Starting phenix.real_space_refine on Sat Mar 2 04:26:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st7_25421/03_2024/7st7_25421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st7_25421/03_2024/7st7_25421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st7_25421/03_2024/7st7_25421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st7_25421/03_2024/7st7_25421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st7_25421/03_2024/7st7_25421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st7_25421/03_2024/7st7_25421_updated.pdb" } resolution = 3.2 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= 0.009 sd= 1.134 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 4732 5.49 5 S 178 5.16 5 C 77856 2.51 5 N 28531 2.21 5 O 42259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 120": "OD1" <-> "OD2" Residue "b GLU 144": "OE1" <-> "OE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 30": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 74": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 99": "OE1" <-> "OE2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 16": "OE1" <-> "OE2" 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 GLU 51": "OE1" <-> "OE2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ASP 91": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 145": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 31": "OE1" <-> "OE2" Residue "e ASP 50": "OD1" <-> "OD2" Residue "e ASP 55": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 122": "OD1" <-> "OD2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 164": "OE1" <-> "OE2" Residue "e ASP 173": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ASP 165": "OD1" <-> "OD2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 55": "OE1" <-> "OE2" Residue "g GLU 76": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 98": "OD1" <-> "OD2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 179": "OD1" <-> "OD2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 63": "OD1" <-> "OD2" Residue "i GLU 140": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 80": "OD1" <-> "OD2" 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 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 86": "OE1" <-> "OE2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ASP 25": "OD1" <-> "OD2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ASP 70": "OD1" <-> "OD2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" 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 ASP 58": "OD1" <-> "OD2" 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 ARG 96": "NH1" <-> "NH2" Residue "n ASP 117": "OD1" <-> "OD2" 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 ARG 81": "NH1" <-> "NH2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 26": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" 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 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r GLU 46": "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 GLU 2": "OE1" <-> "OE2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" 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 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 17": "OD1" <-> "OD2" Residue "u PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 80": "OD1" <-> "OD2" 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 GLU 11": "OE1" <-> "OE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 43": "OD1" <-> "OD2" Residue "v ASP 66": "OD1" <-> "OD2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "w PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 40": "OE1" <-> "OE2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "x GLU 69": "OE1" <-> "OE2" Residue "x TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 24": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" 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 ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "N PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "R ASP 53": "OD1" <-> "OD2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S GLU 25": "OE1" <-> "OE2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "X PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "G TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "P ASP 17": "OD1" <-> "OD2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "T ASP 17": "OD1" <-> "OD2" Residue "T PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "Y GLU 14": "OE1" <-> "OE2" Residue "Y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "8 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 184": "OD1" <-> "OD2" Residue "8 ASP 195": "OD1" <-> "OD2" Residue "8 GLU 247": "OE1" <-> "OE2" Residue "8 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 291": "OD1" <-> "OD2" Residue "8 PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 347": "OD1" <-> "OD2" Residue "8 ARG 359": "NH1" <-> "NH2" Residue "8 ARG 362": "NH1" <-> "NH2" Residue "8 GLU 372": "OE1" <-> "OE2" Residue "8 GLU 376": "OE1" <-> "OE2" Residue "8 ASP 381": "OD1" <-> "OD2" Residue "8 GLU 410": "OE1" <-> "OE2" Residue "8 GLU 413": "OE1" <-> "OE2" Residue "8 ASP 500": "OD1" <-> "OD2" Residue "8 TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 539": "OD1" <-> "OD2" Residue "8 PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 603": "OE1" <-> "OE2" Residue "8 GLU 620": "OE1" <-> "OE2" Residue "8 ASP 630": "OD1" <-> "OD2" Residue "8 ASP 688": "OD1" <-> "OD2" Residue "8 GLU 689": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153556 Number of models: 1 Model: "" Number of chains: 60 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': 232, 'rna2p_pyr': 112, 'rna3p_pur': 1442, 'rna3p_pyr': 1117} Link IDs: {'rna2p': 344, 'rna3p': 2558} 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: "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: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} 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: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: "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: "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: "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: "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: "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: "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': 99, 'rna2p_pyr': 56, 'rna3p_pur': 775, 'rna3p_pyr': 609} Link IDs: {'rna2p': 155, 'rna3p': 1383} 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: "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: "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: "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: "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: "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: "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: 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: "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: "5" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 30, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "h" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'5OH:plan-2': 1, 'UAL:plan-2': 1, 'DPP:plan-1': 1} Unresolved non-hydrogen planarities: 3 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: 57.32, per 1000 atoms: 0.37 Number of scatterers: 153556 At special positions: 0 Unit cell: (269.7, 252.3, 243.6, 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 4732 15.00 O 42259 8.00 N 28531 7.00 C 77856 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=2.18 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 56.90 Conformation dependent library (CDL) restraints added in 8.1 seconds 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB KBE h 1 " pdb=" CB UAL h 5 " Number of C-beta restraints generated: 12220 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: 194 helices and 83 sheets defined 37.7% alpha, 18.9% beta 961 base pairs and 2749 stacking pairs defined. Time for finding SS restraints: 73.87 Creating SS restraints... Processing helix chain 'b' and resid 9 through 16 removed outlier: 7.607A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 removed outlier: 3.823A 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: 4.225A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.712A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 220 through 225' Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.028A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 267' Processing helix chain 'b' and resid 196 through 201 removed outlier: 4.320A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.701A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 105 removed outlier: 4.580A pdb=" N VAL c 104 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LYS c 105 " --> pdb=" O PHE c 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 100 through 105' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 removed outlier: 4.091A pdb=" N PHE d 19 " --> pdb=" O SER d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.608A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 53 removed outlier: 6.240A pdb=" N THR d 53 " --> pdb=" O ARG d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.507A pdb=" N ARG d 102 " --> pdb=" O LYS d 98 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.572A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA d 142 " --> pdb=" O LEU d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 4.233A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.556A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.601A pdb=" N GLN d 195 " --> pdb=" O ASP d 191 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 4.616A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 61 removed outlier: 3.735A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA e 54 " --> pdb=" O ASP e 50 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP e 55 " --> pdb=" O ASN e 51 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 3.989A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.337A 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 161 through 173 Processing helix chain 'e' and resid 133 through 138 removed outlier: 3.692A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE e 137 " --> pdb=" O GLN e 134 " (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 'f' and resid 1 through 7 Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.774A pdb=" N GLY f 65 " --> pdb=" O TRP f 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR f 66 " --> pdb=" O ALA f 62 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU f 71 " --> pdb=" O ALA f 67 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.578A pdb=" N ILE f 140 " --> pdb=" O ASP f 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.540A pdb=" N ASN g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.681A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 74 removed outlier: 3.789A pdb=" N GLU g 55 " --> pdb=" O ARG g 51 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU g 70 " --> pdb=" O ASN g 66 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA g 74 " --> pdb=" O GLU g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.685A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 3.995A pdb=" N VAL g 115 " --> pdb=" O ALA g 111 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ARG g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 111 through 116' Processing helix chain 'a' and resid 6 through 16 removed outlier: 3.876A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 34 removed outlier: 5.049A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU a 29 " --> pdb=" O GLU a 25 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.936A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA a 191 " --> pdb=" O GLU a 187 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU a 192 " --> pdb=" O ASN a 188 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 31 Proline residue: i 25 - end of helix removed outlier: 4.174A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 45 removed outlier: 3.657A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 84 removed outlier: 3.669A pdb=" N LEU i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 116 removed outlier: 3.580A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN i 110 " --> pdb=" O GLN i 106 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP i 115 " --> pdb=" O THR i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.678A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY i 136 " --> pdb=" O ALA i 132 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.889A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.568A pdb=" N ALA j 94 " --> pdb=" O GLU j 90 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.325A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA j 104 " --> pdb=" O VAL j 100 " (cutoff:3.500A) removed outlier: 4.596A 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: 3.525A pdb=" N ALA j 117 " --> pdb=" O PRO j 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE j 119 " --> pdb=" O GLY j 115 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 120 removed outlier: 5.720A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU k 118 " --> pdb=" O LYS k 114 " (cutoff:3.500A) Proline residue: k 120 - end of