 6 removed outlier: 4.778A pdb=" N SER d 10 " --> pdb=" O LEU d 5 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.942A pdb=" N VAL d 186 " --> pdb=" O ARG d 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE d 119 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR d 150 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'e' and resid 32 through 38 removed outlier: 3.539A pdb=" N ILE e 33 " --> pdb=" O LEU e 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU e 90 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET e 37 " --> pdb=" O CYS e 86 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS e 86 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'e' and resid 126 through 130 removed outlier: 3.851A pdb=" N ILE e 153 " --> pdb=" O MET e 129 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'f' and resid 14 through 18 removed outlier: 3.621A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE f 23 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE f 25 " --> pdb=" O LEU f 32 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY f 30 " --> pdb=" O GLY f 27 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 29, first strand: chain 'f' and resid 81 through 88 Processing sheet with id= 30, first strand: chain 'g' and resid 76 through 82 removed outlier: 6.307A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL g 78 " --> pdb=" O ILE g 143 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN g 145 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE g 80 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL g 142 " --> pdb=" O VAL g 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS g 128 " --> pdb=" O VAL g 144 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY g 126 " --> pdb=" O VAL g 146 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'a' and resid 169 through 173 removed outlier: 7.779A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN a 47 " --> pdb=" O LYS a 211 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'i' and resid 7 through 12 removed outlier: 3.937A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL i 56 " --> pdb=" O LEU i 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL i 12 " --> pdb=" O ILE i 54 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE i 54 " --> pdb=" O VAL i 12 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'j' and resid 15 through 18 Processing sheet with id= 34, first strand: chain 'j' and resid 74 through 78 removed outlier: 4.049A pdb=" N ALA j 87 " --> pdb=" O TYR j 74 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS j 85 " --> pdb=" O HIS j 76 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'k' and resid 8 through 11 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'k' and resid 19 through 22 removed outlier: 4.182A pdb=" N MET k 20 " --> pdb=" O THR k 42 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'm' and resid 63 through 66 removed outlier: 7.483A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY m 32 " --> pdb=" O VAL m 131 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL m 131 " --> pdb=" O GLY m 32 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS m 34 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR m 129 " --> pdb=" O LYS m 34 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'o' and resid 49 through 53 removed outlier: 4.320A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR o 36 " --> pdb=" O HIS o 29 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'p' and resid 25 through 29 removed outlier: 3.755A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'p' and resid 44 through 47 removed outlier: 4.931A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA p 57 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'p' and resid 57 through 63 removed outlier: 3.598A pdb=" N PHE p 58 " --> pdb=" O PHE p 73 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'r' and resid 11 through 15 Processing sheet with id= 43, first strand: chain 'r' and resid 32 through 36 removed outlier: 3.656A pdb=" N ALA r 61 " --> pdb=" O VAL r 33 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE r 35 " --> pdb=" O ILE r 59 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR r 83 " --> pdb=" O PHE r 77 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE r 77 " --> pdb=" O TYR r 83 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS r 85 " --> pdb=" O VAL r 75 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL r 75 " --> pdb=" O LYS r 85 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN r 87 " --> pdb=" O LYS r 73 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS r 73 " --> pdb=" O GLN r 87 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA r 65 " --> pdb=" O ASP r 95 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 's' and resid 2 through 8 Processing sheet with id= 45, first strand: chain 't' and resid 29 through 34 removed outlier: 4.105A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG t 77 " --> pdb=" O LYS t 66 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'u' and resid 8 through 12 removed outlier: 4.810A pdb=" N ASP u 8 " --> pdb=" O VAL u 24 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL u 24 " --> pdb=" O ASP u 8 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL u 12 " --> pdb=" O LYS u 20 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS u 20 " --> pdb=" O VAL u 12 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'u' and resid 41 through 44 removed outlier: 3.620A pdb=" N LYS u 60 " --> pdb=" O VAL u 41 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL u 58 " --> pdb=" O LYS u 43 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'v' and resid 6 through 9 removed outlier: 3.598A pdb=" N ARG v 9 " --> pdb=" O ALA v 39 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALA v 39 " --> pdb=" O ARG v 9 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE v 40 " --> pdb=" O ALA v 28 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'v' and resid 61 through 64 Processing sheet with id= 50, first strand: chain 'w' and resid 47 through 50 removed outlier: 6.203A pdb=" N GLY w 48 " --> pdb=" O LEU w 55 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU w 55 " --> pdb=" O GLY w 48 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLY w 50 " --> pdb=" O HIS w 53 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'w' and resid 63 through 68 removed outlier: 3.970A pdb=" N LYS w 68 " --> pdb=" O ARG w 73 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG w 73 " --> pdb=" O LYS w 68 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.704A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'z' and resid 32 through 38 removed outlier: 4.576A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR z 7 " --> pdb=" O LYS z 55 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'A' and resid 11 through 15 Processing sheet with id= 55, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.714A pdb=" N LEU C 10 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'G' and resid 66 through 70 removed outlier: 4.198A pdb=" N LEU G 160 " --> pdb=" O PRO G 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 162 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE G 197 " --> pdb=" O VAL G 182 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'H' and resid 52 through 58 removed outlier: 3.696A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'H' and resid 147 through 154 removed outlier: 3.658A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.712A pdb=" N ILE I 144 " --> pdb=" O MET I 177 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N MET I 177 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP I 173 " --> pdb=" O GLU I 178 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU I 171 " --> pdb=" O THR I 180 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'J' and resid 21 through 24 removed outlier: 3.810A pdb=" N LYS J 22 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'J' and resid 82 through 86 removed outlier: 8.438A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL J 84 " --> pdb=" O MET J 95 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'J' and resid 102 through 106 removed outlier: 4.877A pdb=" N VAL J 122 " --> pdb=" O GLY J 103 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE J 105 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA J 124 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'K' and resid 43 through 46 removed outlier: 3.780A pdb=" N GLY K 43 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET K 62 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL K 64 " --> pdb=" O TYR K 4 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR K 92 " --> pdb=" O HIS K 3 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'L' and resid 71 through 76 removed outlier: 6.669A pdb=" N THR L 71 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL L 90 " --> pdb=" O THR L 71 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'M' and resid 23 through 26 removed outlier: 3.757A pdb=" N VAL M 24 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU M 57 " --> pdb=" O GLU M 51 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU M 59 " --> pdb=" O LYS M 49 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'M' and resid 74 through 77 removed outlier: 3.614A pdb=" N TYR M 127 " --> pdb=" O GLN M 75 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE M 125 " --> pdb=" O VAL M 77 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'N' and resid 6 through 10 removed outlier: 3.792A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL N 18 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'O' and resid 6 through 13 removed outlier: 3.741A pdb=" N ILE O 6 " --> pdb=" O ILE O 76 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P' and resid 41 through 44 removed outlier: 3.829A pdb=" N GLU P 82 " --> pdb=" O GLY P 18 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 28 through 32 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'Q' and resid 50 through 56 removed outlier: 4.542A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Q 56 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.552A pdb=" N ARG U 51 " --> pdb=" O PHE U 38 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'V' and resid 6 through 10 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'V' and resid 19 through 29 removed outlier: 3.546A pdb=" N VAL V 22 " --> pdb=" O LEU V 43 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR V 41 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG V 39 " --> pdb=" O ARG V 26 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL V 28 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE V 37 " --> pdb=" O VAL V 28 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'X' and resid 29 through 33 removed outlier: 3.907A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR X 32 " --> pdb=" O ALA X 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS X 51 " --> pdb=" O THR X 32 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL X 61 " --> pdb=" O LEU X 46 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2351 hydrogen bonds 3838 hydrogen bond angles 0 basepair planarities 978 basepair parallelities 2505 stacking parallelities Total time for adding SS restraints: 198.82 Time building geometry restraints manager: 64.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 31045 1.34 - 1.47: 69806 1.47 - 1.59: 55802 1.59 - 1.72: 9285 1.72 - 1.84: 320 Bond restraints: 166258 Sorted by residual: bond pdb=" O3' C 12064 " pdb=" P C 12065 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 5.96e+01 bond pdb=" O3' G 12102 " pdb=" P C 12103 " ideal model delta sigma weight residual 1.607 1.511 0.096 1.50e-02 4.44e+03 4.13e+01 bond pdb=" CA ALA n 66 " pdb=" C ALA n 66 " ideal model delta sigma weight residual 1.524 1.436 0.088 1.48e-02 4.57e+03 3.55e+01 bond pdb=" CA ARG l 18 " pdb=" CB ARG l 18 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.62e-02 3.81e+03 2.55e+01 bond pdb=" O3' A 1 905 " pdb=" P U 1 906 " ideal model delta sigma weight residual 1.607 1.531 0.076 1.50e-02 4.44e+03 2.55e+01 ... (remaining 166253 not shown) Histogram of bond angle deviations from ideal: 26.14 - 51.21: 1 51.21 - 76.27: 0 76.27 - 101.34: 2456 101.34 - 126.40: 230670 126.40 - 151.47: 14840 Bond angle restraints: 247967 Sorted by residual: angle pdb=" O3' G 12102 " pdb=" P C 12103 " pdb=" O5' C 12103 " ideal model delta sigma weight residual 104.00 26.14 77.86 1.50e+00 4.44e-01 2.69e+03 angle pdb=" C3' U 12187 " pdb=" O3' U 12187 " pdb=" P U 12188 " ideal model delta sigma weight residual 120.20 151.47 -31.27 1.50e+00 4.44e-01 4.35e+02 angle pdb=" C3' G 12102 " pdb=" O3' G 12102 " pdb=" P C 12103 " ideal model delta sigma weight residual 120.20 89.82 30.38 1.50e+00 4.44e-01 4.10e+02 angle pdb=" C3' G 12578 " pdb=" O3' G 12578 " pdb=" P C 12579 " ideal model delta sigma weight residual 120.20 97.28 22.92 1.50e+00 4.44e-01 2.33e+02 angle pdb=" C3' A 1 905 " pdb=" O3' A 1 905 " pdb=" P U 1 906 " ideal model delta sigma weight residual 120.20 138.67 -18.47 1.50e+00 4.44e-01 1.52e+02 ... (remaining 247962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 93811 34.73 - 69.46: 11157 69.46 - 104.19: 1365 104.19 - 138.92: 27 138.92 - 173.65: 21 Dihedral angle restraints: 106381 sinusoidal: 87501 harmonic: 18880 Sorted by residual: dihedral pdb=" CA GLY d 82 " pdb=" C GLY d 82 " pdb=" N VAL d 83 " pdb=" CA VAL d 83 " ideal model delta harmonic sigma weight residual -180.00 -125.97 -54.03 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA ASN J 121 " pdb=" C ASN J 121 " pdb=" N VAL J 122 " pdb=" CA VAL J 122 " ideal model delta harmonic sigma weight residual -180.00 -127.12 -52.88 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA LYS K 53 " pdb=" C LYS K 53 " pdb=" N LEU K 54 " pdb=" CA LEU K 54 " ideal model delta harmonic sigma weight residual 180.00 127.67 52.33 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 106378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 28485 0.125 - 0.250: 2978 0.250 - 0.375: 109 0.375 - 0.500: 6 0.500 - 0.625: 2 Chirality restraints: 31580 Sorted by residual: chirality pdb=" CA PRO x 30 " pdb=" N PRO x 30 " pdb=" C PRO x 30 " pdb=" CB PRO x 30 " both_signs ideal model delta sigma weight residual False 2.72 2.09 0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" P C 5 1 " pdb=" OP1 C 5 1 " pdb=" OP2 C 5 1 " pdb=" O5' C 5 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.03 -0.62 2.00e-01 2.50e+01 9.61e+00 chirality pdb=" C3' A 11020 " pdb=" C4' A 11020 " pdb=" O3' A 11020 " pdb=" C2' A 11020 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.44 2.00e-01 2.50e+01 4.95e+00 ... (remaining 31577 not shown) Planarity restraints: 13864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 11275 " 0.157 2.00e-02 2.50e+03 6.83e-02 1.28e+02 pdb=" N9 A 11275 " -0.009 2.00e-02 2.50e+03 pdb=" C8 A 11275 " -0.055 2.00e-02 2.50e+03 pdb=" N7 A 11275 " -0.055 2.00e-02 2.50e+03 pdb=" C5 A 11275 " -0.036 2.00e-02 2.50e+03 pdb=" C6 A 11275 " 0.024 2.00e-02 2.50e+03 pdb=" N6 A 11275 " 0.102 2.00e-02 2.50e+03 pdb=" N1 A 11275 " 0.019 2.00e-02 2.50e+03 pdb=" C2 A 11275 " -0.028 2.00e-02 2.50e+03 pdb=" N3 A 11275 " -0.061 2.00e-02 2.50e+03 pdb=" C4 A 11275 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11779 " 0.139 2.00e-02 2.50e+03 7.29e-02 1.20e+02 pdb=" N1 U 11779 " -0.009 2.00e-02 2.50e+03 pdb=" C2 U 11779 " -0.027 2.00e-02 2.50e+03 pdb=" O2 U 11779 " -0.056 2.00e-02 2.50e+03 pdb=" N3 U 11779 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U 11779 " -0.015 2.00e-02 2.50e+03 pdb=" O4 U 11779 " 0.122 2.00e-02 2.50e+03 pdb=" C5 U 11779 " -0.069 2.00e-02 2.50e+03 pdb=" C6 U 11779 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 702 " 0.130 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" N1 U 1 702 " -0.005 2.00e-02 2.50e+03 pdb=" C2 U 1 702 " -0.025 2.00e-02 2.50e+03 pdb=" O2 U 1 702 " -0.050 2.00e-02 2.50e+03 pdb=" N3 U 1 702 " -0.022 2.00e-02 2.50e+03 pdb=" C4 U 1 702 " -0.020 2.00e-02 2.50e+03 pdb=" O4 U 1 702 " 0.124 2.00e-02 2.50e+03 pdb=" C5 U 1 702 " -0.069 2.00e-02 2.50e+03 pdb=" C6 U 1 702 " -0.063 2.00e-02 2.50e+03 ... (remaining 13861 not shown) Histogram of nonbonded interaction distances: 0.52 - 1.40: 2 1.40 - 2.27: 30 2.27 - 3.15: 112132 3.15 - 4.02: 464773 4.02 - 4.90: 759895 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1336832 Sorted by model distance: nonbonded pdb=" N2 G 12120 " pdb=" NZ LYS a 167 " model vdw 0.524 3.200 nonbonded pdb=" C2 G 12120 " pdb=" NZ LYS a 167 " model vdw 1.380 3.340 nonbonded pdb=" N3 G 12121 " pdb=" CB LYS a 167 " model vdw 1.713 3.520 nonbonded pdb=" C1' G 12121 " pdb=" CG LYS a 167 " model vdw 1.716 3.870 nonbonded pdb=" N2 G 12120 " pdb=" CE LYS a 167 " model vdw 1.733 3.520 ... (remaining 1336827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.51 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 23.360 Check model and map are aligned: 1.660 Set scattering table: 1.120 Process input model: 499.780 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 536.