helix Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.808A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 3.977A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.033A 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: 3.740A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.747A 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 91 through 99 removed outlier: 4.972A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 4.108A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA l 134 " --> pdb=" O GLY l 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.580A pdb=" N ARG m 50 " --> pdb=" O ILE m 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.799A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.505A pdb=" N ARG n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY n 26 " --> pdb=" O ARG n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 58 removed outlier: 4.487A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.502A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.528A pdb=" N LEU n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 4.158A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU n 82 " --> pdb=" O LYS n 78 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 5.730A 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 20 removed outlier: 4.814A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 62 removed outlier: 3.626A pdb=" N GLU o 60 " --> pdb=" O LYS o 56 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.824A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 1 through 13 removed outlier: 3.632A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN p 9 " --> pdb=" O LYS p 5 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET p 12 " --> pdb=" O GLU p 8 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.517A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 103' Processing helix chain 'q' and resid 6 through 21 removed outlier: 3.787A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.062A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 60 removed outlier: 4.107A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 72 removed outlier: 3.617A pdb=" N ALA q 66 " --> pdb=" O ALA q 62 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.556A pdb=" N ALA q 85 " --> pdb=" O GLY q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.767A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.848A pdb=" N ALA q 107 " --> pdb=" O VAL q 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU q 108 " --> pdb=" O ALA q 104 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.724A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 4.229A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR s 37 " --> pdb=" O LEU s 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.888A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 11 removed outlier: 3.552A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 Processing helix chain 't' and resid 39 through 50 removed outlier: 3.508A pdb=" N LYS t 44 " --> pdb=" O LYS t 40 " (cutoff:3.500A) Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.763A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 4.899A 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: 3.635A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 52 removed outlier: 3.942A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 59 removed outlier: 4.535A pdb=" N TYR v 57 " --> pdb=" O LYS v 53 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU v 59 " --> pdb=" O GLU v 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 3.646A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE x 58 " --> pdb=" O GLY x 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 removed outlier: 3.529A pdb=" N ARG x 71 " --> pdb=" O LEU x 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 1 through 9 removed outlier: 3.931A pdb=" N GLU y 5 " --> pdb=" O MET y 1 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LYS y 9 " --> pdb=" O GLU y 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 1 through 9' Processing helix chain 'y' and resid 10 through 35 removed outlier: 3.780A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 61 removed outlier: 3.945A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN y 45 " --> pdb=" O HIS y 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG y 47 " --> pdb=" O LEU y 43 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 removed outlier: 3.587A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.656A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 removed outlier: 4.712A pdb=" N PHE A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.739A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.567A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 3.570A pdb=" N ARG D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.515A pdb=" N LYS D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.718A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 5.212A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 4.936A 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 45 removed outlier: 3.837A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.922A pdb=" N LEU E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.948A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.601A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.551A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.754A pdb=" N LYS H 85 " --> pdb=" O GLU H 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.609A pdb=" N ASP H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ALA H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 112' Processing helix chain 'H' and resid 113 through 126 removed outlier: 3.746A pdb=" N SER H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.692A pdb=" N LYS H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.819A pdb=" N ALA L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 53 removed outlier: 4.030A pdb=" N ALA L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN L 51 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 69 removed outlier: 4.461A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 4.292A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.660A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.884A pdb=" N LYS L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU L 138 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 4.180A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 55 removed outlier: 4.514A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.950A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 87 removed outlier: 4.710A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 removed outlier: 4.553A pdb=" N ARG N 94 " --> pdb=" O ASP N 90 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.862A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 4.001A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 21 removed outlier: 4.000A pdb=" N THR R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.618A pdb=" N LYS R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 4.983A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 60 removed outlier: 4.990A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 4.537A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.627A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.646A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 33 removed outlier: 3.879A pdb=" N ILE S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE S 30 " --> pdb=" O LEU S 26 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASP S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL S 33 " --> pdb=" O ILE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.640A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN S 42 " --> pdb=" O GLU S 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.725A 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 55 through 60 removed outlier: 3.559A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 55 through 60' Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.725A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.510A pdb=" N LEU X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY X 25 " --> pdb=" O ALA X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.884A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'G' and resid 42 through 63 Proline residue: G 47 - end of helix removed outlier: 3.635A pdb=" N ALA G 54 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 removed outlier: 5.901A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 4.963A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.681A pdb=" N THR G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.967A pdb=" N GLU G 168 " --> pdb=" O ASP G 164 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.726A pdb=" N ALA G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 4.278A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY G 214 " --> pdb=" O THR G 210 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY G 223 " --> pdb=" O THR G 219 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.919A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.592A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.625A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR I 74 " --> pdb=" O GLN I 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR I 75 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 4.084A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.556A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.757A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 5.616A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 204 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.656A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.190A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 removed outlier: 3.545A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 11 through 18 removed outlier: 4.295A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 removed outlier: 3.610A pdb=" N GLU K 23 " --> pdb=" O PRO K 19 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.647A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.682A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.532A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 4.385A 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: 3.909A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.858A 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 77 removed outlier: 3.565A pdb=" N ALA P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 103 removed outlier: 4.137A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.884A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.983A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.615A 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 'T' and resid 3 through 15 removed outlier: 3.576A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 46 removed outlier: 4.727A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE T 42 " --> pdb=" O LEU T 38 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.862A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.533A pdb=" N ILE T 81 " --> pdb=" O TYR T 77 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.937A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.501A pdb=" N ASN U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 17 removed outlier: 6.138A pdb=" N GLU W 15 " --> pdb=" O ARG W 11 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) removed outlier: 4.593A 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 33 removed outlier: 4.332A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 65 removed outlier: 3.760A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER W 65 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 41 removed outlier: 4.781A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA Y 16 " --> pdb=" O GLN Y 12 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 removed outlier: 3.554A pdb=" N GLN Y 54 " --> pdb=" O PHE Y 50 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.573A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Y 61 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 3.692A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA Y 80 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 23 Processing helix chain 'Z' and resid 24 through 33 removed outlier: 4.603A pdb=" N LEU Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Z 31 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.742A pdb=" N LYS Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG Z 46 " --> pdb=" O THR Z 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS Z 57 " --> pdb=" O LYS Z 53 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG Z 61 " --> pdb=" O LYS Z 57 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 35 removed outlier: 3.510A pdb=" N GLU 8 28 " --> pdb=" O THR 8 24 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG 8 29 " --> pdb=" O THR 8 25 " (cutoff:3.500A) Processing helix chain '8' and resid 53 through 60 Processing helix chain '8' and resid 95 through 107 removed outlier: 3.517A pdb=" N SER 8 102 " --> pdb=" O GLU 8 98 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL 8 105 " --> pdb=" O ARG 8 101 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU 8 106 " --> pdb=" O