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 : 0.009 0.116 166258 Z= 0.528 Angle : 1.016 77.858 247967 Z= 0.638 Chirality : 0.079 0.625 31580 Planarity : 0.011 0.115 13864 Dihedral : 23.029 173.655 94204 Min Nonbonded Distance : 0.524 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.61 % Favored : 87.21 % Rotamer: Outliers : 1.11 % Allowed : 14.03 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.08), residues: 6520 helix: -4.35 (0.06), residues: 1552 sheet: -2.94 (0.15), residues: 936 loop : -3.27 (0.08), residues: 4032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP b 212 HIS 0.014 0.002 HIS g 128 PHE 0.035 0.003 PHE Z 36 TYR 0.041 0.003 TYR L 84 ARG 0.011 0.001 ARG 8 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1666 time to evaluate : 6.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 113 TYR cc_start: 0.7896 (m-80) cc_final: 0.7157 (m-80) REVERT: 8 193 TRP cc_start: 0.7074 (m100) cc_final: 0.6815 (m100) REVERT: 8 309 ARG cc_start: 0.5901 (mtp180) cc_final: 0.5344 (mtp180) REVERT: 8 337 ARG cc_start: 0.7477 (tmt170) cc_final: 0.7124 (tpt-90) REVERT: 8 445 PHE cc_start: 0.7223 (t80) cc_final: 0.6938 (t80) REVERT: 8 469 ILE cc_start: 0.7202 (tp) cc_final: 0.6710 (tp) REVERT: 8 574 MET cc_start: 0.5197 (ttp) cc_final: 0.4304 (pmm) REVERT: 8 606 LYS cc_start: 0.6406 (mptt) cc_final: 0.6186 (mptt) REVERT: b 83 ASP cc_start: 0.7600 (t0) cc_final: 0.6761 (p0) REVERT: b 144 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7339 (mt-10) REVERT: b 146 LYS cc_start: 0.7554 (mttt) cc_final: 0.6658 (mmtt) REVERT: b 194 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7292 (t) REVERT: b 213 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8274 (mtp85) REVERT: b 268 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7865 (ttp80) REVERT: c 7 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7730 (ttpp) REVERT: c 81 GLU cc_start: 0.7487 (tp30) cc_final: 0.7260 (tp30) REVERT: c 89 GLU cc_start: 0.8459 (pm20) cc_final: 0.7971 (pm20) REVERT: c 199 SER cc_start: 0.9163 (m) cc_final: 0.8950 (m) REVERT: d 57 LYS cc_start: 0.5536 (mmtm) cc_final: 0.5131 (mmtt) REVERT: d 102 ARG cc_start: 0.7794 (mtt180) cc_final: 0.6615 (mtm180) REVERT: d 195 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7534 (tm-30) REVERT: e 6 TYR cc_start: 0.7779 (t80) cc_final: 0.7328 (t80) REVERT: e 25 MET cc_start: 0.8228 (tpp) cc_final: 0.6751 (ptp) REVERT: e 63 LYS cc_start: 0.7691 (tttm) cc_final: 0.6779 (ptmt) REVERT: e 76 PHE cc_start: 0.6898 (m-80) cc_final: 0.6684 (m-80) REVERT: e 95 MET cc_start: 0.7118 (ppp) cc_final: 0.6892 (pmm) REVERT: e 111 ARG cc_start: 0.6996 (ptt180) cc_final: 0.6616 (mtp85) REVERT: e 126 ASN cc_start: 0.6052 (m-40) cc_final: 0.5795 (m-40) REVERT: f 25 ILE cc_start: 0.6347 (mt) cc_final: 0.5564 (mm) REVERT: f 26 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8464 (mmmt) REVERT: f 106 LEU cc_start: 0.8408 (mm) cc_final: 0.7802 (mm) REVERT: f 142 GLN cc_start: 0.8270 (tp40) cc_final: 0.7835 (tp40) REVERT: f 146 ASP cc_start: 0.7745 (m-30) cc_final: 0.7363 (m-30) REVERT: g 47 PHE cc_start: 0.7805 (t80) cc_final: 0.7594 (t80) REVERT: j 27 ARG cc_start: 0.8017 (mpt-90) cc_final: 0.7507 (mmt-90) REVERT: j 106 LYS cc_start: 0.8566 (tttt) cc_final: 0.8087 (tttp) REVERT: j 136 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8181 (tm-30) REVERT: k 23 LYS cc_start: 0.7118 (mmmm) cc_final: 0.6742 (mmtp) REVERT: k 93 GLN cc_start: 0.7607 (pp30) cc_final: 0.7379 (pp30) REVERT: k 98 ARG cc_start: 0.7756 (tpt170) cc_final: 0.7251 (ttm110) REVERT: l 12 SER cc_start: 0.9218 (p) cc_final: 0.9007 (p) REVERT: l 81 ASP cc_start: 0.7434 (t70) cc_final: 0.7018 (t70) REVERT: m 22 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7593 (tp40) REVERT: m 68 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: m 73 ILE cc_start: 0.8245 (mt) cc_final: 0.7979 (mp) REVERT: n 1 MET cc_start: 0.8665 (ptp) cc_final: 0.8169 (ptp) REVERT: n 4 ARG cc_start: 0.7699 (mmt180) cc_final: 0.7390 (tpm170) REVERT: o 4 LYS cc_start: 0.8442 (tppp) cc_final: 0.8223 (ttpt) REVERT: o 56 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7575 (pptt) REVERT: p 3 ILE cc_start: 0.8481 (mm) cc_final: 0.8237 (mm) REVERT: p 23 ASP cc_start: 0.8290 (m-30) cc_final: 0.7984 (m-30) REVERT: p 43 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8075 (tp30) REVERT: p 58 PHE cc_start: 0.8689 (p90) cc_final: 0.8377 (p90) REVERT: p 61 ARG cc_start: 0.7842 (ttt-90) cc_final: 0.7297 (ttm-80) REVERT: p 62 LYS cc_start: 0.7736 (tttt) cc_final: 0.7202 (tptm) REVERT: q 5 ARG cc_start: 0.7521 (mtm110) cc_final: 0.6501 (mtm-85) REVERT: q 55 GLN cc_start: 0.8948 (tp40) cc_final: 0.8587 (tp40) REVERT: q 57 ARG cc_start: 0.8124 (ttt90) cc_final: 0.7384 (ttt-90) REVERT: r 1 MET cc_start: 0.7945 (tpp) cc_final: 0.7587 (tpp) REVERT: r 41 ILE cc_start: 0.8435 (mt) cc_final: 0.8205 (mm) REVERT: r 53 PHE cc_start: 0.8452 (m-10) cc_final: 0.8107 (m-80) REVERT: r 101 ILE cc_start: 0.7328 (mm) cc_final: 0.6717 (mm) REVERT: s 4 ILE cc_start: 0.8967 (mp) cc_final: 0.8444 (tp) REVERT: s 22 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.6934 (t70) REVERT: t 42 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7541 (mm-30) REVERT: t 89 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8488 (mm-30) REVERT: u 4 ILE cc_start: 0.8845 (mm) cc_final: 0.8636 (mt) REVERT: u 27 VAL cc_start: 0.4086 (OUTLIER) cc_final: 0.3833 (m) REVERT: v 24 ASN cc_start: 0.7704 (t0) cc_final: 0.7333 (t0) REVERT: v 57 TYR cc_start: 0.7468 (m-80) cc_final: 0.7077 (m-10) REVERT: x 2 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: x 15 ASN cc_start: 0.8161 (m-40) cc_final: 0.7686 (t0) REVERT: x 31 ASN cc_start: 0.8167 (t0) cc_final: 0.7525 (t0) REVERT: x 70 LEU cc_start: 0.8811 (mt) cc_final: 0.8517 (mp) REVERT: y 2 LYS cc_start: 0.8339 (ptpt) cc_final: 0.8023 (pttm) REVERT: y 5 GLU cc_start: 0.8241 (tt0) cc_final: 0.7418 (tt0) REVERT: y 52 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7276 (ttt180) REVERT: z 10 ARG cc_start: 0.8321 (mtt180) cc_final: 0.8073 (mtt90) REVERT: B 11 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8296 (tmtt) REVERT: B 12 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8167 (ttp80) REVERT: B 39 ARG cc_start: 0.7808 (ttt90) cc_final: 0.6768 (ttt90) REVERT: C 6 GLU cc_start: 0.7334 (pp20) cc_final: 0.6932 (pp20) REVERT: C 24 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7224 (ttpp) REVERT: C 37 LYS cc_start: 0.6751 (mttt) cc_final: 0.6452 (mtpt) REVERT: G 55 GLU cc_start: 0.9132 (tp30) cc_final: 0.8355 (tp30) REVERT: G 112 ARG cc_start: 0.9427 (mpt180) cc_final: 0.9070 (mmp80) REVERT: G 117 GLU cc_start: 0.8632 (mt-10) cc_final: 0.7045 (tp30) REVERT: G 138 ARG cc_start: 0.7792 (tpm170) cc_final: 0.7436 (tpm170) REVERT: G 153 MET cc_start: 0.5996 (tmm) cc_final: 0.5514 (tmm) REVERT: G 168 GLU cc_start: 0.8697 (mp0) cc_final: 0.8321 (mp0) REVERT: H 10 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8021 (mtm180) REVERT: H 151 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7245 (tp30) REVERT: H 183 TYR cc_start: 0.7106 (t80) cc_final: 0.6787 (t80) REVERT: H 198 LYS cc_start: 0.6408 (mttt) cc_final: 0.6039 (mttt) REVERT: I 13 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.6908 (tpm170) REVERT: I 35 GLN cc_start: 0.8110 (mm110) cc_final: 0.7396 (pp30) REVERT: I 62 ARG cc_start: 0.8344 (mpp80) cc_final: 0.7960 (mtm-85) REVERT: I 69 ARG cc_start: 0.7127 (tpp-160) cc_final: 0.5857 (ttp-170) REVERT: I 106 PHE cc_start: 0.8260 (m-80) cc_final: 0.7686 (m-80) REVERT: I 115 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7466 (mm-40) REVERT: I 195 ASN cc_start: 0.8458 (p0) cc_final: 0.8016 (p0) REVERT: J 92 ARG cc_start: 0.6673 (mpt180) cc_final: 0.6380 (mpt180) REVERT: J 127 TYR cc_start: 0.7707 (m-80) cc_final: 0.7397 (m-80) REVERT: J 150 GLU cc_start: 0.8683 (mp0) cc_final: 0.8427 (mp0) REVERT: K 17 GLN cc_start: 0.7326 (pt0) cc_final: 0.6838 (pm20) REVERT: K 90 MET cc_start: 0.6736 (mmt) cc_final: 0.6518 (mmp) REVERT: L 39 GLU cc_start: 0.6360 (pp20) cc_final: 0.5510 (pp20) REVERT: L 117 LEU cc_start: 0.8328 (tp) cc_final: 0.8110 (tp) REVERT: M 17 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7366 (mt0) REVERT: M 59 GLU cc_start: 0.7956 (tt0) cc_final: 0.7578 (tm-30) REVERT: N 49 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7864 (tp40) REVERT: N 98 ARG cc_start: 0.3870 (tpm170) cc_final: 0.1195 (tpt-90) REVERT: P 26 PHE cc_start: 0.8496 (m-80) cc_final: 0.8247 (m-10) REVERT: R 22 TYR cc_start: 0.6587 (t80) cc_final: 0.6105 (t80) REVERT: S 27 LYS cc_start: 0.8129 (pptt) cc_final: 0.7551 (ptmm) REVERT: V 10 ARG cc_start: 0.6887 (tmt-80) cc_final: 0.6683 (tmt170) REVERT: V 17 GLU cc_start: 0.7203 (tt0) cc_final: 0.6823 (tt0) REVERT: V 35 LYS cc_start: 0.8159 (tttm) cc_final: 0.7925 (tptp) REVERT: V 37 ILE cc_start: 0.6326 (pt) cc_final: 0.6088 (pt) REVERT: V 42 LYS cc_start: 0.7025 (mttp) cc_final: 0.6641 (mtpt) REVERT: V 72 TRP cc_start: 0.7862 (m-10) cc_final: 0.7341 (m-10) REVERT: W 23 LYS cc_start: 0.7230 (ptpp) cc_final: 0.6661 (ptmt) REVERT: W 47 ARG cc_start: 0.7168 (mmp-170) cc_final: 0.6769 (mmt180) REVERT: Y 54 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8635 (tm-30) REVERT: Y 56 ILE cc_start: 0.8641 (mt) cc_final: 0.8190 (mt) REVERT: Z 39 LYS cc_start: 0.7349 (mtpt) cc_final: 0.7126 (ttpt) REVERT: Z 54 ARG cc_start: 0.7242 (mtt90) cc_final: 0.6991 (mtt180) outliers start: 60 outliers final: 27 residues processed: 1708 average time/residue: 1.4794 time to fit residues: 4218.9057 Evaluate side-chains 1369 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1338 time to evaluate : 6.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 173 ILE Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 936 optimal weight: 6.9990 chunk 840 optimal weight: 6.9990 chunk 466 optimal weight: 30.0000 chunk 287 optimal weight: 10.0000 chunk 567 optimal weight: 0.8980 chunk 449 optimal weight: 20.0000 chunk 869 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 528 optimal weight: 20.0000 chunk 646 optimal weight: 3.9990 chunk 1007 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 37 ASN 8 57 GLN ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 192 ASN ** 8 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 365 GLN 8 508 GLN 8 514 GLN ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 HIS b 52 HIS ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 250 GLN c 32 ASN c 49 GLN c 67 HIS c 136 ASN ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN e 22 ASN f 21 GLN f 63 GLN g 33 GLN g 66 ASN a 24 ASN a 168 ASN a 172 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 135 GLN l 93 ASN n 9 GLN n 23 ASN n 73 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 80 ASN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS t 59 ASN t 70 HIS ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN u 73 ASN ** u 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 24 ASN ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS G 14 HIS G 57 ASN G 102 ASN G 169 HIS H 18 ASN H 101 ASN H 122 GLN H 138 GLN H 139 ASN H 184 ASN I 125 ASN I 130 ASN I 197 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN P 27 ASN P 80 ASN ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS R 13 HIS R 90 HIS ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN U 59 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN W 53 GLN X 51 HIS Y 12 GLN Y 74 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 166258 Z= 0.299 Angle : 0.783 19.873 247967 Z= 0.399 Chirality : 0.044 0.312 31580 Planarity : 0.006 0.107 13864 Dihedral : 23.498 177.231 81288 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.35 % Favored : 88.56 % Rotamer: Outliers : 4.91 % Allowed : 22.26 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.16 % 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: -4.50 (0.08), residues: 6520 helix: -3.17 (0.09), residues: 1720 sheet: -2.89 (0.15), residues: 937 loop : -3.02 (0.08), residues: 3863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 212 HIS 0.011 0.002 HIS 8 44 PHE 0.032 0.002 PHE a 180 TYR 0.022 0.002 TYR b 102 ARG 0.017 0.001 ARG f 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1450 time to evaluate : 6.