SER 8 102 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP 8 107 " --> pdb=" O MET 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 121 through 134 removed outlier: 4.513A pdb=" N THR 8 125 " --> pdb=" O PRO 8 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL 8 126 " --> pdb=" O GLN 8 122 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR 8 133 " --> pdb=" O GLN 8 129 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 161 removed outlier: 3.695A pdb=" N VAL 8 154 " --> pdb=" O ASN 8 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL 8 155 " --> pdb=" O PHE 8 151 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN 8 156 " --> pdb=" O LEU 8 152 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 8 159 " --> pdb=" O VAL 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 208 through 231 removed outlier: 3.676A pdb=" N VAL 8 212 " --> pdb=" O PRO 8 208 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU 8 213 " --> pdb=" O ALA 8 209 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU 8 214 " --> pdb=" O ASP 8 210 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN 8 221 " --> pdb=" O GLU 8 217 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA 8 229 " --> pdb=" O SER 8 225 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER 8 230 " --> pdb=" O ALA 8 226 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU 8 231 " --> pdb=" O ALA 8 227 " (cutoff:3.500A) Processing helix chain '8' and resid 232 through 240 Processing helix chain '8' and resid 244 through 259 removed outlier: 3.591A pdb=" N ARG 8 255 " --> pdb=" O ALA 8 251 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN 8 258 " --> pdb=" O GLN 8 254 " (cutoff:3.500A) Processing helix chain '8' and resid 274 through 285 removed outlier: 3.736A pdb=" N MET 8 278 " --> pdb=" O GLY 8 274 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE 8 283 " --> pdb=" O LEU 8 279 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR 8 285 " --> pdb=" O ALA 8 281 " (cutoff:3.500A) Processing helix chain '8' and resid 424 through 443 removed outlier: 4.469A pdb=" N GLN 8 428 " --> pdb=" O THR 8 424 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU 8 429 " --> pdb=" O LYS 8 425 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYS 8 430 " --> pdb=" O ALA 8 426 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU 8 441 " --> pdb=" O ARG 8 437 " (cutoff:3.500A) removed outlier: 3.749A 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 477 removed outlier: 3.606A pdb=" N ILE 8 469 " --> pdb=" O HIS 8 465 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL 8 470 " --> pdb=" O LEU 8 466 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 8 475 " --> pdb=" O ASP 8 471 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU 8 476 " --> pdb=" O ARG 8 472 " (cutoff:3.500A) Processing helix chain '8' and resid 546 through 562 removed outlier: 4.196A pdb=" N ILE 8 550 " --> pdb=" O PRO 8 546 " (cutoff:3.500A) Proline residue: 8 551 - end of helix removed outlier: 3.527A pdb=" N GLY 8 556 " --> pdb=" O ALA 8 552 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN 8 560 " --> pdb=" O GLY 8 556 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU 8 561 " --> pdb=" O ILE 8 557 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS 8 562 " --> pdb=" O GLN 8 558 " (cutoff:3.500A) Processing helix chain '8' and resid 589 through 609 removed outlier: 3.665A pdb=" N SER 8 598 " --> pdb=" O LYS 8 594 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE 8 599 " --> pdb=" O LEU 8 595 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY 8 604 " --> pdb=" O ALA 8 600 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE 8 605 " --> pdb=" O PHE 8 601 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA 8 608 " --> pdb=" O GLY 8 604 " (cutoff:3.500A) Processing helix chain '8' and resid 627 through 639 removed outlier: 3.598A pdb=" N ARG 8 637 " --> pdb=" O GLY 8 633 " (cutoff:3.500A) Processing helix chain '8' and resid 659 through 664 removed outlier: 4.340A pdb=" N PHE 8 664 " --> pdb=" O LEU 8 660 " (cutoff:3.500A) Processing helix chain '8' and resid 665 through 675 removed outlier: 3.510A pdb=" N ARG 8 671 " --> pdb=" O ALA 8 667 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER 8 672 " --> pdb=" O THR 8 668 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU 8 673 " --> pdb=" O GLN 8 669 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS 8 675 " --> pdb=" O ARG 8 671 " (cutoff:3.500A) Processing helix chain '8' and resid 691 through 699 removed outlier: 3.629A pdb=" N ALA 8 697 " --> pdb=" O ASN 8 693 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL 8 698 " --> pdb=" O VAL 8 694 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE 8 699 " --> pdb=" O ALA 8 695 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 3.587A pdb=" N ARG b 79 " --> pdb=" O LEU b 92 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.294A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.541A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 3 through 7 Processing sheet with id= 6, first strand: chain 'c' and resid 10 through 16 removed outlier: 3.623A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 79 through 83 removed outlier: 6.398A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'd' and resid 166 through 171 removed outlier: 3.678A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'e' and resid 32 through 37 removed outlier: 3.754A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR e 154 " --> pdb=" O THR e 34 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU e 151 " --> pdb=" O VAL e 131 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR e 157 " --> pdb=" O GLY e 125 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLY e 125 " --> pdb=" O THR e 157 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.918A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'f' and resid 14 through 18 removed outlier: 3.602A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY f 30 " --> pdb=" O GLY f 27 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'f' and resid 40 through 44 removed outlier: 3.578A pdb=" N THR f 50 " --> pdb=" O LYS f 43 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'f' and resid 81 through 88 removed outlier: 3.600A pdb=" N LYS f 84 " --> pdb=" O LEU f 132 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE f 130 " --> pdb=" O LEU f 86 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 93 through 97 removed outlier: 3.514A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA f 96 " --> pdb=" O ASN f 103 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'g' and resid 3 through 6 removed outlier: 3.545A pdb=" N ILE g 4 " --> pdb=" O VAL g 37 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'g' and resid 76 through 83 removed outlier: 3.629A pdb=" N VAL g 78 " --> pdb=" O ILE g 143 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL g 147 " --> pdb=" O ILE g 80 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU g 149 " --> pdb=" O SER g 82 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'a' and resid 59 through 64 removed outlier: 7.800A pdb=" N VAL a 59 " --> pdb=" O ASN a 165 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN a 165 " --> pdb=" O VAL a 59 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR a 163 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR a 63 " --> pdb=" O VAL a 161 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'a' and resid 169 through 174 removed outlier: 5.876A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL a 46 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR a 173 " --> pdb=" O VAL a 44 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'i' and resid 7 through 12 removed outlier: 3.711A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL i 56 " --> pdb=" O LEU i 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL i 69 " --> pdb=" O VAL i 57 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'i' and resid 97 through 101 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'j' and resid 52 through 57 removed outlier: 5.238A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'j' and resid 74 through 78 removed outlier: 8.141A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'k' and resid 56 through 60 removed outlier: 4.707A pdb=" N ASP k 56 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS k 21 " --> pdb=" O THR k 6 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'k' and resid 68 through 71 removed outlier: 3.743A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'm' and resid 37 through 40 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'm' and resid 62 through 65 removed outlier: 4.518A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'm' and resid 30 through 36 removed outlier: 7.123A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'n' and resid 33 through 36 removed outlier: 7.019A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL n 116 " --> pdb=" O TYR n 94 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR n 94 " --> pdb=" O VAL n 116 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.576A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'p' and resid 39 through 44 removed outlier: 6.373A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'p' and resid 48 through 51 removed outlier: 3.769A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.736A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'r' and resid 18 through 22 removed outlier: 4.215A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'r' and resid 57 through 60 removed outlier: 6.542A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY r 100 " --> pdb=" O LYS r 60 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'r' and resid 65 through 68 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'r' and resid 71 through 78 removed outlier: 4.200A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 's' and resid 2 through 8 removed outlier: 6.786A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 's' and resid 74 through 88 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 't' and resid 12 through 15 removed outlier: 5.565A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER t 78 " --> pdb=" O GLY t 65 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY t 65 " --> pdb=" O SER t 78 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'u' and resid 39 through 44 removed outlier: 5.072A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'v' and resid 37 through 41 removed outlier: 3.585A pdb=" N ILE v 40 " --> pdb=" O ALA v 28 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE v 29 " --> pdb=" O ILE v 89 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'v' and resid 61 through 64 Processing sheet with id= 43, first strand: chain 'w' and resid 47 through 50 removed outlier: 4.358A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'w' and resid 62 through 67 removed outlier: 3.724A pdb=" N LYS w 62 " --> pdb=" O GLU w 79 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'x' and resid 11 through 18 removed outlier: 6.321A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'z' and resid 34 through 38 removed outlier: 3.859A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.238A pdb=" N ASN A 20 " --> pdb=" O CYS A 16 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.684A pdb=" N GLU B 35 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 19 through 23 removed outlier: 6.938A pdb=" N ILE C 47 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.902A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'F' and resid 14 through 18 Processing sheet with id= 52, first strand: chain 'H' and resid 53 through 58 removed outlier: 3.837A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.835A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY H 193 " --> pdb=" O THR H 190 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL H 199 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'L' and resid 71 through 76 removed outlier: 7.137A pdb=" N THR L 71 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.525A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'O' and resid 42 through 52 removed outlier: 4.979A pdb=" N LEU O 71 " --> pdb=" O PRO O 43 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'X' and resid 30 through 33 removed outlier: 4.008A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 30 through 33 removed outlier: 4.090A pdb=" N ILE G 39 " --> pdb=" O PHE G 31 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA G 33 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.518A pdb=" N LEU G 160 " --> pdb=" O PRO G 181 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'I' and resid 139 through 143 removed outlier: 6.312A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP I 173 " --> pdb=" O GLU I 178 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'J' and resid 10 through 15 removed outlier: 4.091A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY J 39 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN J 18 " --> pdb=" O THR J 33 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'J' and resid 82 through 87 removed outlier: 6.716A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU J 123 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 