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 32 PHE cc_start: 0.6374 (t80) cc_final: 0.6053 (t80) REVERT: 8 53 MET cc_start: 0.1275 (mtm) cc_final: 0.0653 (mtm) REVERT: 8 101 ARG cc_start: 0.8157 (ppt170) cc_final: 0.7863 (ppt170) REVERT: 8 113 TYR cc_start: 0.7737 (m-80) cc_final: 0.7142 (m-80) REVERT: 8 309 ARG cc_start: 0.5725 (mtp180) cc_final: 0.5498 (mtp180) REVERT: 8 337 ARG cc_start: 0.7591 (tmt170) cc_final: 0.7167 (tpt-90) REVERT: 8 365 GLN cc_start: 0.0994 (OUTLIER) cc_final: 0.0602 (tm130) REVERT: 8 469 ILE cc_start: 0.7272 (tp) cc_final: 0.6830 (tp) REVERT: 8 523 TYR cc_start: 0.2208 (OUTLIER) cc_final: 0.1460 (m-10) REVERT: 8 574 MET cc_start: 0.5529 (ttp) cc_final: 0.4274 (pmm) REVERT: b 146 LYS cc_start: 0.7444 (mttt) cc_final: 0.6957 (mmtt) REVERT: b 259 ASN cc_start: 0.6828 (p0) cc_final: 0.6296 (p0) REVERT: c 7 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8004 (ttpp) REVERT: c 48 ILE cc_start: 0.8319 (pt) cc_final: 0.8104 (mm) REVERT: c 81 GLU cc_start: 0.7267 (tp30) cc_final: 0.6983 (tp30) REVERT: c 89 GLU cc_start: 0.8477 (pm20) cc_final: 0.7958 (pm20) REVERT: c 149 ASN cc_start: 0.9044 (t0) cc_final: 0.8814 (t0) REVERT: d 102 ARG cc_start: 0.7899 (mtt180) cc_final: 0.6734 (mtm180) REVERT: d 195 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7441 (tm-30) REVERT: e 37 MET cc_start: 0.6817 (mtp) cc_final: 0.5834 (mtp) REVERT: e 51 ASN cc_start: 0.8568 (t0) cc_final: 0.8258 (t0) REVERT: e 63 LYS cc_start: 0.7681 (tttm) cc_final: 0.6817 (ptmt) REVERT: e 76 PHE cc_start: 0.7336 (m-80) cc_final: 0.6877 (m-80) REVERT: e 164 GLU cc_start: 0.7996 (tp30) cc_final: 0.7787 (tp30) REVERT: f 106 LEU cc_start: 0.8206 (mm) cc_final: 0.7815 (mm) REVERT: f 142 GLN cc_start: 0.7680 (tp40) cc_final: 0.7261 (tp40) REVERT: f 146 ASP cc_start: 0.8091 (m-30) cc_final: 0.7584 (m-30) REVERT: i 16 MET cc_start: 0.3186 (tpp) cc_final: 0.2470 (tmm) REVERT: j 58 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7474 (t0) REVERT: j 86 GLN cc_start: 0.8803 (pp30) cc_final: 0.8553 (pp30) REVERT: j 106 LYS cc_start: 0.8549 (tttt) cc_final: 0.8074 (tttp) REVERT: j 136 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8392 (tm-30) REVERT: l 14 LYS cc_start: 0.8614 (tptp) cc_final: 0.8409 (tptp) REVERT: l 36 LYS cc_start: 0.6417 (mtpt) cc_final: 0.5886 (pttm) REVERT: l 81 ASP cc_start: 0.7379 (t70) cc_final: 0.7087 (t70) REVERT: m 68 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: m 73 ILE cc_start: 0.8200 (mt) cc_final: 0.7995 (mp) REVERT: n 1 MET cc_start: 0.8545 (ptp) cc_final: 0.8262 (ptp) REVERT: n 4 ARG cc_start: 0.7813 (mmt180) cc_final: 0.7478 (tpm170) REVERT: n 67 PHE cc_start: 0.8370 (t80) cc_final: 0.8169 (t80) REVERT: n 71 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7759 (tpt170) REVERT: o 25 ARG cc_start: 0.7220 (ptt180) cc_final: 0.6882 (ptt-90) REVERT: o 56 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7743 (pptt) REVERT: o 64 TYR cc_start: 0.5762 (t80) cc_final: 0.5484 (t80) REVERT: p 23 ASP cc_start: 0.8364 (m-30) cc_final: 0.8019 (m-30) REVERT: p 61 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.7250 (ttm-80) REVERT: p 62 LYS cc_start: 0.7720 (tttt) cc_final: 0.7140 (tptm) REVERT: q 40 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8568 (mmmm) REVERT: r 11 GLN cc_start: 0.8499 (mt0) cc_final: 0.8188 (mt0) REVERT: r 40 MET cc_start: 0.5741 (tpt) cc_final: 0.4675 (tpt) REVERT: s 4 ILE cc_start: 0.8940 (mp) cc_final: 0.8433 (tp) REVERT: s 22 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.6826 (t70) REVERT: s 48 LYS cc_start: 0.8239 (tttp) cc_final: 0.7938 (ttpt) REVERT: t 89 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8528 (mm-30) REVERT: u 52 ASN cc_start: 0.6795 (t0) cc_final: 0.6580 (t0) REVERT: v 24 ASN cc_start: 0.7626 (t0) cc_final: 0.7242 (t0) REVERT: v 57 TYR cc_start: 0.7799 (m-80) cc_final: 0.7239 (m-10) REVERT: x 31 ASN cc_start: 0.8594 (t0) cc_final: 0.7935 (t0) REVERT: y 5 GLU cc_start: 0.8349 (tt0) cc_final: 0.7683 (tt0) REVERT: y 52 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7082 (ttt180) REVERT: A 9 TYR cc_start: 0.6874 (m-10) cc_final: 0.6479 (m-10) REVERT: B 11 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8269 (tttm) REVERT: B 16 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7369 (ttm-80) REVERT: C 24 LYS cc_start: 0.7341 (ttpp) cc_final: 0.7121 (ttpp) REVERT: D 41 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6979 (ptm160) REVERT: G 55 GLU cc_start: 0.8942 (tp30) cc_final: 0.8687 (tp30) REVERT: G 110 ILE cc_start: 0.8888 (mt) cc_final: 0.8363 (mt) REVERT: G 112 ARG cc_start: 0.9520 (mpt180) cc_final: 0.9227 (mmp-170) REVERT: G 117 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7210 (tp30) REVERT: G 138 ARG cc_start: 0.7728 (tpm170) cc_final: 0.7338 (tpm170) REVERT: G 153 MET cc_start: 0.5834 (tmm) cc_final: 0.5203 (tmm) REVERT: G 168 GLU cc_start: 0.8717 (mp0) cc_final: 0.8327 (mp0) REVERT: H 160 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6900 (tp30) REVERT: H 183 TYR cc_start: 0.7142 (t80) cc_final: 0.6741 (t80) REVERT: I 13 ARG cc_start: 0.7919 (tpp-160) cc_final: 0.7117 (tpm170) REVERT: I 62 ARG cc_start: 0.8334 (mpp80) cc_final: 0.8040 (mtm-85) REVERT: I 106 PHE cc_start: 0.8257 (m-80) cc_final: 0.7756 (m-80) REVERT: I 134 TYR cc_start: 0.8036 (t80) cc_final: 0.7689 (t80) REVERT: I 195 ASN cc_start: 0.8168 (p0) cc_final: 0.7777 (p0) REVERT: I 205 LYS cc_start: 0.7140 (ptmt) cc_final: 0.6918 (ptpt) REVERT: J 127 TYR cc_start: 0.7732 (m-80) cc_final: 0.7426 (m-80) REVERT: K 11 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7594 (m-70) REVERT: K 63 ASN cc_start: 0.6628 (t0) cc_final: 0.6337 (t0) REVERT: L 39 GLU cc_start: 0.5997 (pp20) cc_final: 0.5227 (pp20) REVERT: M 30 LYS cc_start: 0.7764 (tttt) cc_final: 0.7545 (ttpt) REVERT: M 45 ILE cc_start: 0.4334 (OUTLIER) cc_final: 0.3985 (tp) REVERT: M 59 GLU cc_start: 0.7814 (tt0) cc_final: 0.7420 (tm-30) REVERT: N 49 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7848 (tp-100) REVERT: N 98 ARG cc_start: 0.3657 (tpm170) cc_final: 0.0843 (tpt-90) REVERT: N 129 ARG cc_start: 0.4344 (ptt-90) cc_final: 0.4110 (ptt-90) REVERT: Q 58 ASN cc_start: 0.8032 (p0) cc_final: 0.7573 (t0) REVERT: S 27 LYS cc_start: 0.8164 (pptt) cc_final: 0.7620 (ptmm) REVERT: S 58 ARG cc_start: 0.6620 (tpt170) cc_final: 0.6093 (tpp-160) REVERT: U 18 GLN cc_start: 0.7508 (tt0) cc_final: 0.7124 (tm-30) REVERT: V 10 ARG cc_start: 0.7067 (tmt-80) cc_final: 0.6751 (tmt170) REVERT: V 17 GLU cc_start: 0.7060 (tt0) cc_final: 0.6702 (tt0) REVERT: V 37 ILE cc_start: 0.6530 (pt) cc_final: 0.6182 (pt) REVERT: V 72 TRP cc_start: 0.8035 (m-10) cc_final: 0.7451 (m-10) REVERT: W 23 LYS cc_start: 0.7298 (ptpp) cc_final: 0.6813 (ptmt) REVERT: W 52 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7161 (mmm160) REVERT: W 53 GLN cc_start: 0.6830 (tt0) cc_final: 0.6596 (tt0) REVERT: Y 54 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8786 (tm-30) outliers start: 266 outliers final: 166 residues processed: 1595 average time/residue: 1.4548 time to fit residues: 3944.7015 Evaluate side-chains 1463 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1289 time to evaluate : 6.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 173 ILE Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 365 GLN Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 134 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 110 VAL Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 91 LYS Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 43 LYS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 189 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 85 TYR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 559 optimal weight: 0.7980 chunk 312 optimal weight: 10.0000 chunk 838 optimal weight: 6.9990 chunk 685 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 1008 optimal weight: 10.0000 chunk 1089 optimal weight: 2.9990 chunk 898 optimal weight: 0.5980 chunk 1000 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 809 optimal weight: 20.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 ASN ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 HIS c 67 HIS ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 97 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 13 HIS n 9 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 104 GLN ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 98 ASN A 30 HIS ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN H 122 GLN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN K 94 HIS N 109 GLN ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN S 70 HIS T 19 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 HIS ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN V 30 HIS V 46 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 166258 Z= 0.240 Angle : 0.671 21.361 247967 Z= 0.346 Chirality : 0.039 0.321 31580 Planarity : 0.006 0.119 13864 Dihedral : 23.583 178.683 81281 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.64 % Favored : 88.27 % Rotamer: Outliers : 6.41 % Allowed : 24.72 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.92 (0.09), residues: 6520 helix: -2.41 (0.10), residues: 1739 sheet: -2.64 (0.15), residues: 900 loop : -2.78 (0.09), residues: 3881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 212 HIS 0.040 0.002 HIS U 59 PHE 0.033 0.002 PHE 8 664 TYR 0.020 0.002 TYR b 102 ARG 0.013 0.001 ARG N 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1431 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 32 PHE cc_start: 0.6332 (t80) cc_final: 0.6090 (t80) REVERT: 8 50 MET cc_start: 0.6679 (tpp) cc_final: 0.6418 (tpp) REVERT: 8 98 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6601 (pt0) REVERT: 8 101 ARG cc_start: 0.7969 (ppt170) cc_final: 0.7719 (ppt170) REVERT: 8 113 TYR cc_start: 0.7717 (m-80) cc_final: 0.7125 (m-80) REVERT: 8 337 ARG cc_start: 0.7606 (tmt170) cc_final: 0.7158 (tpt-90) REVERT: 8 461 MET cc_start: 0.4196 (tmm) cc_final: 0.3845 (tmm) REVERT: 8 523 TYR cc_start: 0.1951 (OUTLIER) cc_final: 0.1306 (m-10) REVERT: 8 574 MET cc_start: 0.5539 (ttp) cc_final: 0.3727 (ptp) REVERT: 8 682 MET cc_start: 0.1539 (mmt) cc_final: 0.1129 (mmp) REVERT: b 146 LYS cc_start: 0.7430 (mttt) cc_final: 0.6995 (mmtt) REVERT: b 206 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8471 (pttp) REVERT: b 259 ASN cc_start: 0.6762 (p0) cc_final: 0.6185 (p0) REVERT: c 1 MET cc_start: 0.5838 (tmm) cc_final: 0.5058 (ptm) REVERT: c 7 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7982 (ttpp) REVERT: c 18 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8416 (p0) REVERT: c 81 GLU cc_start: 0.7133 (tp30) cc_final: 0.6899 (tp30) REVERT: c 89 GLU cc_start: 0.8449 (pm20) cc_final: 0.7911 (pm20) REVERT: c 149 ASN cc_start: 0.8968 (t0) cc_final: 0.8662 (t0) REVERT: c 150 GLN cc_start: 0.8692 (mt0) cc_final: 0.8356 (mt0) REVERT: d 77 ILE cc_start: 0.8974 (mt) cc_final: 0.8736 (mm) REVERT: d 95 LYS cc_start: 0.6470 (tttp) cc_final: 0.6080 (tmtt) REVERT: d 102 ARG cc_start: 0.7929 (mtt180) cc_final: 0.6580 (mtp-110) REVERT: d 195 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7503 (tm-30) REVERT: e 16 MET cc_start: 0.7463 (tpp) cc_final: 0.7089 (tpp) REVERT: e 30 VAL cc_start: 0.6733 (p) cc_final: 0.6497 (t) REVERT: e 37 MET cc_start: 0.6881 (mtp) cc_final: 0.6080 (mtp) REVERT: e 51 ASN cc_start: 0.8481 (m-40) cc_final: 0.8203 (t0) REVERT: e 76 PHE cc_start: 0.7539 (m-80) cc_final: 0.6961 (m-80) REVERT: e 95 MET cc_start: 0.7713 (ppp) cc_final: 0.7403 (pmm) REVERT: e 111 ARG cc_start: 0.7256 (ptp90) cc_final: 0.7041 (mtm-85) REVERT: f 106 LEU cc_start: 0.8195 (mm) cc_final: 0.7598 (mm) REVERT: i 16 MET cc_start: 0.3192 (tpp) cc_final: 0.2502 (tmm) REVERT: j 58 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6213 (t0) REVERT: j 60 ASP cc_start: 0.8198 (p0) cc_final: 0.7757 (p0) REVERT: j 86 GLN cc_start: 0.8816 (pp30) cc_final: 0.8576 (pp30) REVERT: j 106 LYS cc_start: 0.8581 (tttt) cc_final: 0.8153 (tttp) REVERT: j 136 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8424 (tm-30) REVERT: l 10 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7283 (tm-30) REVERT: l 36 LYS cc_start: 0.6367 (mtpt) cc_final: 0.5825 (pttm) REVERT: m 9 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5707 (t80) REVERT: m 68 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: m 73 ILE cc_start: 0.8179 (mt) cc_final: 0.7890 (mp) REVERT: n 1 MET cc_start: 0.8495 (ptp) cc_final: 0.8141 (ptp) REVERT: n 4 ARG cc_start: 0.7777 (mmt180) cc_final: 0.7438 (tpm170) REVERT: n 71 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7878 (tpt170) REVERT: o 56 LYS cc_start: 0.8327 (mtmm) cc_final: 0.7673 (pptt) REVERT: p 23 ASP cc_start: 0.8425 (m-30) cc_final: 0.8073 (m-30) REVERT: p 61 ARG cc_start: 0.7742 (ttt-90) cc_final: 0.7168 (ttm-80) REVERT: p 62 LYS cc_start: 0.7738 (tttt) cc_final: 0.7098 (tptm) REVERT: q 60 TRP cc_start: 0.8794 (m-10) cc_final: 0.8493 (m-10) REVERT: r 1 MET cc_start: 0.8259 (tpp) cc_final: 0.7889 (tpp) REVERT: r 40 MET cc_start: 0.5510 (tpt) cc_final: 0.5112 (tpt) REVERT: s 4 ILE cc_start: 0.8969 (mp) cc_final: 0.8470 (tp) REVERT: s 22 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.6754 (t70) REVERT: s 103 ILE cc_start: 0.8587 (mp) cc_final: 0.8119 (tt) REVERT: t 42 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7455 (mm-30) REVERT: t 91 GLN cc_start: 0.7844 (mt0) cc_final: 0.7361 (mt0) REVERT: u 21 ARG cc_start: 0.6755 (ptm-80) cc_final: 0.6146 (mtp-110) REVERT: u 52 ASN cc_start: 0.6879 (t0) cc_final: 0.6668 (t0) REVERT: v 57 TYR cc_start: 0.7707 (m-80) cc_final: 0.7260 (m-10) REVERT: x 31 ASN cc_start: 0.8277 (t0) cc_final: 0.7656 (t0) REVERT: y 5 GLU cc_start: 0.8219 (tt0) cc_final: 0.7325 (tt0) REVERT: y 52 ARG cc_start: 0.7391 (ttt180) cc_final: 0.7021 (ttt180) REVERT: z 10 ARG cc_start: 0.8329 (mtt180) cc_final: 0.8029 (mtt180) REVERT: B 11 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8193 (tttm) REVERT: C 24 LYS cc_start: 0.7424 (ttpp) cc_final: 0.7173 (ttpp) REVERT: D 41 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6885 (ptm160) REVERT: G 55 GLU cc_start: 0.8930 (tp30) cc_final: 0.8465 (tp30) REVERT: G 112 ARG cc_start: 0.9529 (mpt180) cc_final: 0.9108 (mmp80) REVERT: G 117 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7201 (tp30) REVERT: G 153 MET cc_start: 0.5802 (tmm) cc_final: 0.5241 (tmm) REVERT: G 168 GLU cc_start: 0.8740 (mp0) cc_final: 0.8346 (mp0) REVERT: H 183 TYR cc_start: 0.7273 (t80) cc_final: 0.6976 (t80) REVERT: I 13 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7030 (tpm170) REVERT: I 62 ARG cc_start: 0.8318 (mpp80) cc_final: 0.8046 (mpp80) REVERT: I 69 ARG cc_start: 0.7427 (tpp-160) cc_final: 0.6065 (ttp-170) REVERT: I 106 PHE cc_start: 0.8279 (m-80) cc_final: 0.7837 (m-80) REVERT: I 195 ASN cc_start: 0.8371 (p0) cc_final: 0.8038 (p0) REVERT: J 92 ARG cc_start: 0.6752 (mpt180) cc_final: 0.6547 (mpt180) REVERT: J 127 TYR cc_start: 0.7712 (m-80) cc_final: 0.7303 (m-80) REVERT: K 9 MET cc_start: 0.6104 (ptp) cc_final: 0.5690 (mtm) REVERT: K 90 MET cc_start: 0.7177 (mmt) cc_final: 0.6551 (mmt) REVERT: L 21 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7329 (pp) REVERT: L 39 GLU cc_start: 0.6013 (pp20) cc_final: 0.5190 (pp20) REVERT: M 45 ILE cc_start: 0.4364 (OUTLIER) cc_final: 0.4001 (tp) REVERT: M 59 GLU cc_start: 0.7792 (tt0) cc_final: 0.7501 (tm-30) REVERT: N 98 ARG cc_start: 0.3931 (tpm170) cc_final: 0.1040 (tpt-90) REVERT: O 72 ARG cc_start: 0.4963 (mmt-90) cc_final: 0.4606 (mmt-90) REVERT: P 28 ASN cc_start: 0.7361 (t0) cc_final: 0.6918 (m-40) REVERT: P 86 LYS cc_start: 0.8207 (tttp) cc_final: 0.7898 (tttt) REVERT: P 108 ASN cc_start: 0.8323 (p0) cc_final: 0.7534 (p0) REVERT: Q 53 ARG cc_start: 0.7829 (ttt90) cc_final: 0.7538 (ttt180) REVERT: Q 58 ASN cc_start: 0.7927 (p0) cc_final: 0.7604 (t0) REVERT: S 27 LYS cc_start: 0.8081 (pptt) cc_final: 0.7528 (ptmm) REVERT: S 58 ARG cc_start: 0.6415 (tpt170) cc_final: 0.5332 (tpp80) REVERT: U 18 GLN cc_start: 0.7404 (tt0) cc_final: 0.7071 (tm-30) REVERT: U 51 ARG cc_start: 0.6358 (tpp80) cc_final: 0.6015 (tpp80) REVERT: U 54 LEU cc_start: 0.8398 (mt) cc_final: 0.8036 (mt) REVERT: U 63 GLN cc_start: 0.8064 (mt0) cc_final: 0.7853 (mt0) REVERT: V 10 ARG cc_start: 0.7004 (tmt-80) cc_final: 0.6712 (tmt170) REVERT: V 17 GLU cc_start: 0.7131 (tt0) cc_final: 0.6702 (tt0) REVERT: V 72 TRP cc_start: 0.7901 (m-10) cc_final: 0.7316 (m-10) REVERT: W 23 LYS cc_start: 0.7179 (ptpp) cc_final: 0.6642 (ptmt) REVERT: W 42 ARG cc_start: 0.8824 (tmm-80) cc_final: 0.8545 (tmm-80) REVERT: W 47 ARG cc_start: 0.7162 (mmp-170) cc_final: 0.6832 (mmt180) REVERT: W 53 GLN cc_start: 0.6832 (tt0) cc_final: 0.6483 (tt0) REVERT: X 43 MET cc_start: 0.3550 (mmm) cc_final: 0.3015 (mmt) REVERT: Y 24 ARG cc_start: 0.8786 (ttm110) cc_final: 0.8555 (ttm110) REVERT: Y 54 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8723 (tm-30) outliers start: 347 outliers final: 230 residues processed: 1643 average time/residue: 1.4037 time to fit residues: 3930.2655 Evaluate side-chains 1538 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1297 time to evaluate : 6.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 98 GLU Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 173 ILE Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 363 ILE Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 479 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 91 LYS Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 189 HIS Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 996 optimal weight: 20.0000 chunk 758 optimal weight: 7.9990 chunk 523 optimal weight: 0.9980 chunk 111 optimal weight: 30.0000 chunk 481 optimal weight: 9.9990 chunk 677 optimal weight: 10.0000 chunk 1012 optimal weight: 50.0000 chunk 1071 optimal weight: 0.9980 chunk 529 optimal weight: 20.0000 chunk 959 optimal weight: 9.9990 chunk 288 optimal weight: 10.0000 overall best weight: 5.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 HIS b 57 HIS b 133 ASN ** b 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 ASN c 67 HIS ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN t 15 HIS t 59 ASN t 92 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 166258 Z= 0.316 Angle : 0.745 18.644 247967 Z= 0.378 Chirality : 0.041 0.392 31580 Planarity : 0.006 0.088 13864 Dihedral : 23.780 179.921 81280 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.79 % Favored : 87.12 % Rotamer: Outliers : 7.70 % Allowed : 25.94 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.77 (0.09), residues: 6520 helix: -2.12 (0.11), residues: 1723 sheet: -2.58 (0.15), residues: 929 loop : -2.76 (0.09), residues: 3868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 8 193 HIS 0.015 0.002 HIS X 51 PHE 0.026 0.002 PHE p 19 TYR 0.021 0.002 TYR b 102 ARG 0.014 0.001 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1745 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 1328 time to evaluate : 6.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 50 MET cc_start: 0.6597 (tpp) cc_final: 0.6342 (tpp) REVERT: 8 98 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6865 (pt0) REVERT: 8 101 ARG cc_start: 0.8022 (ppt170) cc_final: 0.7684 (ppt170) REVERT: 8 113 TYR cc_start: 0.7724 (m-80) cc_final: 0.7125 (m-80) REVERT: 8 120 GLN cc_start: 0.6942 (mm110) cc_final: 0.6693 (mm110) REVERT: 8 337 ARG cc_start: 0.7508 (tmt170) cc_final: 0.7112 (tpt-90) REVERT: 8 523 TYR cc_start: 0.1680 (OUTLIER) cc_final: 0.1025 (m-10) REVERT: 8 682 MET cc_start: 0.1661 (mmt) cc_final: 0.1447 (mmm) REVERT: b 144 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7580 (mt-10) REVERT: b 146 LYS cc_start: 0.7432 (mttt) cc_final: 0.6975 (mmtt) REVERT: b 206 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8130 (pttt) REVERT: b 254 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7889 (mtpt) REVERT: c 7 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7924 (ttpp) REVERT: c 81 GLU cc_start: 0.7087 (tp30) cc_final: 0.6881 (tp30) REVERT: c 89 GLU cc_start: 0.8431 (pm20) cc_final: 0.7911 (pm20) REVERT: c 149 ASN cc_start: 0.9095 (t0) cc_final: 0.8706 (t0) REVERT: c 150 GLN cc_start: 0.8774 (mt0) cc_final: 0.8460 (mt0) REVERT: d 77 ILE cc_start: 0.9131 (mt) cc_final: 0.8896 (mt) REVERT: d 102 ARG cc_start: 0.7961 (mtt180) cc_final: 0.6648 (mtp-110) REVERT: d 195 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7615 (tm-30) REVERT: e 6 TYR cc_start: 0.8005 (t80) cc_final: 0.7733 (t80) REVERT: e 16 MET cc_start: 0.7471 (tpp) cc_final: 0.7125 (tpp) REVERT: e 37 MET cc_start: 0.7017 (mtp) cc_final: 0.6683 (ttt) REVERT: e 51 ASN cc_start: 0.8474 (m-40) cc_final: 0.8236 (t0) REVERT: e 76 PHE cc_start: 0.7921 (m-80) cc_final: 0.7043 (m-80) REVERT: e 164 GLU cc_start: 0.8149 (tp30) cc_final: 0.7884 (tm-30) REVERT: f 74 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7870 (ptt) REVERT: f 106 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7911 (mm) REVERT: i 16 MET cc_start: 0.3225 (tpp) cc_final: 0.2577 (tmm) REVERT: j 27 ARG cc_start: 0.7815 (mpt-90) cc_final: 0.7484 (mmm-85) REVERT: j 31 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: j 58 ASN cc_start: 0.7799 (t0) cc_final: 0.6751 (t0) REVERT: j 106 LYS cc_start: 0.8597 (tttt) cc_final: 0.8193 (tttp) REVERT: j 136 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8418 (tm-30) REVERT: l 10 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7350 (tm-30) REVERT: l 14 LYS cc_start: 0.8701 (tptp) cc_final: 0.8390 (tptp) REVERT: l 36 LYS cc_start: 0.6470 (mtpt) cc_final: 0.5866 (pttm) REVERT: m 9 PHE cc_start: 0.6301 (OUTLIER) cc_final: 0.5923 (t80) REVERT: m 68 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: m 73 ILE cc_start: 0.8200 (mt) cc_final: 0.7976 (mt) REVERT: n 71 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7953 (tpt170) REVERT: o 56 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7301 (ptmm) REVERT: o 60 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5899 (mp0) REVERT: o 64 TYR cc_start: 0.6161 (t80) cc_final: 0.5870 (t80) REVERT: p 23 ASP cc_start: 0.8392 (m-30) cc_final: 0.8056 (m-30) REVERT: p 61 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7448 (ttt-90) REVERT: p 62 LYS cc_start: 0.7805 (tttt) cc_final: 0.7116 (tptm) REVERT: q 31 TYR cc_start: 0.7604 (t80) cc_final: 0.7083 (t80) REVERT: r 1 MET cc_start: 0.8461 (tpp) cc_final: 0.7960 (tpp) REVERT: r 40 MET cc_start: 0.5681 (tpt) cc_final: 0.5161 (tpt) REVERT: s 4 ILE cc_start: 0.9003 (mp) cc_final: 0.8416 (tp) REVERT: s 42 LYS cc_start: 0.7475 (ttmt) cc_final: 0.7093 (ttpt) REVERT: s 48 LYS cc_start: 0.8343 (tttp) cc_final: 0.8024 (ttpt) REVERT: s 103 ILE cc_start: 0.8634 (mp) cc_final: 0.8185 (tt) REVERT: t 74 ILE cc_start: 0.7089 (mp) cc_final: 0.6814 (mt) REVERT: u 52 ASN cc_start: 0.6870 (t0) cc_final: 0.6632 (t0) REVERT: v 24 ASN cc_start: 0.7908 (p0) cc_final: 0.7615 (p0) REVERT: x 31 ASN cc_start: 0.8495 (t0) cc_final: 0.7830 (t0) REVERT: x 36 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.6585 (ttp-110) REVERT: y 5 GLU cc_start: 0.8270 (tt0) cc_final: 0.7493 (tt0) REVERT: y 52 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7130 (ttt180) REVERT: z 10 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8085 (mtt90) REVERT: B 11 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8246 (tttm) REVERT: B 16 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7551 (ttm-80) REVERT: E 21 PHE cc_start: 0.6398 (m-80) cc_final: 0.6178 (m-10) REVERT: E 41 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8252 (ttp80) REVERT: G 55 GLU cc_start: 0.8876 (tp30) cc_final: 0.8528 (tp30) REVERT: G 94 ARG cc_start: 0.4702 (OUTLIER) cc_final: 0.2653 (ttt-90) REVERT: G 112 ARG cc_start: 0.9528 (mpt180) cc_final: 0.9160 (mmp80) REVERT: G 117 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7141 (tp30) REVERT: G 168 GLU cc_start: 0.8788 (mp0) cc_final: 0.8275 (mp0) REVERT: H 183 TYR cc_start: 0.7304 (t80) cc_final: 0.6731 (t80) REVERT: H 198 LYS cc_start: 0.7454 (mttt) cc_final: 0.6977 (mttt) REVERT: H 202 PHE cc_start: 0.7380 (t80) cc_final: 0.6477 (t80) REVERT: I 13 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.6993 (tpm170) REVERT: I 61 ARG cc_start: 0.7861 (ttt-90) cc_final: 0.7542 (ttt-90) REVERT: I 62 ARG cc_start: 0.8319 (mpp80) cc_final: 0.7914 (mtm-85) REVERT: I 106 PHE cc_start: 0.8382 (m-80) cc_final: 0.7707 (m-80) REVERT: I 112 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8355 (mt-10) REVERT: I 195 ASN cc_start: 0.8457 (p0) cc_final: 0.8111 (p0) REVERT: I 205 LYS cc_start: 0.6790 (ptpt) cc_final: 0.6588 (ptpt) REVERT: J 127 TYR cc_start: 0.7793 (m-80) cc_final: 0.7368 (m-80) REVERT: K 9 MET cc_start: 0.6156 (ptp) cc_final: 0.5349 (mtm) REVERT: K 11 HIS cc_start: 0.7663 (m-70) cc_final: 0.6987 (m-70) REVERT: K 90 MET cc_start: 0.7080 (mmt) cc_final: 0.6459 (mmt) REVERT: L 10 LYS cc_start: 0.5741 (ptmm) cc_final: 0.5501 (ptmm) REVERT: L 21 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7376 (pp) REVERT: L 39 GLU cc_start: 0.6064 (pp20) cc_final: 0.5184 (pp20) REVERT: L 105 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8946 (mm-30) REVERT: M 30 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7647 (mtmt) REVERT: M 45 ILE cc_start: 0.4296 (OUTLIER) cc_final: 0.4056 (tp) REVERT: M 59 GLU cc_start: 0.7974 (tt0) cc_final: 0.7740 (tm-30) REVERT: N 98 ARG cc_start: 0.4039 (tpm170) cc_final: 0.1162 (tpt-90) REVERT: P 28 ASN cc_start: 0.7272 (t0) cc_final: 0.6818 (m-40) REVERT: Q 58 ASN cc_start: 0.7896 (p0) cc_final: 0.7658 (t0) REVERT: Q 110 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7645 (mmtm) REVERT: R 30 LYS cc_start: 0.7804 (mptt) cc_final: 0.7465 (mptt) REVERT: S 27 LYS cc_start: 0.8080 (pptt) cc_final: 0.7646 (ptmm) REVERT: S 58 ARG cc_start: 0.6344 (tpt170) cc_final: 0.6113 (tpp-160) REVERT: T 30 LEU cc_start: 0.8481 (tp) cc_final: 0.8176 (tp) REVERT: T 49 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.6563 (m-70) REVERT: T 64 LYS cc_start: 0.8059 (mtmm) cc_final: 0.6338 (mmtt) REVERT: V 10 ARG cc_start: 0.7193 (tmt-80) cc_final: 0.6828 (tmt170) REVERT: V 17 GLU cc_start: 0.6952 (tt0) cc_final: 0.6574 (tt0) REVERT: V 72 TRP cc_start: 0.7968 (m-10) cc_final: 0.7261 (m-10) REVERT: W 23 LYS cc_start: 0.7312 (ptpp) cc_final: 0.6476 (ptmt) REVERT: W 42 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8476 (tmm-80) REVERT: W 47 ARG cc_start: 0.7139 (mmp-170) cc_final: 0.6677 (mmt180) REVERT: W 52 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7684 (mtt180) REVERT: W 53 GLN cc_start: 0.6860 (tt0) cc_final: 0.6353 (tp-100) REVERT: Y 19 HIS cc_start: 0.8547 (t-90) cc_final: 0.6994 (t-170) REVERT: Y 54 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8786 (tm-30) REVERT: Z 28 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8808 (mm) outliers start: 417 outliers final: 301 residues processed: 1594 average time/residue: 1.3953 time to fit residues: 3782.9934 Evaluate side-chains 1580 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1266 time to evaluate : 6.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 98 GLU Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 212 VAL Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 363 ILE Chi-restraints excluded: chain 8 residue 369 ASN Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 427 ASP Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 467 ASP Chi-restraints excluded: chain 8 residue 479 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 654 ILE Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 160 TYR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 74 MET Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 91 LYS Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 20 ASP Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 49 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 892 optimal weight: 8.9990 chunk 608 optimal weight: 0.0670 chunk 15 optimal weight: 20.0000 chunk 798 optimal weight: 9.9990 chunk 442 optimal weight: 20.0000 chunk 914 optimal weight: 4.9990 chunk 740 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 547 optimal weight: 5.9990 chunk 962 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 HIS c 148 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 80 ASN t 59 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN Q 28 GLN T 36 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 166258 Z= 0.254 Angle : 0.677 16.851 247967 Z= 0.345 Chirality : 0.039 0.388 31580 Planarity : 0.005 0.080 13864 Dihedral : 23.813 178.163 81278 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.67 % Favored : 88.25 % Rotamer: Outliers : 7.70 % Allowed : 26.86 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.52 (0.09), residues: 6520 helix: -1.84 (0.11), residues: 1714 sheet: -2.51 (0.15), residues: 919 loop : -2.62 (0.09), residues: 3887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP 8 193 HIS 0.014 0.001 HIS X 51 PHE 0.049 0.002 PHE p 19 TYR 0.026 0.002 TYR q 44 ARG 0.014 0.001 ARG S 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1773 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 1356 time to evaluate : 6.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 32 PHE cc_start: 0.6005 (t80) cc_final: 0.5737 (t80) REVERT: 8 50 MET cc_start: 0.6604 (tpp) cc_final: 0.6355 (tpp) REVERT: 8 113 TYR cc_start: 0.7736 (m-80) cc_final: 0.7172 (m-80) REVERT: 8 120 GLN cc_start: 0.6811 (mm110) cc_final: 0.6599 (mm110) REVERT: 8 144 MET cc_start: 0.5883 (tpp) cc_final: 0.5665 (tpp) REVERT: 8 337 ARG cc_start: 0.7353 (tmt170) cc_final: 0.6946 (tpt-90) REVERT: 8 523 TYR cc_start: 0.1692 (OUTLIER) cc_final: 0.1141 (m-10) REVERT: 8 574 MET cc_start: 0.5339 (ttp) cc_final: 0.3677 (ptt) REVERT: 8 682 MET cc_start: 0.1583 (mmt) cc_final: 0.1358 (mmm) REVERT: b 144 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7627 (mt-10) REVERT: b 146 LYS cc_start: 0.7439 (mttt) cc_final: 0.7003 (mmtt) REVERT: b 206 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8328 (pttp) REVERT: b 254 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7807 (mtpt) REVERT: b 268 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7966 (ttp80) REVERT: c 1 MET cc_start: 0.6196 (tmm) cc_final: 0.4915 (ptt) REVERT: c 7 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7900 (ttpp) REVERT: c 89 GLU cc_start: 0.8393 (pm20) cc_final: 0.7874 (pm20) REVERT: c 149 ASN cc_start: 0.9103 (t0) cc_final: 0.8693 (t0) REVERT: c 150 GLN cc_start: 0.8732 (mt0) cc_final: 0.8455 (mt0) REVERT: d 95 LYS cc_start: 0.6611 (tttp) cc_final: 0.6129 (tmtt) REVERT: d 102 ARG cc_start: 0.8004 (mtt180) cc_final: 0.6589 (mtp-110) REVERT: d 188 MET cc_start: 0.7149 (mmp) cc_final: 0.6445 (mmp) REVERT: d 195 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7655 (tm-30) REVERT: e 6 TYR cc_start: 0.8067 (t80) cc_final: 0.7865 (t80) REVERT: e 11 VAL cc_start: 0.7227 (t) cc_final: 0.6757 (p) REVERT: e 16 MET cc_start: 0.7464 (tpp) cc_final: 0.7172 (tpp) REVERT: e 51 ASN cc_start: 0.8440 (m-40) cc_final: 0.8226 (t0) REVERT: e 164 GLU cc_start: 0.8453 (tp30) cc_final: 0.8032 (tm-30) REVERT: f 74 MET cc_start: 0.8236 (ptt) cc_final: 0.7845 (ptt) REVERT: f 106 LEU cc_start: 0.8542 (mm) cc_final: 0.8004 (mm) REVERT: i 16 MET cc_start: 0.3181 (tpp) cc_final: 0.2690 (tmm) REVERT: j 27 ARG cc_start: 0.7730 (mpt-90) cc_final: 0.7461 (mmm-85) REVERT: j 31 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: j 57 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8802 (tp) REVERT: j 106 LYS cc_start: 0.8599 (tttt) cc_final: 0.8174 (tttp) REVERT: j 136 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8397 (tm-30) REVERT: l 10 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7330 (tm-30) REVERT: l 14 LYS cc_start: 0.8730 (tptp) cc_final: 0.8482 (tptp) REVERT: l 36 LYS cc_start: 0.6314 (mtpt) cc_final: 0.5800 (pttm) REVERT: l 112 LEU cc_start: 0.6964 (tp) cc_final: 0.6756 (tp) REVERT: m 9 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.6034 (t80) REVERT: m 62 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8464 (mtmt) REVERT: m 68 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: m 73 ILE cc_start: 0.8232 (mt) cc_final: 0.8006 (mt) REVERT: n 43 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: n 71 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7883 (tpt170) REVERT: o 56 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7292 (pptt) REVERT: o 60 GLU cc_start: 0.6315 (mm-30) cc_final: 0.5749 (mp0) REVERT: o 64 TYR cc_start: 0.6171 (t80) cc_final: 0.5891 (t80) REVERT: p 23 ASP cc_start: 0.8324 (m-30) cc_final: 0.8007 (m-30) REVERT: p 61 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7462 (ttt-90) REVERT: p 62 LYS cc_start: 0.7774 (tttt) cc_final: 0.7119 (tptm) REVERT: q 60 TRP cc_start: 0.8725 (m-10) cc_final: 0.8402 (m-10) REVERT: r 1 MET cc_start: 0.8472 (tpp) cc_final: 0.7885 (tpp) REVERT: s 1 MET cc_start: 0.8114 (tpt) cc_final: 0.7338 (mtp) REVERT: s 9 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6357 (m-70) REVERT: s 48 LYS cc_start: 0.8362 (tttp) cc_final: 0.7741 (tptt) REVERT: s 103 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8178 (tt) REVERT: u 52 ASN cc_start: 0.6852 (t0) cc_final: 0.6618 (t0) REVERT: v 29 ILE cc_start: 0.8376 (tp) cc_final: 0.8107 (tp) REVERT: v 30 ILE cc_start: 0.8419 (mm) cc_final: 0.8150 (mm) REVERT: v 91 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6158 (t80) REVERT: w 73 ARG cc_start: 0.8410 (mmt180) cc_final: 0.7942 (mmt180) REVERT: x 31 ASN cc_start: 0.8349 (t0) cc_final: 0.7700 (t0) REVERT: y 5 