32 through 39 Processing sheet with id= 64, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.660A pdb=" N LYS K 35 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASN K 63 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS K 58 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR K 92 " --> pdb=" O HIS K 3 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'K' and resid 39 through 42 removed outlier: 3.794A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP K 42 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'K' and resid 43 through 46 removed outlier: 4.117A pdb=" N GLY K 43 " --> pdb=" O TYR K 59 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'M' and resid 22 through 28 removed outlier: 7.163A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.799A pdb=" N TYR M 127 " --> pdb=" O GLN M 75 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P' and resid 41 through 44 Processing sheet with id= 70, first strand: chain 'Q' and resid 28 through 32 Processing sheet with id= 71, first strand: chain 'Q' and resid 34 through 40 removed outlier: 4.500A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.537A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE U 38 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG U 51 " --> pdb=" O PHE U 38 " (cutoff:3.500A) removed outlier: 6.458A 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 removed outlier: 3.533A pdb=" N ILE V 60 " --> pdb=" O LEU V 7 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY V 9 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL V 58 " --> pdb=" O GLY V 9 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'V' and resid 19 through 27 No H-bonds generated for sheet with id= 74 Processing sheet with id= 75, first strand: chain '8' and resid 65 through 73 removed outlier: 6.674A pdb=" N ARG 8 9 " --> pdb=" O PRO 8 81 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG 8 83 " --> pdb=" O ARG 8 9 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR 8 89 " --> pdb=" O ILE 8 15 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA 8 17 " --> pdb=" O THR 8 89 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY 8 91 " --> pdb=" O ALA 8 17 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY 8 108 " --> pdb=" O ASN 8 12 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER 8 16 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL 8 112 " --> pdb=" O SER 8 16 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS 8 18 " --> pdb=" O VAL 8 112 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG 8 137 " --> pdb=" O ILE 8 261 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 8 263 " --> pdb=" O ARG 8 137 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N CYS 8 266 " --> pdb=" O LEU 8 169 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '8' and resid 170 through 173 removed outlier: 4.512A pdb=" N GLY 8 181 " --> pdb=" O ILE 8 173 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS 8 189 " --> pdb=" O ASP 8 184 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '8' and resid 294 through 298 removed outlier: 3.923A pdb=" N ILE 8 295 " --> pdb=" O ARG 8 309 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '8' and resid 323 through 327 removed outlier: 5.059A pdb=" N LYS 8 323 " --> pdb=" O PHE 8 335 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE 8 335 " --> pdb=" O LYS 8 323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY 8 331 " --> pdb=" O ASP 8 327 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE 8 317 " --> pdb=" O ASP 8 399 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '8' and resid 341 through 344 removed outlier: 7.151A pdb=" N GLY 8 341 " --> pdb=" O ALA 8 379 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '8' and resid 348 through 351 Processing sheet with id= 81, first strand: chain '8' and resid 445 through 450 removed outlier: 4.865A pdb=" N ARG 8 446 " --> pdb=" O ALA 8 459 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN 8 455 " --> pdb=" O ASP 8 450 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR 8 456 " --> pdb=" O VAL 8 420 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE 8 416 " --> pdb=" O GLY 8 460 " (cutoff:3.500A) removed outlier: 20.672A pdb=" N VAL 8 415 " --> pdb=" O VAL 8 488 " (cutoff:3.500A) removed outlier: 16.766A pdb=" N VAL 8 488 " --> pdb=" O VAL 8 415 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N SER 8 417 " --> pdb=" O PRO 8 486 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN 8 482 " --> pdb=" O GLU 8 421 " (cutoff:3.500A) removed outlier: 36.925A pdb=" N ALA 8 481 " --> pdb=" O THR 8 623 " (cutoff:3.500A) removed outlier: 32.708A pdb=" N THR 8 623 " --> pdb=" O ALA 8 481 " (cutoff:3.500A) removed outlier: 29.493A pdb=" N VAL 8 483 " --> pdb=" O VAL 8 621 " (cutoff:3.500A) removed outlier: 25.824A pdb=" N VAL 8 621 " --> pdb=" O VAL 8 483 " (cutoff:3.500A) removed outlier: 22.443A pdb=" N LYS 8 485 " --> pdb=" O VAL 8 619 " (cutoff:3.500A) removed outlier: 19.951A pdb=" N VAL 8 619 " --> pdb=" O LYS 8 485 " (cutoff:3.500A) removed outlier: 15.922A pdb=" N GLN 8 487 " --> pdb=" O MET 8 617 " (cutoff:3.500A) removed outlier: 11.460A pdb=" N MET 8 617 " --> pdb=" O GLN 8 487 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA 8 489 " --> pdb=" O PRO 8 615 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY 8 651 " --> pdb=" O GLU 8 648 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS 8 655 " --> pdb=" O GLY 8 644 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY 8 644 " --> pdb=" O HIS 8 655 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '8' and resid 501 through 508 removed outlier: 3.745A pdb=" N VAL 8 501 " --> pdb=" O ILE 8 520 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS 8 507 " --> pdb=" O GLN 8 514 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN 8 514 " --> pdb=" O LYS 8 507 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU 8 535 " --> pdb=" O MET 8 574 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '8' and resid 617 through 623 1761 hydrogen bonds defined for protein. 5220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2260 hydrogen bonds 3614 hydrogen bond angles 0 basepair planarities 961 basepair parallelities 2749 stacking parallelities Total time for adding SS restraints: 216.46 Time building geometry restraints manager: 62.