GLU cc_start: 0.8212 (tt0) cc_final: 0.7640 (tt0) REVERT: y 52 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7034 (ttt180) REVERT: z 10 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8143 (mtt90) REVERT: B 11 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8226 (tttm) REVERT: B 16 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7573 (ttm-80) REVERT: E 21 PHE cc_start: 0.6529 (m-80) cc_final: 0.6260 (m-10) REVERT: E 41 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8246 (ttp80) REVERT: G 55 GLU cc_start: 0.8853 (tp30) cc_final: 0.8527 (tp30) REVERT: G 94 ARG cc_start: 0.4540 (OUTLIER) cc_final: 0.2666 (ttt90) REVERT: G 112 ARG cc_start: 0.9522 (mpt180) cc_final: 0.9205 (mmp-170) REVERT: G 117 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7136 (tp30) REVERT: G 140 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8395 (mt) REVERT: G 168 GLU cc_start: 0.8796 (mp0) cc_final: 0.8314 (mp0) REVERT: H 183 TYR cc_start: 0.7369 (t80) cc_final: 0.6835 (t80) REVERT: H 198 LYS cc_start: 0.7316 (mttt) cc_final: 0.6829 (mttt) REVERT: H 202 PHE cc_start: 0.7508 (t80) cc_final: 0.6977 (t80) REVERT: I 13 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.6978 (tpm170) REVERT: I 61 ARG cc_start: 0.7864 (ttt-90) cc_final: 0.7631 (ttt-90) REVERT: I 62 ARG cc_start: 0.8293 (mpp80) cc_final: 0.7906 (mtm-85) REVERT: I 106 PHE cc_start: 0.8403 (m-80) cc_final: 0.7682 (m-80) REVERT: I 195 ASN cc_start: 0.8495 (p0) cc_final: 0.8193 (p0) REVERT: I 205 LYS cc_start: 0.6635 (ptpt) cc_final: 0.6420 (ptpt) REVERT: J 127 TYR cc_start: 0.7742 (m-80) cc_final: 0.7363 (m-80) REVERT: K 9 MET cc_start: 0.6247 (ptp) cc_final: 0.5954 (ptp) REVERT: K 11 HIS cc_start: 0.7629 (m-70) cc_final: 0.7007 (m-70) REVERT: K 62 MET cc_start: 0.4441 (OUTLIER) cc_final: 0.4039 (tpp) REVERT: K 90 MET cc_start: 0.7147 (mmt) cc_final: 0.6614 (mmt) REVERT: L 21 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7389 (pp) REVERT: L 105 GLU cc_start: 0.9232 (mm-30) cc_final: 0.9017 (mm-30) REVERT: M 30 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7595 (mtmt) REVERT: M 45 ILE cc_start: 0.4353 (OUTLIER) cc_final: 0.3956 (tp) REVERT: M 59 GLU cc_start: 0.8022 (tt0) cc_final: 0.7762 (tm-30) REVERT: N 74 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8303 (mm-40) REVERT: N 98 ARG cc_start: 0.4004 (tpm170) cc_final: 0.1140 (tpt-90) REVERT: O 37 ARG cc_start: 0.5122 (mmm-85) cc_final: 0.4493 (tpt-90) REVERT: Q 110 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7588 (mmtm) REVERT: S 5 MET cc_start: 0.8164 (mmm) cc_final: 0.7702 (mmt) REVERT: S 27 LYS cc_start: 0.8060 (pptt) cc_final: 0.7552 (ptmm) REVERT: S 58 ARG cc_start: 0.6227 (tpt170) cc_final: 0.5422 (tpp80) REVERT: T 49 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.6524 (m-70) REVERT: T 64 LYS cc_start: 0.8073 (mtmm) cc_final: 0.6338 (mmtt) REVERT: U 18 GLN cc_start: 0.7412 (tt0) cc_final: 0.7017 (tm-30) REVERT: V 10 ARG cc_start: 0.7090 (tmt-80) cc_final: 0.6751 (tmt170) REVERT: V 17 GLU cc_start: 0.6996 (tt0) cc_final: 0.6580 (tt0) REVERT: V 54 ILE cc_start: 0.8342 (mt) cc_final: 0.7953 (mm) REVERT: V 72 TRP cc_start: 0.7945 (m100) cc_final: 0.7304 (m-10) REVERT: W 23 LYS cc_start: 0.7101 (ptpp) cc_final: 0.6430 (ptmt) REVERT: W 42 ARG cc_start: 0.8845 (tmm-80) cc_final: 0.8459 (tmm-80) REVERT: W 47 ARG cc_start: 0.7166 (mmp-170) cc_final: 0.6708 (mmt180) REVERT: W 52 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7644 (mtt180) REVERT: W 53 GLN cc_start: 0.6766 (tt0) cc_final: 0.6299 (tp-100) REVERT: X 39 ILE cc_start: 0.7837 (mp) cc_final: 0.7541 (pt) REVERT: Y 19 HIS cc_start: 0.8083 (t-90) cc_final: 0.7104 (t-90) REVERT: Y 54 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8771 (tm-30) REVERT: Z 28 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8741 (mm) outliers start: 417 outliers final: 322 residues processed: 1607 average time/residue: 1.3913 time to fit residues: 3810.9402 Evaluate side-chains 1616 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1276 time to evaluate : 6.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 363 ILE Chi-restraints excluded: chain 8 residue 369 ASN Chi-restraints excluded: chain 8 residue 395 ASP Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 427 ASP Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 479 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 572 VAL Chi-restraints excluded: chain 8 residue 654 ILE Chi-restraints excluded: chain 8 residue 655 HIS Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain 8 residue 683 GLU Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 160 TYR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 92 HIS Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 44 LYS Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 58 TYR Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 91 LYS Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 91 PHE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 49 CYS Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 53 HIS Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 43 LYS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 189 HIS Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 PHE Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 49 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 15 LYS Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 360 optimal weight: 10.0000 chunk 965 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 629 optimal weight: 7.9990 chunk 264 optimal weight: 30.0000 chunk 1073 optimal weight: 0.0020 chunk 890 optimal weight: 9.9990 chunk 496 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 563 optimal weight: 20.0000 overall best weight: 7.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 655 HIS ** b 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 GLN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 98 ASN ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 166258 Z= 0.370 Angle : 0.815 17.179 247967 Z= 0.407 Chirality : 0.043 0.340 31580 Planarity : 0.006 0.101 13864 Dihedral : 23.975 178.427 81278 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.79 % Favored : 86.10 % Rotamer: Outliers : 8.68 % Allowed : 27.67 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.64 (0.09), residues: 6520 helix: -1.91 (0.11), residues: 1730 sheet: -2.59 (0.15), residues: 926 loop : -2.72 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 96 HIS 0.019 0.002 HIS e 4 PHE 0.035 0.002 PHE p 19 TYR 0.030 0.003 TYR I 75 ARG 0.018 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1780 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 470 poor density : 1310 time to evaluate : 7.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 50 MET cc_start: 0.6595 (tpp) cc_final: 0.6352 (tpp) REVERT: 8 113 TYR cc_start: 0.7746 (m-80) cc_final: 0.7159 (m-80) REVERT: 8 337 ARG cc_start: 0.7469 (tmt170) cc_final: 0.7045 (tpt-90) REVERT: 8 501 VAL cc_start: -0.0335 (OUTLIER) cc_final: -0.0925 (p) REVERT: 8 523 TYR cc_start: 0.1690 (OUTLIER) cc_final: 0.0918 (m-10) REVERT: 8 682 MET cc_start: 0.1469 (mmt) cc_final: 0.1267 (mmm) REVERT: b 206 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8238 (pttp) REVERT: b 254 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7873 (mtpt) REVERT: b 259 ASN cc_start: 0.6917 (p0) cc_final: 0.6300 (p0) REVERT: c 1 MET cc_start: 0.6152 (tmm) cc_final: 0.5189 (ptt) REVERT: c 7 LYS cc_start: 0.8364 (ttpt) cc_final: 0.7918 (ttpp) REVERT: c 149 ASN cc_start: 0.9198 (t0) cc_final: 0.8779 (t0) REVERT: c 150 GLN cc_start: 0.8793 (mt0) cc_final: 0.8541 (mt0) REVERT: d 102 ARG cc_start: 0.7972 (mtt180) cc_final: 0.6680 (mtp-110) REVERT: d 188 MET cc_start: 0.7327 (mmp) cc_final: 0.6537 (mmp) REVERT: d 195 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7796 (tm-30) REVERT: e 6 TYR cc_start: 0.8032 (t80) cc_final: 0.7734 (t80) REVERT: e 51 ASN cc_start: 0.8488 (m-40) cc_final: 0.8271 (t0) REVERT: e 164 GLU cc_start: 0.8487 (tp30) cc_final: 0.8112 (tm-30) REVERT: f 74 MET cc_start: 0.8236 (ptt) cc_final: 0.7874 (ptt) REVERT: f 106 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8112 (mm) REVERT: a 53 ARG cc_start: 0.4596 (OUTLIER) cc_final: 0.4252 (ptt180) REVERT: i 16 MET cc_start: 0.3212 (tpp) cc_final: 0.2825 (tmm) REVERT: j 27 ARG cc_start: 0.7814 (mpt-90) cc_final: 0.7584 (mmm-85) REVERT: j 57 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8829 (tp) REVERT: j 106 LYS cc_start: 0.8637 (tttt) cc_final: 0.8270 (tttp) REVERT: j 136 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8445 (tm-30) REVERT: l 10 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7449 (tm-30) REVERT: l 36 LYS cc_start: 0.6305 (mtpt) cc_final: 0.5878 (pttm) REVERT: m 9 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.6116 (t80) REVERT: m 68 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: m 73 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7977 (mp) REVERT: n 71 ARG cc_start: 0.8361 (mmm160) cc_final: 0.8023 (tpt170) REVERT: o 56 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7417 (pptt) REVERT: o 60 GLU cc_start: 0.6330 (mm-30) cc_final: 0.5943 (mp0) REVERT: p 23 ASP cc_start: 0.8305 (m-30) cc_final: 0.7990 (m-30) REVERT: p 61 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7423 (ttm-80) REVERT: p 62 LYS cc_start: 0.7795 (tttt) cc_final: 0.7198 (tptm) REVERT: r 1 MET cc_start: 0.8488 (tpp) cc_final: 0.7902 (tpp) REVERT: r 37 GLU cc_start: 0.8045 (mp0) cc_final: 0.7723 (mm-30) REVERT: r 40 MET cc_start: 0.5561 (tpt) cc_final: 0.5208 (tpt) REVERT: s 1 MET cc_start: 0.8084 (tpt) cc_final: 0.7187 (mtm) REVERT: s 9 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6498 (m-70) REVERT: s 42 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7185 (ttpt) REVERT: s 48 LYS cc_start: 0.8333 (tttp) cc_final: 0.7948 (ttpt) REVERT: s 82 MET cc_start: 0.7222 (ttm) cc_final: 0.6277 (mtp) REVERT: t 69 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7323 (mmm-85) REVERT: u 8 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6535 (t0) REVERT: u 52 ASN cc_start: 0.6977 (t0) cc_final: 0.6738 (t0) REVERT: v 29 ILE cc_start: 0.8420 (tp) cc_final: 0.8199 (tp) REVERT: v 30 ILE cc_start: 0.8480 (mm) cc_final: 0.8203 (mm) REVERT: v 57 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: v 91 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6134 (t80) REVERT: w 73 ARG cc_start: 0.8387 (mmt180) cc_final: 0.7817 (mmt180) REVERT: x 31 ASN cc_start: 0.8487 (t0) cc_final: 0.7678 (t0) REVERT: y 4 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8810 (mtmm) REVERT: z 10 ARG cc_start: 0.8467 (mtt180) cc_final: 0.7610 (mtt90) REVERT: B 3 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: B 11 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8294 (tttm) REVERT: B 16 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7539 (ttm-80) REVERT: B 47 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6936 (m-10) REVERT: G 55 GLU cc_start: 0.8845 (tp30) cc_final: 0.8004 (tp30) REVERT: G 94 ARG cc_start: 0.4666 (OUTLIER) cc_final: 0.2717 (ttt90) REVERT: G 107 ARG cc_start: 0.9017 (ttp-170) cc_final: 0.8804 (ptm160) REVERT: G 112 ARG cc_start: 0.9519 (mpt180) cc_final: 0.9161 (mmp80) REVERT: G 117 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7134 (tp30) REVERT: H 53 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.5758 (ttm170) REVERT: H 78 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8713 (tmmt) REVERT: H 183 TYR cc_start: 0.7413 (t80) cc_final: 0.6887 (t80) REVERT: H 198 LYS cc_start: 0.7273 (mttt) cc_final: 0.6706 (mttt) REVERT: H 202 PHE cc_start: 0.7418 (t80) cc_final: 0.7088 (t80) REVERT: I 13 ARG cc_start: 0.7815 (tpp-160) cc_final: 0.6944 (tpm170) REVERT: I 32 LYS cc_start: 0.5753 (tptt) cc_final: 0.5038 (tptt) REVERT: I 61 ARG cc_start: 0.7954 (ttt-90) cc_final: 0.7574 (ttt-90) REVERT: I 62 ARG cc_start: 0.8339 (mpp80) cc_final: 0.7943 (mtm-85) REVERT: I 106 PHE cc_start: 0.8400 (m-80) cc_final: 0.7660 (m-80) REVERT: I 195 ASN cc_start: 0.8537 (p0) cc_final: 0.8242 (p0) REVERT: I 205 LYS cc_start: 0.6833 (ptpt) cc_final: 0.6603 (ptpt) REVERT: J 127 TYR cc_start: 0.7826 (m-80) cc_final: 0.7458 (m-80) REVERT: K 11 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7111 (m-70) REVERT: K 90 MET cc_start: 0.7250 (mmt) cc_final: 0.6632 (mmt) REVERT: L 21 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7395 (pp) REVERT: L 105 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8882 (mm-30) REVERT: M 30 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7634 (mtmt) REVERT: M 45 ILE cc_start: 0.4226 (OUTLIER) cc_final: 0.3822 (tp) REVERT: M 59 GLU cc_start: 0.8101 (tt0) cc_final: 0.7718 (tm-30) REVERT: N 74 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8356 (mm-40) REVERT: N 98 ARG cc_start: 0.4184 (tpm170) cc_final: 0.1349 (tpt-90) REVERT: Q 110 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7673 (mmtm) REVERT: S 5 MET cc_start: 0.8752 (mmm) cc_final: 0.8284 (mmt) REVERT: S 27 LYS cc_start: 0.8115 (pptt) cc_final: 0.7711 (ptmm) REVERT: S 58 ARG cc_start: 0.6284 (tpt170) cc_final: 0.5137 (tpp80) REVERT: S 60 ARG cc_start: 0.5675 (mmm160) cc_final: 0.4805 (mmm160) REVERT: T 49 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6546 (m-70) REVERT: T 64 LYS cc_start: 0.8053 (mtmm) cc_final: 0.6328 (mmtt) REVERT: V 17 GLU cc_start: 0.6874 (tt0) cc_final: 0.6578 (tt0) REVERT: V 72 TRP cc_start: 0.8030 (m100) cc_final: 0.7330 (m-10) REVERT: W 23 LYS cc_start: 0.7183 (ptpp) cc_final: 0.6497 (ptmt) REVERT: W 42 ARG cc_start: 0.8878 (tmm-80) cc_final: 0.8454 (tmm-80) REVERT: W 47 ARG cc_start: 0.7214 (mmp-170) cc_final: 0.6705 (mmt90) REVERT: W 51 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6273 (tp40) REVERT: W 52 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7721 (mtt180) REVERT: W 53 GLN cc_start: 0.6844 (tt0) cc_final: 0.6317 (tp-100) REVERT: X 39 ILE cc_start: 0.7947 (mp) cc_final: 0.7630 (pt) REVERT: Y 23 ARG cc_start: 0.8569 (ptp-170) cc_final: 0.8212 (ptp-170) REVERT: Y 54 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8817 (tm-30) REVERT: Z 34 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.4136 (ptp90) outliers start: 470 outliers final: 367 residues processed: 1603 average time/residue: 1.3770 time to fit residues: 3770.3339 Evaluate side-chains 1660 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1270 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 54 GLU Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 222 LEU Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 363 ILE Chi-restraints excluded: chain 8 residue 369 ASN Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 406 LEU Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 427 ASP Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 479 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 612 LEU Chi-restraints excluded: chain 8 residue 654 ILE Chi-restraints excluded: chain 8 residue 655 HIS Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain 8 residue 669 GLN Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 160 TYR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 92 HIS Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 44 LYS Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 58 TYR Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 47 VAL Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 13 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 57 TYR Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 91 PHE Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 53 HIS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 43 LYS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 49 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 15 LYS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 34 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 1034 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 611 optimal weight: 10.0000 chunk 783 optimal weight: 5.9990 chunk 607 optimal weight: 6.9990 chunk 903 optimal weight: 0.0270 chunk 599 optimal weight: 9.9990 chunk 1068 optimal weight: 20.0000 chunk 668 optimal weight: 10.0000 chunk 651 optimal weight: 1.9990 chunk 493 optimal weight: 20.0000 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 655 HIS ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 67 HIS ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 HIS ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 98 ASN ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 166258 Z= 0.263 Angle : 0.700 17.690 247967 Z= 0.355 Chirality : 0.039 0.358 31580 Planarity : 0.005 0.101 13864 Dihedral : 23.958 178.416 81278 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.93 % Favored : 88.01 % Rotamer: Outliers : 8.05 % Allowed : 28.47 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.43 (0.09), residues: 6520 helix: -1.68 (0.11), residues: 1698 sheet: -2.44 (0.15), residues: 920 loop : -2.62 (0.09), residues: 3902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP 8 193 HIS 0.019 0.002 HIS e 4 PHE 0.041 0.002 PHE M 65 TYR 0.031 0.002 TYR I 75 ARG 0.019 0.001 ARG U 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1775 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1339 time to evaluate : 6.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 50 MET cc_start: 0.6564 (tpp) cc_final: 0.6324 (tpp) REVERT: 8 113 TYR cc_start: 0.7765 (m-80) cc_final: 0.7259 (m-80) REVERT: 8 120 GLN cc_start: 0.6594 (mm110) cc_final: 0.6107 (mm-40) REVERT: 8 323 LYS cc_start: 0.8700 (pttp) cc_final: 0.8488 (pttp) REVERT: 8 337 ARG cc_start: 0.7420 (tmt170) cc_final: 0.7023 (tpt-90) REVERT: 8 523 TYR cc_start: 0.1694 (OUTLIER) cc_final: 0.0653 (m-10) REVERT: 8 574 MET cc_start: 0.5294 (ttp) cc_final: 0.3628 (ptt) REVERT: 8 620 GLU cc_start: 0.5526 (mp0) cc_final: 0.5238 (mp0) REVERT: b 144 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7710 (mt-10) REVERT: b 206 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8363 (pttp) REVERT: b 259 ASN cc_start: 0.6720 (p0) cc_final: 0.6103 (p0) REVERT: c 1 MET cc_start: 0.6171 (tmm) cc_final: 0.5259 (ptt) REVERT: c 7 LYS cc_start: 0.8352 (ttpt) cc_final: 0.7942 (ttpp) REVERT: c 149 ASN cc_start: 0.9198 (t0) cc_final: 0.8771 (t0) REVERT: c 150 GLN cc_start: 0.8776 (mt0) cc_final: 0.8336 (mt0) REVERT: d 102 ARG cc_start: 0.7957 (mtt180) cc_final: 0.6664 (mtp-110) REVERT: d 188 MET cc_start: 0.7441 (mmp) cc_final: 0.6594 (mmp) REVERT: d 195 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7770 (tm-30) REVERT: e 16 MET cc_start: 0.7387 (tpp) cc_final: 0.6985 (tpp) REVERT: e 95 MET cc_start: 0.8169 (ppp) cc_final: 0.7604 (ppp) REVERT: e 142 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.3996 (t80) REVERT: e 147 ARG cc_start: 0.7099 (tpm170) cc_final: 0.6130 (tpt170) REVERT: e 164 GLU cc_start: 0.8464 (tp30) cc_final: 0.8050 (tm-30) REVERT: f 74 MET cc_start: 0.8206 (ptt) cc_final: 0.7952 (ptt) REVERT: f 106 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8196 (mm) REVERT: a 53 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.1030 (tpm170) REVERT: i 16 MET cc_start: 0.3301 (tpp) cc_final: 0.2933 (tmm) REVERT: j 27 ARG cc_start: 0.7782 (mpt-90) cc_final: 0.7505 (mmm-85) REVERT: j 57 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8986 (tp) REVERT: j 106 LYS cc_start: 0.8580 (tttt) cc_final: 0.8189 (tttp) REVERT: j 136 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8408 (tm-30) REVERT: l 10 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7641 (tm-30) REVERT: l 14 LYS cc_start: 0.8750 (tptp) cc_final: 0.8494 (tptp) REVERT: l 36 LYS cc_start: 0.6305 (mtpt) cc_final: 0.5782 (pttm) REVERT: l 112 LEU cc_start: 0.6910 (tp) cc_final: 0.6656 (tp) REVERT: m 62 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8508 (mtmt) REVERT: m 68 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: m 119 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5894 (mp) REVERT: n 4 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7382 (tpm170) REVERT: n 71 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7972 (tpt170) REVERT: o 56 LYS cc_start: 0.8301 (mtmm) cc_final: 0.7629 (pptt) REVERT: p 23 ASP cc_start: 0.8272 (m-30) cc_final: 0.7999 (m-30) REVERT: p 61 ARG cc_start: 0.7876 (ttt-90) cc_final: 0.7467 (ttt-90) REVERT: p 62 LYS cc_start: 0.7777 (tttt) cc_final: 0.7143 (tptm) REVERT: q 31 TYR cc_start: 0.7610 (t80) cc_final: 0.7073 (t80) REVERT: q 60 TRP cc_start: 0.8731 (m-10) cc_final: 0.8305 (m-10) REVERT: r 1 MET cc_start: 0.8453 (tpp) cc_final: 0.7882 (tpp) REVERT: r 37 GLU cc_start: 0.8089 (mp0) cc_final: 0.7682 (mm-30) REVERT: s 1 MET cc_start: 0.8011 (tpt) cc_final: 0.7280 (mtm) REVERT: s 9 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6395 (m-70) REVERT: s 48 LYS cc_start: 0.8286 (tttp) cc_final: 0.8042 (ttmt) REVERT: s 103 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8148 (tt) REVERT: u 8 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6362 (t0) REVERT: u 52 ASN cc_start: 0.6876 (t0) cc_final: 0.6645 (t0) REVERT: v 29 ILE cc_start: 0.8390 (tp) cc_final: 0.8151 (tp) REVERT: v 30 ILE cc_start: 0.8473 (mm) cc_final: 0.8206 (mm) REVERT: v 91 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6174 (t80) REVERT: w 73 ARG cc_start: 0.8074 (mmt180) cc_final: 0.7757 (mmt180) REVERT: z 10 ARG cc_start: 0.8473 (mtt180) cc_final: 0.8197 (mtt90) REVERT: B 3 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: B 11 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8245 (tmtt) REVERT: B 16 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7610 (ttm-80) REVERT: E 21 PHE cc_start: 0.6580 (m-80) cc_final: 0.6165 (m-10) REVERT: E 61 LEU cc_start: 0.8916 (tt) cc_final: 0.8682 (pp) REVERT: G 21 TYR cc_start: 0.7127 (p90) cc_final: 0.6815 (p90) REVERT: G 94 ARG cc_start: 0.4418 (OUTLIER) cc_final: 0.2655 (ttt90) REVERT: G 112 ARG cc_start: 0.9512 (mpt180) cc_final: 0.9207 (mmp-170) REVERT: G 117 GLU cc_start: 0.8624 (mt-10) cc_final: 0.7195 (tp30) REVERT: G 153 MET cc_start: 0.5636 (tmm) cc_final: 0.4769 (tmm) REVERT: H 53 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5791 (ttm170) REVERT: H 183 TYR cc_start: 0.7478 (t80) cc_final: 0.7005 (t80) REVERT: H 198 LYS cc_start: 0.7255 (mttt) cc_final: 0.6835 (mttt) REVERT: I 13 ARG cc_start: 0.7785 (tpp-160) cc_final: 0.6975 (tpm170) REVERT: I 32 LYS cc_start: 0.5818 (tptt) cc_final: 0.5103 (tptt) REVERT: I 62 ARG cc_start: 0.8262 (mpp80) cc_final: 0.7874 (mtm-85) REVERT: I 106 PHE cc_start: 0.8360 (m-80) cc_final: 0.7931 (m-80) REVERT: I 115 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7676 (mm-40) REVERT: I 145 ARG cc_start: 0.6955 (mmm-85) cc_final: 0.6525 (mmm-85) REVERT: I 195 ASN cc_start: 0.8509 (p0) cc_final: 0.8198 (p0) REVERT: I 205 LYS cc_start: 0.6736 (ptpt) cc_final: 0.6466 (ptpt) REVERT: J 127 TYR cc_start: 0.7719 (m-80) cc_final: 0.7416 (m-80) REVERT: K 9 MET cc_start: 0.6252 (ptp) cc_final: 0.5885 (ptp) REVERT: K 11 HIS cc_start: 0.7663 (m-70) cc_final: 0.7137 (m-70) REVERT: K 62 MET cc_start: 0.4213 (OUTLIER) cc_final: 0.3871 (tpp) REVERT: K 90 MET cc_start: 0.7177 (mmt) cc_final: 0.6635 (mmt) REVERT: L 21 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7383 (pp) REVERT: L 105 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8995 (mm-30) REVERT: M 30 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7661 (mtmt) REVERT: M 45 ILE cc_start: 0.4291 (OUTLIER) cc_final: 0.3879 (tp) REVERT: N 74 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8272 (mm-40) REVERT: N 98 ARG cc_start: 0.4129 (tpm170) cc_final: 0.1282 (tpt-90) REVERT: Q 110 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7684 (mmtm) REVERT: S 5 MET cc_start: 0.8688 (mmm) cc_final: 0.8226 (mmt) REVERT: S 27 LYS cc_start: 0.8028 (pptt) cc_final: 0.7524 (ptmm) REVERT: S 58 ARG cc_start: 0.6317 (tpt170) cc_final: 0.5937 (tpp-160) REVERT: T 30 LEU cc_start: 0.8445 (tp) cc_final: 0.8019 (tp) REVERT: T 49 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.6588 (m-70) REVERT: T 64 LYS cc_start: 0.8012 (mtmm) cc_final: 0.6294 (mmtt) REVERT: U 18 GLN cc_start: 0.7426 (tt0) cc_final: 0.7063 (tm-30) REVERT: U 63 GLN cc_start: 0.8067 (mt0) cc_final: 0.7714 (tt0) REVERT: V 10 ARG cc_start: 0.7009 (tmt-80) cc_final: 0.6677 (tmt170) REVERT: V 17 GLU cc_start: 0.7005 (tt0) cc_final: 0.6649 (tt0) REVERT: V 54 ILE cc_start: 0.8369 (mt) cc_final: 0.7956 (mm) REVERT: V 72 TRP cc_start: 0.7995 (m100) cc_final: 0.7282 (m-10) REVERT: W 23 LYS cc_start: 0.7122 (ptpp) cc_final: 0.6439 (ptmt) REVERT: W 42 ARG cc_start: 0.8871 (tmm-80) cc_final: 0.8507 (tmm-80) REVERT: W 47 ARG cc_start: 0.7188 (mmp-170) cc_final: 0.6648 (mmt180) REVERT: W 51 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6106 (tp40) REVERT: W 52 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7630 (mtt180) REVERT: W 53 GLN cc_start: 0.6766 (tt0) cc_final: 0.6278 (tp-100) REVERT: X 39 ILE cc_start: 0.7870 (mp) cc_final: 0.7588 (pt) REVERT: Y 19 HIS cc_start: 0.8227 (t-90) cc_final: 0.7412 (t-90) REVERT: Y 23 ARG cc_start: 0.8707 (ptp-170) cc_final: 0.8238 (mtm180) REVERT: Y 54 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8786 (tm-30) outliers start: 436 outliers final: 362 residues processed: 1598 average time/residue: 1.3894 time to fit residues: 3812.4675 Evaluate side-chains 1655 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 1273 time to evaluate : 6.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 72 TRP Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 212 VAL Chi-restraints excluded: chain 8 residue 222 LEU Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 363 ILE Chi-restraints excluded: chain 8 residue 369 ASN Chi-restraints excluded: chain 8 residue 395 ASP Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 406 LEU Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 427 ASP Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 479 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 654 ILE Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 160 TYR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 92 HIS Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 134 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 44 LYS Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 58 TYR Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 27 SER Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 13 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 91 PHE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 49 CYS Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 43 LYS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 49 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 15 LYS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 661 optimal weight: 7.9990 chunk 426 optimal weight: 10.0000 chunk 638 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 679 optimal weight: 7.9990 chunk 728 optimal weight: 3.9990 chunk 528 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 840 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 219 HIS ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 67 HIS ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 98 ASN ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 166258 Z= 0.290 Angle : 0.729 18.521 247967 Z= 0.368 Chirality : 0.040 0.329 31580 Planarity : 0.006 0.136 13864 Dihedral : 23.988 178.365 81278 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.07 % Favored : 86.89 % Rotamer: Outliers : 8.10 % Allowed : 28.84 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.44 (0.09), residues: 6520 helix: -1.67 (0.11), residues: 1718 sheet: -2.45 (0.15), residues: 935 loop : -2.63 (0.09), residues: 3867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP 8 193 HIS 0.055 0.002 HIS e 4 PHE 0.036 0.002 PHE M 65 TYR 0.032 0.002 TYR I 75 ARG 0.017 0.001 ARG R 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 439 poor density : 1307 time to evaluate : 6.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 50 MET cc_start: 0.6516 (tpp) cc_final: 0.6289 (tpp) REVERT: 8 113 TYR cc_start: 0.7800 (m-80) cc_final: 0.7238 (m-80) REVERT: 8 120 GLN cc_start: 0.6669 (mm110) cc_final: 0.6161 (mm110) REVERT: 8 337 ARG cc_start: 0.7400 (tmt170) cc_final: 0.7043 (tpt-90) REVERT: 8 523 TYR cc_start: 0.0927 (OUTLIER) cc_final: 0.0368 (m-10) REVERT: 8 620 GLU cc_start: 0.5758 (mp0) cc_final: 0.5264 (mp0) REVERT: b 144 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7723 (mt-10) REVERT: b 206 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8358 (pttp) REVERT: b 254 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7857 (mtpt) REVERT: c 1 MET cc_start: 0.6275 (tmm) cc_final: 0.5448 (ptt) REVERT: c 7 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7904 (ttpp) REVERT: c 74 GLU cc_start: 0.7443 (tp30) cc_final: 0.7240 (tp30) REVERT: c 149 ASN cc_start: 0.9207 (t0) cc_final: 0.8828 (t0) REVERT: c 150 GLN cc_start: 0.8748 (mt0) cc_final: 0.8327 (mt0) REVERT: d 188 MET cc_start: 0.7385 (mmp) cc_final: 0.6524 (mmp) REVERT: d 195 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7807 (tm-30) REVERT: e 16 MET cc_start: 0.7532 (tpp) cc_final: 0.7082 (tpp) REVERT: e 37 MET cc_start: 0.6742 (mtp) cc_final: 0.6135 (mtp) REVERT: e 51 ASN cc_start: 0.8522 (t0) cc_final: 0.8288 (t0) REVERT: e 95 MET cc_start: 0.7969 (ppp) cc_final: 0.7551 (ppp) REVERT: e 142 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.3916 (t80) REVERT: e 147 ARG cc_start: 0.7138 (tpm170) cc_final: 0.6140 (tpt170) REVERT: e 164 GLU cc_start: 0.8462 (tp30) cc_final: 0.8062 (tm-30) REVERT: f 34 ARG cc_start: 0.7996 (mmt180) cc_final: 0.7224 (mtp85) REVERT: f 106 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8260 (mm) REVERT: a 53 ARG cc_start: 0.4604 (OUTLIER) cc_final: 0.1093 (tpm170) REVERT: j 27 ARG cc_start: 0.7794 (mpt-90) cc_final: 0.7563 (mmm-85) REVERT: j 52 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8175 (p0) REVERT: j 57 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8958 (tp) REVERT: j 106 LYS cc_start: 0.8579 (tttt) cc_final: 0.8180 (tttp) REVERT: j 136 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8413 (tm-30) REVERT: l 10 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7447 (tm-30) REVERT: l 14 LYS cc_start: 0.8748 (tptp) cc_final: 0.8462 (tptp) REVERT: l 36 LYS cc_start: 0.6322 (mtpt) cc_final: 0.5790 (pttm) REVERT: l 112 LEU cc_start: 0.6912 (tp) cc_final: 0.6615 (tp) REVERT: m 62 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8356 (mtmt) REVERT: m 68 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: n 71 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7952 (tpt170) REVERT: n 73 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7531 (t0) REVERT: o 56 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7276 (ptmm) REVERT: o 60 GLU cc_start: 0.6259 (mm-30) cc_final: 0.5823 (mp0) REVERT: p 23 ASP cc_start: 0.8292 (m-30) cc_final: 0.8002 (m-30) REVERT: p 61 ARG cc_start: 0.7889 (ttt-90) cc_final: 0.7426 (ttm-80) REVERT: p 62 LYS cc_start: 0.7762 (tttt) cc_final: 0.7112 (tptm) REVERT: q 60 TRP cc_start: 0.8753 (m-10) cc_final: 0.8265 (m-10) REVERT: r 1 MET cc_start: 0.8445 (tpp) cc_final: 0.7872 (tpp) REVERT: r 31 GLU cc_start: 0.7545 (tp30) cc_final: 0.6950 (pt0) REVERT: r 37 GLU cc_start: 0.8077 (mp0) cc_final: 0.7697 (mm-30) REVERT: s 1 MET cc_start: 0.7999 (tpt) cc_final: 0.7397 (mtp) REVERT: s 9 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6393 (m-70) REVERT: s 48 LYS cc_start: 0.8346 (tttp) cc_final: 0.7782 (tptt) REVERT: s 103 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8124 (tt) REVERT: u 8 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6449 (t0) REVERT: u 52 ASN cc_start: 0.6891 (t0) cc_final: 0.6661 (t0) REVERT: v 29 ILE cc_start: 0.8401 (tp) cc_final: 0.8164 (tp) REVERT: v 30 ILE cc_start: 0.8475 (mm) cc_final: 0.8207 (mm) REVERT: v 91 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6199 (t80) REVERT: w 73 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7721 (mmt180) REVERT: x 9 LYS cc_start: 0.8877 (ttpp) cc_final: 0.8387 (ttpp) REVERT: z 10 ARG cc_start: 0.8490 (mtt180) cc_final: 0.8149 (mtt180) REVERT: B 3 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: B 11 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8271 (tttm) REVERT: B 16 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7616 (ttm-80) REVERT: E 21 PHE cc_start: 0.6579 (m-80) cc_final: 0.6218 (m-10) REVERT: G 21 TYR cc_start: 0.7119 (p90) cc_final: 0.6840 (p90) REVERT: G 94 ARG cc_start: 0.4393 (OUTLIER) cc_final: 0.2630 (ttt90) REVERT: G 112 ARG cc_start: 0.9506 (mpt180) cc_final: 0.9125 (mmp-170) REVERT: G 153 MET cc_start: 0.5732 (tmm) cc_final: 0.4903 (tmm) REVERT: H 53 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5879 (ttm170) REVERT: H 183 TYR cc_start: 0.7478 (t80) cc_final: 0.7012 (t80) REVERT: H 198 LYS cc_start: 0.7281 (mttt) cc_final: 0.6850 (mttt) REVERT: I 13 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.6965 (tpm170) REVERT: I 32 LYS cc_start: 0.5875 (tptt) cc_final: 0.5161 (tptt) REVERT: I 61 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7640 (ttt-90) REVERT: I 62 ARG cc_start: 0.8270 (mpp80) cc_final: 0.7885 (mtm-85) REVERT: I 106 PHE cc_start: 0.8363 (m-80) cc_final: 0.7673 (m-80) REVERT: I 115 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7671 (mm-40) REVERT: I 195 ASN cc_start: 0.8514 (p0) cc_final: 0.8208 (p0) REVERT: I 205 LYS cc_start: 0.6750 (ptpt) cc_final: 0.6512 (ptpt) REVERT: J 92 ARG cc_start: 0.6869 (mpt180) cc_final: 0.6640 (mpt180) REVERT: J 127 TYR cc_start: 0.7770 (m-80) cc_final: 0.7430 (m-80) REVERT: K 9 MET cc_start: 0.6293 (ptp) cc_final: 0.5910 (ptp) REVERT: K 11 HIS cc_start: 0.7661 (m-70) cc_final: 0.7122 (m-70) REVERT: K 90 MET cc_start: 0.7169 (mmt) cc_final: 0.6620 (mmt) REVERT: L 21 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7375 (pp) REVERT: L 105 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8995 (mm-30) REVERT: M 30 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7651 (mtmt) REVERT: M 45 ILE cc_start: 0.4354 (OUTLIER) cc_final: 0.3968 (tp) REVERT: N 74 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8269 (mm-40) REVERT: N 98 ARG cc_start: 0.4226 (tpm170) cc_final: 0.1432 (tpt-90) REVERT: Q 110 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7702 (mmtm) REVERT: S 5 MET cc_start: 0.8692 (mmm) cc_final: 0.8251 (mmt) REVERT: S 27 LYS cc_start: 0.8025 (pptt) cc_final: 0.7587 (ptmm) REVERT: S 58 ARG cc_start: 0.6310 (tpt170) cc_final: 0.5969 (tpp-160) REVERT: T 30 LEU cc_start: 0.8419 (tp) cc_final: 0.8006 (tp) REVERT: T 49 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6606 (m-70) REVERT: U 18 GLN cc_start: 0.7404 (tt0) cc_final: 0.7042 (tm-30) REVERT: U 63 GLN cc_start: 0.8083 (mt0) cc_final: 0.7569 (tt0) REVERT: V 17 GLU cc_start: 0.7017 (tt0) cc_final: 0.6639 (tt0) REVERT: V 54 ILE cc_start: 0.8405 (mt) cc_final: 0.8047 (mm) REVERT: V 72 TRP cc_start: 0.7975 (m100) cc_final: 0.7297 (m-10) REVERT: W 23 LYS cc_start: 0.7161 (ptpp) cc_final: 0.6474 (ptmt) REVERT: W 42 ARG cc_start: 0.8875 (tmm-80) cc_final: 0.8504 (tmm-80) REVERT: W 47 ARG cc_start: 0.7165 (mmp-170) cc_final: 0.6649 (mmt180) REVERT: W 51 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6153 (tp40) REVERT: W 52 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7688 (mtt180) REVERT: W 53 GLN cc_start: 0.6772 (tt0) cc_final: 0.6279 (tp-100) REVERT: X 39 ILE cc_start: 0.7886 (mp) cc_final: 0.7595 (pt) REVERT: Y 19 HIS cc_start: 0.8250 (t-90) cc_final: 0.7827 (t-90) REVERT: Y 54 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8788 (tm-30) outliers start: 439 outliers final: 379 residues processed: 1575 average time/residue: 1.3632 time to fit residues: 3669.8394 Evaluate side-chains 1678 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 1279 time to evaluate : 6.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 88 ASP Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 212 VAL Chi-restraints excluded: chain 8 residue 222 LEU Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 363 ILE Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 406 LEU Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 427 ASP Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 479 VAL Chi-restraints excluded: chain 8 residue 499 THR Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 521 ASP Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 606 LYS Chi-restraints excluded: chain 8 residue 635 LEU Chi-restraints excluded: chain 8 residue 654 ILE Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain 8 residue 669 GLN Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 199 HIS Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 92 HIS Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 44 LYS Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 58 TYR Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 27 SER Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 13 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 91 LYS Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 91 PHE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 49 CYS Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 53 HIS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 43 LYS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 49 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 15 LYS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 972 optimal weight: 5.9990 chunk 1024 optimal weight: 6.9990 chunk 934 optimal weight: 8.9990 chunk 996 optimal weight: 9.9990 chunk 1023 optimal weight: 20.0000 chunk 599 optimal weight: 10.0000 chunk 433 optimal weight: 20.0000 chunk 782 optimal weight: 7.9990 chunk 305 optimal weight: 20.0000 chunk 900 optimal weight: 8.9990 chunk 942 optimal weight: 0.0870 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 517 HIS ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 ASN c 67 HIS ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 166258 Z= 0.307 Angle : 0.752 18.453 247967 Z= 0.378 Chirality : 0.041 0.579 31580 Planarity : 0.006 0.100 13864 Dihedral : 24.026 178.499 81278 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.04 % Favored : 86.89 % Rotamer: Outliers : 8.25 % Allowed : 28.93 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.48 (0.09), residues: 6520 helix: -1.68 (0.11), residues: 1717 sheet: -2.51 (0.15), residues: 948 loop : -2.65 (0.09), residues: 3855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP 8 193 HIS 0.017 0.002 HIS e 4 PHE 0.030 0.002 PHE a 180 TYR 0.038 0.002 TYR I 75 ARG 0.014 0.001 ARG M 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1742 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 447 poor density : 1295 time to evaluate : 8.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 50 MET cc_start: 0.6491 (tpp) cc_final: 0.6274 (tpp) REVERT: 8 113 TYR cc_start: 0.7801 (m-80) cc_final: 0.7233 (m-80) REVERT: 8 337 ARG cc_start: 0.7364 (tmt170) cc_final: 0.6988 (tpt-90) REVERT: 8 574 MET cc_start: 0.5341 (ttp) cc_final: 0.3920 (ptt) REVERT: 8 579 HIS cc_start: 0.8179 (t-90) cc_final: 0.7599 (t-90) REVERT: 8 620 GLU cc_start: 0.5802 (mp0) cc_final: 0.5177 (mp0) REVERT: b 144 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7721 (mt-10) REVERT: b 206 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8359 (pttp) REVERT: b 254 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7811 (mtpt) REVERT: c 1 MET cc_start: 0.6255 (tmm) cc_final: 0.5536 (ptm) REVERT: c 7 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7925 (ttpp) REVERT: c 11 MET cc_start: 0.6431 (mmm) cc_final: 0.6228 (mmm) REVERT: c 74 GLU cc_start: 0.7419 (tp30) cc_final: 0.7197 (tp30) REVERT: c 149 ASN cc_start: 0.9236 (t0) cc_final: 0.8794 (t0) REVERT: c 184 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8022 (ptp-170) REVERT: d 188 MET cc_start: 0.7335 (mmp) cc_final: 0.6453 (mmp) REVERT: d 195 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7832 (tm-30) REVERT: e 16 MET cc_start: 0.7616 (tpp) cc_final: 0.7151 (tpp) REVERT: e 26 GLN cc_start: 0.6877 (tt0) cc_final: 0.5891 (tp40) REVERT: e 51 ASN cc_start: 0.8470 (t0) cc_final: 0.8187 (t0) REVERT: e 95 MET cc_start: 0.8012 (ppp) cc_final: 0.7480 (ppp) REVERT: e 142 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.3798 (t80) REVERT: e 147 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6180 (tpt170) REVERT: e 164 GLU cc_start: 0.8483 (tp30) cc_final: 0.8019 (tm-30) REVERT: f 26 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8413 (mmmt) REVERT: f 34 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7257 (mtp85) REVERT: f 74 MET cc_start: 0.8259 (ptt) cc_final: 0.8057 (ptt) REVERT: f 106 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8277 (mm) REVERT: a 53 ARG cc_start: 0.4589 (OUTLIER) cc_final: 0.1105 (tpm170) REVERT: j 27 ARG cc_start: 0.7804 (mpt-90) cc_final: 0.7593 (mmm-85) REVERT: j 52 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8218 (p0) REVERT: j 57 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8958 (tp) REVERT: j 106 LYS cc_start: 0.8587 (tttt) cc_final: 0.8253 (tttp) REVERT: j 136 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8410 (tm-30) REVERT: l 10 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7471 (tm-30) REVERT: l 14 LYS cc_start: 0.8794 (tptp) cc_final: 0.8526 (tptp) REVERT: l 36 LYS cc_start: 0.6377 (mtpt) cc_final: 0.5806 (pttm) REVERT: l 112 LEU cc_start: 0.6930 (tp) cc_final: 0.6623 (tp) REVERT: m 62 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8318 (mtmt) REVERT: m 68 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: n 4 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7379 (tpm170) REVERT: n 71 ARG cc_start: 0.8312 (mmm160) cc_final: 0.7937 (tpt170) REVERT: n 73 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7531 (t0) REVERT: o 56 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7221 (ptmm) REVERT: o 60 GLU cc_start: 0.6257 (mm-30) cc_final: 0.5797 (mp0) REVERT: p 23 ASP cc_start: 0.8302 (m-30) cc_final: 0.8011 (m-30) REVERT: p 61 ARG cc_start: 0.7887 (ttt-90) cc_final: 0.7413 (ttm-80) REVERT: p 62 LYS cc_start: 0.7763 (tttt) cc_final: 0.7114 (tptm) REVERT: q 60 TRP cc_start: 0.8764 (m-10) cc_final: 0.8257 (m-10) REVERT: r 1 MET cc_start: 0.8448 (tpp) cc_final: 0.7879 (tpp) REVERT: r 37 GLU cc_start: 0.8106 (mp0) cc_final: 0.7687 (mm-30) REVERT: s 1 MET cc_start: 0.7972 (tpt) cc_final: 0.7372 (mtp) REVERT: s 9 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6385 (m-70) REVERT: s 103 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8115 (tt) REVERT: t 9 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6506 (mtmm) REVERT: t 68 LYS cc_start: 0.6548 (mmtp) cc_final: 0.5949 (mmtp) REVERT: u 8 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6469 (t0) REVERT: u 52 ASN cc_start: 0.6882 (t0) cc_final: 0.6654 (t0) REVERT: v 29 ILE cc_start: 0.8395 (tp) cc_final: 0.8150 (tp) REVERT: v 30 ILE cc_start: 0.8484 (mm) cc_final: 0.8214 (mm) REVERT: v 91 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6178 (t80) REVERT: w 73 ARG cc_start: 0.8062 (mmt180) cc_final: 0.7711 (mmt180) REVERT: x 9 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8446 (ttpp) REVERT: z 10 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7673 (mtt90) REVERT: B 3 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: B 11 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8268 (tttm) REVERT: B 16 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7619 (ttm-80) REVERT: G 21 TYR cc_start: 0.7186 (p90) cc_final: 0.6940 (p90) REVERT: G 94 ARG cc_start: 0.4431 (OUTLIER) cc_final: 0.2645 (ttt90) REVERT: G 112 ARG cc_start: 0.9334 (mpt180) cc_final: 0.9050 (mmp80) REVERT: G 117 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7200 (tp30) REVERT: H 53 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5910 (ttm170) REVERT: H 183 TYR cc_start: 0.7487 (t80) cc_final: 0.7035 (t80) REVERT: H 198 LYS cc_start: 0.7236 (mttt) cc_final: 0.6784 (mttt) REVERT: I 13 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.6951 (tpm170) REVERT: I 32 LYS cc_start: 0.5870 (tptt) cc_final: 0.5183 (tptt) REVERT: I 62 ARG cc_start: 0.8272 (mpp80) cc_final: 0.7890 (mtm-85) REVERT: I 106 PHE cc_start: 0.8408 (m-80) cc_final: 0.7736 (m-80) REVERT: I 195 ASN cc_start: 0.8511 (p0) cc_final: 0.8218 (p0) REVERT: I 205 LYS cc_start: 0.6774 (ptpt) cc_final: 0.6513 (ptpt) REVERT: J 92 ARG cc_start: 0.6925 (mpt180) cc_final: 0.6672 (mpt180) REVERT: J 127 TYR cc_start: 0.7764 (m-80) cc_final: 0.7435 (m-80) REVERT: K 9 MET cc_start: 0.6280 (ptp) cc_final: 0.5918 (ptp) REVERT: K 11 HIS cc_start: 0.7671 (m-70) cc_final: 0.7129 (m-70) REVERT: K 55 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7177 (m-70) REVERT: K 90 MET cc_start: 0.7270 (mmt) cc_final: 0.6737 (mmt) REVERT: L 105 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8997 (mm-30) REVERT: M 30 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7645 (mtpt) REVERT: M 45 ILE cc_start: 0.4367 (OUTLIER) cc_final: 0.3958 (tp) REVERT: N 74 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8294 (mm-40) REVERT: N 98 ARG cc_start: 0.4296 (tpm170) cc_final: 0.1487 (tpt-90) REVERT: Q 110 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7710 (mmtm) REVERT: S 5 MET cc_start: 0.8679 (mmm) cc_final: 0.8253 (mmt) REVERT: S 27 LYS cc_start: 0.8052 (pptt) cc_final: 0.7616 (ptmm) REVERT: S 58 ARG cc_start: 0.6225 (tpt170) cc_final: 0.5875 (tpp-160) REVERT: T 49 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6590 (m-70) REVERT: U 18 GLN cc_start: 0.7432 (tt0) cc_final: 0.7051 (tm-30) REVERT: U 63 GLN cc_start: 0.8104 (mt0) cc_final: 0.7605 (tt0) REVERT: V 17 GLU cc_start: 0.6961 (tt0) cc_final: 0.6600 (tt0) REVERT: V 54 ILE cc_start: 0.8401 (mt) cc_final: 0.8039 (mm) REVERT: V 72 TRP cc_start: 0.7991 (m100) cc_final: 0.7308 (m-10) REVERT: W 23 LYS cc_start: 0.7164 (ptpp) cc_final: 0.6461 (ptmt) REVERT: W 42 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8486 (tmm-80) REVERT: W 47 ARG cc_start: 0.7169 (mmp-170) cc_final: 0.6646 (mmt180) REVERT: W 51 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6113 (tp40) REVERT: W 52 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7619 (mtt180) REVERT: W 53 GLN cc_start: 0.6774 (tt0) cc_final: 0.6284 (tp-100) REVERT: X 39 ILE cc_start: 0.7961 (mp) cc_final: 0.7649 (pt) REVERT: Y 19 HIS cc_start: 0.8271 (t-90) cc_final: 0.8029 (t-90) REVERT: Y 54 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8787 (tm-30) REVERT: Z 34 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.3944 (ptp90) outliers start: 447 outliers final: 389 residues processed: 1573 average time/residue: 1.3477 time to fit residues: 3620.2187 Evaluate side-chains 1683 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 1272 time to evaluate : 6.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 88 ASP Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 126 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 191 ILE Chi-restraints excluded: chain 8 residue 222 LEU Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 363 ILE Chi-restraints excluded: chain 8 residue 369 ASN Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 406 LEU Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 427 ASP Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 479 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 612 LEU Chi-restraints excluded: chain 8 residue 654 ILE Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain 8 residue 669 GLN Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 199 HIS Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 92 HIS Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 134 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 44 LYS Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 58 TYR Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 27 SER Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 13 LEU Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 91 PHE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 49 CYS Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 53 HIS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 43 LYS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 71 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 49 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 15 LYS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 34 ARG Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 992 optimal weight: 6.9990 chunk 654 optimal weight: 30.0000 chunk 1053 optimal weight: 3.9990 chunk 642 optimal weight: 10.0000 chunk 499 optimal weight: 0.0040 chunk 732 optimal weight: 8.9990 chunk 1104 optimal weight: 20.0000 chunk 1016 optimal weight: 0.9980 chunk 879 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 679 optimal weight: 10.0000 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 GLN ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 166258 Z= 0.229 Angle : 0.675 18.705 247967 Z= 0.342 Chirality : 0.038 0.301 31580 Planarity : 0.005 0.114 13864 Dihedral : 23.970 178.392 81278 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.87 % Favored : 88.05 % Rotamer: Outliers : 7.25 % Allowed : 30.09 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.31 (0.10), residues: 6520 helix: -1.48 (0.12), residues: 1698 sheet: -2.49 (0.15), residues: 949 loop : -2.55 (0.09), residues: 3873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 8 193 HIS 0.011 0.001 HIS X 51 PHE 0.030 0.002 PHE a 180 TYR 0.034 0.002 TYR I 75 ARG 0.013 0.001 ARG M 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13040 Ramachandran restraints generated. 6520 Oldfield, 0 Emsley, 6520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 1326 time to evaluate : 6.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 113 TYR cc_start: 0.7793 (m-80) cc_final: 0.7237 (m-80) REVERT: 8 120 GLN cc_start: 0.6540 (mm110) cc_final: 0.6316 (mm-40) REVERT: 8 284 ASP cc_start: 0.7239 (m-30) cc_final: 0.6854 (t0) REVERT: 8 309 ARG cc_start: 0.5697 (mtp180) cc_final: 0.5202 (ptm160) REVERT: 8 337 ARG cc_start: 0.7344 (tmt170) cc_final: 0.6996 (tpt-90) REVERT: 8 425 LYS cc_start: 0.4544 (mmmm) cc_final: 0.4130 (mmtt) REVERT: 8 461 MET cc_start: 0.4225 (tmm) cc_final: 0.3893 (tmm) REVERT: 8 620 GLU cc_start: 0.5657 (mp0) cc_final: 0.5211 (mp0) REVERT: b 141 HIS cc_start: 0.7687 (p90) cc_final: 0.7151 (p90) REVERT: b 144 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7682 (mt-10) REVERT: b 206 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8311 (pttp) REVERT: b 254 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7765 (mtpt) REVERT: b 269 ARG cc_start: 0.6738 (tpt170) cc_final: 0.5937 (tpt90) REVERT: c 1 MET cc_start: 0.6239 (tmm) cc_final: 0.5476 (ptm) REVERT: c 7 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7946 (ttpp) REVERT: c 74 GLU cc_start: 0.7471 (tp30) cc_final: 0.7180 (tp30) REVERT: c 149 ASN cc_start: 0.9167 (t0) cc_final: 0.8786 (t0) REVERT: c 150 GLN cc_start: 0.8692 (mt0) cc_final: 0.8250 (mt0) REVERT: d 95 LYS cc_start: 0.6795 (tttp) cc_final: 0.6336 (tmtt) REVERT: d 188 MET cc_start: 0.7315 (mmp) cc_final: 0.6426 (mmp) REVERT: d 195 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7735 (tm-30) REVERT: e 16 MET cc_start: 0.7707 (tpp) cc_final: 0.7183 (tpp) REVERT: e 26 GLN cc_start: 0.6849 (tt0) cc_final: 0.5848 (tp40) REVERT: e 51 ASN cc_start: 0.8525 (t0) cc_final: 0.8260 (t0) REVERT: e 63 LYS cc_start: 0.7510 (tttt) cc_final: 0.6309 (ptpt) REVERT: e 95 MET cc_start: 0.8055 (ppp) cc_final: 0.7794 (ppp) REVERT: e 142 TYR cc_start: 0.5995 (OUTLIER) cc_final: 0.3631 (t80) REVERT: e 147 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.5936 (tpt170) REVERT: e 164 GLU cc_start: 0.8530 (tp30) cc_final: 0.8060 (tm-30) REVERT: f 34 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7141 (mtp85) REVERT: f 106 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8318 (mm) REVERT: a 53 ARG cc_start: 0.4661 (OUTLIER) cc_final: 0.4248 (ptt180) REVERT: i 16 MET cc_start: 0.3286 (tpp) cc_final: 0.2828 (tmm) REVERT: j 27 ARG cc_start: 0.7754 (mpt-90) cc_final: 0.7554 (mmm-85) REVERT: j 52 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8215 (p0) REVERT: j 57 LEU cc_start: 0.9336 (mt) cc_final: 0.8925 (tp) REVERT: j 106 LYS cc_start: 0.8611 (tttt) cc_final: 0.8240 (tttp) REVERT: j 136 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8399 (tm-30) REVERT: l 10 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7425 (tm-30) REVERT: l 14 LYS cc_start: 0.8759 (tptp) cc_final: 0.8510 (tptp) REVERT: l 36 LYS cc_start: 0.6299 (mtpt) cc_final: 0.5747 (pttm) REVERT: l 112 LEU cc_start: 0.6848 (tp) cc_final: 0.6554 (tp) REVERT: m 62 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8262 (mtmt) REVERT: m 68 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: n 4 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7280 (tpm170) REVERT: n 71 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7904 (tpt170) REVERT: n 73 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7400 (t0) REVERT: o 56 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7501 (ptmm) REVERT: p 23 ASP cc_start: 0.8295 (m-30) cc_final: 0.7984 (m-30) REVERT: p 61 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7517 (ttt-90) REVERT: p 62 LYS cc_start: 0.7778 (tttt) cc_final: 0.7178 (tptm) REVERT: q 60 TRP cc_start: 0.8646 (m-10) cc_final: 0.8244 (m-10) REVERT: r 1 MET cc_start: 0.8444 (tpp) cc_final: 0.7834 (tpp) REVERT: r 31 GLU cc_start: 0.7607 (tp30) cc_final: 0.7250 (pm20) REVERT: r 37 GLU cc_start: 0.8056 (mp0) cc_final: 0.7663 (mm-30) REVERT: s 1 MET cc_start: 0.7991 (tpt) cc_final: 0.7443 (mtp) REVERT: s 9 HIS cc_start: 0.6932 (OUTLIER) cc_final: 0.6257 (m-70) REVERT: s 48 LYS cc_start: 0.8278 (tttp) cc_final: 0.7942 (ttpt) REVERT: t 9 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6398 (mtmm) REVERT: t 68 LYS cc_start: 0.6397 (mmtp) cc_final: 0.5652 (mmtp) REVERT: u 8 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6242 (t0) REVERT: u 52 ASN cc_start: 0.6909 (t0) cc_final: 0.6693 (t0) REVERT: v 29 ILE cc_start: 0.8372 (tp) cc_final: 0.8113 (tp) REVERT: v 30 ILE cc_start: 0.8487 (mm) cc_final: 0.8228 (mm) REVERT: v 91 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6196 (t80) REVERT: w 72 ASN cc_start: 0.8687 (t0) cc_final: 0.7893 (p0) REVERT: w 73 ARG cc_start: 0.7976 (mmt180) cc_final: 0.7693 (mmt180) REVERT: x 9 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8478 (ttpp) REVERT: z 10 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8208 (mtt90) REVERT: B 3 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: B 11 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8257 (tmtt) REVERT: B 16 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7587 (ttm-80) REVERT: G 21 TYR cc_start: 0.7246 (p90) cc_final: 0.6963 (p90) REVERT: G 94 ARG cc_start: 0.4278 (OUTLIER) cc_final: 0.2644 (ttt90) REVERT: G 99 MET cc_start: 0.7598 (ptp) cc_final: 0.7353 (ptp) REVERT: G 112 ARG cc_start: 0.9332 (mpt180) cc_final: 0.9035 (mmp80) REVERT: H 21 TRP cc_start: 0.7236 (p-90) cc_final: 0.6621 (p-90) REVERT: H 53 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5906 (ttm170) REVERT: H 183 TYR cc_start: 0.7496 (t80) cc_final: 0.7057 (t80) REVERT: H 198 LYS cc_start: 0.7283 (mttt) cc_final: 0.6917 (mttt) REVERT: I 13 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.6926 (tpm170) REVERT: I 32 LYS cc_start: 0.5903 (tptt) cc_final: 0.5209 (tptt) REVERT: I 62 ARG cc_start: 0.8265 (mpp80) cc_final: 0.7893 (mtm-85) REVERT: I 106 PHE cc_start: 0.8391 (m-80) cc_final: 0.7685 (m-80) REVERT: I 115 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7494 (mm-40) REVERT: I 195 ASN cc_start: 0.8490 (p0) cc_final: 0.8199 (p0) REVERT: I 205 LYS cc_start: 0.6583 (ptpt) cc_final: 0.6348 (ptpt) REVERT: J 92 ARG cc_start: 0.6907 (mpt180) cc_final: 0.6694 (mpt180) REVERT: J 127 TYR cc_start: 0.7688 (m-80) cc_final: 0.7387 (m-80) REVERT: J 146 MET cc_start: 0.7973 (ptm) cc_final: 0.7668 (ppp) REVERT: K 11 HIS cc_start: 0.7636 (m-70) cc_final: 0.7228 (m-70) REVERT: K 62 MET cc_start: 0.4227 (OUTLIER) cc_final: 0.3827 (tpp) REVERT: K 90 MET cc_start: 0.7269 (mmt) cc_final: 0.6716 (mmt) REVERT: M 30 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7579 (mtpt) REVERT: M 45 ILE cc_start: 0.4188 (OUTLIER) cc_final: 0.3813 (tp) REVERT: N 74 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8290 (mm-40) REVERT: N 98 ARG cc_start: 0.4177 (tpm170) cc_final: 0.1453 (tpt-90) REVERT: O 89 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6124 (ptp90) REVERT: Q 110 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7622 (mmtm) REVERT: S 5 MET cc_start: 0.8633 (mmm) cc_final: 0.8227 (mmt) REVERT: S 27 LYS cc_start: 0.8055 (pptt) cc_final: 0.7606 (ptmm) REVERT: S 58 ARG cc_start: 0.6408 (tpt170) cc_final: 0.6059 (tpp-160) REVERT: S 60 ARG cc_start: 0.4969 (mmm160) cc_final: 0.4246 (mmm-85) REVERT: T 49 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6636 (m-70) REVERT: U 18 GLN cc_start: 0.7385 (tt0) cc_final: 0.7023 (tm-30) REVERT: U 63 GLN cc_start: 0.8200 (mt0) cc_final: 0.7742 (tt0) REVERT: V 5 ARG cc_start: 0.7730 (mmt180) cc_final: 0.7473 (mmt-90) REVERT: V 10 ARG cc_start: 0.7020 (tmt-80) cc_final: 0.6708 (tmt170) REVERT: V 17 GLU cc_start: 0.6862 (tt0) cc_final: 0.6449 (tt0) REVERT: V 42 LYS cc_start: 0.6213 (mtpp) cc_final: 0.5802 (mtpp) REVERT: V 54 ILE cc_start: 0.8365 (mt) cc_final: 0.7943 (mm) REVERT: V 72 TRP cc_start: 0.7962 (m100) cc_final: 0.7229 (m-10) REVERT: W 23 LYS cc_start: 0.7104 (ptpp) cc_final: 0.6840 (mtpt) REVERT: W 42 ARG cc_start: 0.8873 (tmm-80) cc_final: 0.8491 (tmm-80) REVERT: W 47 ARG cc_start: 0.7215 (mmp-170) cc_final: 0.6669 (mmt180) REVERT: W 51 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6099 (tp-100) REVERT: W 52 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7779 (mtt180) REVERT: W 53 GLN cc_start: 0.6716 (tt0) cc_final: 0.6217 (tp-100) REVERT: X 39 ILE cc_start: 0.7865 (mp) cc_final: 0.7564 (pt) REVERT: X 43 MET cc_start: 0.2764 (mmm) cc_final: 0.2403 (mpp) REVERT: Y 19 HIS cc_start: 0.8212 (t-90) cc_final: 0.8001 (t-90) REVERT: Y 54 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8777 (tm-30) REVERT: Z 3 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.5968 (tp) outliers start: 393 outliers final: 343 residues processed: 1564 average time/residue: 1.3756 time to fit residues: 3670.6889 Evaluate side-chains 1645 residues out of total 5417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1281 time to evaluate : 6.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 26 THR Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 72 TRP Chi-restraints excluded: chain 8 residue 88 ASP Chi-restraints excluded: chain 8 residue 112 VAL Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 151 PHE Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 191 ILE Chi-restraints excluded: chain 8 residue 212 VAL Chi-restraints excluded: chain 8 residue 222 LEU Chi-restraints excluded: chain 8 residue 279 LEU Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 404 ILE Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 424 THR Chi-restraints excluded: chain 8 residue 427 ASP Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 544 VAL Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 586 VAL Chi-restraints excluded: chain 8 residue 612 LEU Chi-restraints excluded: chain 8 residue 635 LEU Chi-restraints excluded: chain 8 residue 654 ILE Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain 8 residue 683 GLU Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 206 LYS Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 92 HIS Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 78 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 128 HIS Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 180 PHE Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 44 LYS Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 105 VAL Chi-restraints excluded: chain j residue 132 HIS Chi-restraints excluded: chain j residue 141 ASP Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 78 ARG Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 58 TYR Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 27 SER Chi-restraints excluded: chain m residue 68 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain p residue 99 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 68 ASP Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 28 ASN Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 59 ASN Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ASP Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 26 ASN Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 2 PHE Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 91 PHE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 49 CYS Chi-restraints excluded: chain w residue 52 ASP Chi-restraints excluded: chain w residue 53 HIS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 58 ILE Chi-restraints excluded: chain x residue 59 ASP Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 24 LEU Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 89 ARG Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 49 HIS Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 15 LYS Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 3 ILE Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1109 random chunks: chunk 539 optimal weight: 0.5980 chunk 698 optimal weight: 0.0040 chunk 937 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 811 optimal weight: 40.0000 chunk 129 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 881 optimal weight: 6.9990 chunk 368 optimal weight: 40.0000 chunk 904 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 overall best weight: 5.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 67 HIS ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.158879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132963 restraints weight = 391163.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.135884 restraints weight = 150222.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.136611 restraints weight = 87266.679| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 166258 Z= 0.284 Angle : 0.725 19.388 247967 Z= 0.364 Chirality : 0.039 0.308 31580 Planarity : 0.005 0.083 13864 Dihedral : 24.003 178.155 81278 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.87 % Favored : 87.06 % Rotamer: Outliers : 7.33 % Allowed : 30.13 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.31 (0.10), residues: 6520 helix: -1.49 (0.12), residues: 1695 sheet: -2.48 (0.15), residues: 953 loop : -2.54 (0.09), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 8 193 HIS 0.014 0.002 HIS X 51 PHE 0.035 0.002 PHE E 21 TYR 0.044 0.002 TYR 8 490 ARG 0.013 0.001 ARG Y 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49556.50 seconds wall clock time: 863 minutes 32.47 seconds (51812.47 seconds total)