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16170 1.32 - 1.45: 70734 1.45 - 1.57: 69712 1.57 - 1.69: 9527 1.69 - 1.82: 322 Bond restraints: 166465 Sorted by residual: bond pdb=" O3' U 11082 " pdb=" P U 11083 " ideal model delta sigma weight residual 1.607 1.713 -0.106 1.50e-02 4.44e+03 4.98e+01 bond pdb=" CA SER h 3 " pdb=" C SER h 3 " ideal model delta sigma weight residual 1.525 1.384 0.141 2.10e-02 2.27e+03 4.48e+01 bond pdb=" CA 5OH h 6 " pdb=" C 5OH h 6 " ideal model delta sigma weight residual 1.525 1.387 0.138 2.10e-02 2.27e+03 4.31e+01 bond pdb=" C3' C 11104 " pdb=" O3' C 11104 " ideal model delta sigma weight residual 1.417 1.515 -0.098 1.50e-02 4.44e+03 4.26e+01 bond pdb=" CA DPP h 2 " pdb=" C DPP h 2 " ideal model delta sigma weight residual 1.525 1.389 0.136 2.10e-02 2.27e+03 4.18e+01 ... (remaining 166460 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.63: 21148 104.63 - 112.63: 95629 112.63 - 120.64: 77437 120.64 - 128.65: 48939 128.65 - 136.66: 5083 Bond angle restraints: 248236 Sorted by residual: angle pdb=" O3' U 11082 " pdb=" C3' U 11082 " pdb=" C2' U 11082 " ideal model delta sigma weight residual 113.70 134.17 -20.47 1.50e+00 4.44e-01 1.86e+02 angle pdb=" N ILE z 13 " pdb=" CA ILE z 13 " pdb=" C ILE z 13 " ideal model delta sigma weight residual 110.30 122.30 -12.00 9.70e-01 1.06e+00 1.53e+02 angle pdb=" N GLN G 18 " pdb=" CA GLN G 18 " pdb=" CB GLN G 18 " ideal model delta sigma weight residual 114.17 101.08 13.09 1.14e+00 7.69e-01 1.32e+02 angle pdb=" N GLY 8 174 " pdb=" CA GLY 8 174 " pdb=" C GLY 8 174 " ideal model delta sigma weight residual 111.35 123.44 -12.09 1.20e+00 6.94e-01 1.01e+02 angle pdb=" N LYS Q 43 " pdb=" CA LYS Q 43 " pdb=" C LYS Q 43 " ideal model delta sigma weight residual 113.16 127.33 -14.17 1.42e+00 4.96e-01 9.96e+01 ... (remaining 248231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 94946 35.75 - 71.50: 10207 71.50 - 107.24: 1303 107.24 - 142.99: 17 142.99 - 178.74: 28 Dihedral angle restraints: 106501 sinusoidal: 87548 harmonic: 18953 Sorted by residual: dihedral pdb=" O4' U 11911 " pdb=" C1' U 11911 " pdb=" N1 U 11911 " pdb=" C2 U 11911 " ideal model delta sinusoidal sigma weight residual 200.00 28.40 171.60 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U 11917 " pdb=" C1' U 11917 " pdb=" N1 U 11917 " pdb=" C2 U 11917 " ideal model delta sinusoidal sigma weight residual 200.00 32.56 167.44 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' C 31382 " pdb=" C1' C 31382 " pdb=" N1 C 31382 " pdb=" C2 C 31382 " ideal model delta sinusoidal sigma weight residual -160.00 4.51 -164.51 1 1.50e+01 4.44e-03 8.38e+01 ... (remaining 106498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 30811 0.194 - 0.388: 732 0.388 - 0.583: 43 0.583 - 0.777: 14 0.777 - 0.971: 5 Chirality restraints: 31605 Sorted by residual: chirality pdb=" CA PRO e 175 " pdb=" N PRO e 175 " pdb=" C PRO e 175 " pdb=" CB PRO e 175 " both_signs ideal model delta sigma weight residual False 2.72 1.75 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CA PRO 8 121 " pdb=" N PRO 8 121 " pdb=" C PRO 8 121 " pdb=" CB PRO 8 121 " both_signs ideal model delta sigma weight residual False 2.72 1.75 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA PRO 8 524 " pdb=" N PRO 8 524 " pdb=" C PRO 8 524 " pdb=" CB PRO 8 524 " both_signs ideal model delta sigma weight residual False 2.72 1.79 0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 31602 not shown) Planarity restraints: 13907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N UAL h 5 " -0.058 2.00e-02 2.50e+03 2.02e-01 5.09e+02 pdb=" CA UAL h 5 " 0.038 2.00e-02 2.50e+03 pdb=" C UAL h 5 " 0.129 2.00e-02 2.50e+03 pdb=" CB UAL h 5 " -0.351 2.00e-02 2.50e+03 pdb=" N1 UAL h 5 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 202 " -0.137 2.00e-02 2.50e+03 7.66e-02 1.32e+02 pdb=" N1 U 1 202 " 0.004 2.00e-02 2.50e+03 pdb=" C2 U 1 202 " 0.027 2.00e-02 2.50e+03 pdb=" O2 U 1 202 " 0.049 2.00e-02 2.50e+03 pdb=" N3 U 1 202 " 0.030 2.00e-02 2.50e+03 pdb=" C4 U 1 202 " 0.030 2.00e-02 2.50e+03 pdb=" O4 U 1 202 " -0.140 2.00e-02 2.50e+03 pdb=" C5 U 1 202 " 0.074 2.00e-02 2.50e+03 pdb=" C6 U 1 202 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 511 " -0.119 2.00e-02 2.50e+03 6.63e-02 9.88e+01 pdb=" N1 U 1 511 " 0.005 2.00e-02 2.50e+03 pdb=" C2 U 1 511 " 0.024 2.00e-02 2.50e+03 pdb=" O2 U 1 511 " 0.043 2.00e-02 2.50e+03 pdb=" N3 U 1 511 " 0.024 2.00e-02 2.50e+03 pdb=" C4 U 1 511 " 0.024 2.00e-02 2.50e+03 pdb=" O4 U 1 511 " -0.120 2.00e-02 2.50e+03 pdb=" C5 U 1 511 " 0.064 2.00e-02 2.50e+03 pdb=" C6 U 1 511 " 0.056 2.00e-02 2.50e+03 ... (remaining 13904 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 6 2.13 - 2.82: 39339 2.82 - 3.51: 200909 3.51 - 4.21: 484201 4.21 - 4.90: 654152 Nonbonded interactions: 1378607 Sorted by model distance: nonbonded pdb=" OXT KBE h 1 " pdb=" CA DPP h 2 " model vdw 1.436 2.776 nonbonded pdb=" O2 C 11072 " pdb=" O6 G 11091 " model vdw 1.764 3.040 nonbonded pdb=" O2 U 11082 " pdb=" N1 A 11086 " model vdw 1.981 2.496 nonbonded pdb=" OP1 G 11062 " pdb=" OP2 G 11063 " model vdw 2.058 3.040 nonbonded pdb=" C6 G 11047 " pdb=" O6 G 11110 " model vdw 2.062 3.260 ... (remaining 1378602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 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: 0.120 Extract box with map and model: 22.490 Check model and map are aligned: 1.630 Set scattering table: 0.960 Process input model: 510.200 Find NCS groups from input model: 3.410 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 545.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.007 0.141 166465 Z= 0.417 Angle : 1.034 23.177 248236 Z= 0.665 Chirality : 0.086 0.971 31605 Planarity : 0.010 0.202 13907 Dihedral : 22.620 178.739 94278 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 1.12 % Allowed : 11.01 % Favored : 87.88 % Rotamer: Outliers : 1.01 % Allowed : 10.17 % Favored : 88.82 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.08), residues: 6542 helix: -4.28 (0.05), residues: 1905 sheet: -2.66 (0.14), residues: 1150 loop : -3.11 (0.09), residues: 3487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 212 HIS 0.004 0.001 HIS G 17 PHE 0.051 0.003 PHE Z 36 TYR 0.023 0.003 TYR G 21 ARG 0.010 0.001 ARG p 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2026 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1971 time to evaluate : 6.730 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: b 99 GLU cc_start: 0.6515 (tt0) cc_final: 0.6229 (tt0) REVERT: b 152 GLN cc_start: 0.8042 (mp10) cc_final: 0.7552 (mp10) REVERT: b 179 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8089 (tm-30) REVERT: b 196 ASN cc_start: 0.8644 (t0) cc_final: 0.8267 (t0) REVERT: c 42 ASN cc_start: 0.8304 (m110) cc_final: 0.8103 (m110) REVERT: c 129 THR cc_start: 0.8887 (m) cc_final: 0.8640 (p) REVERT: d 194 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8704 (tptm) REVERT: e 10 GLU cc_start: 0.8628 (mp0) cc_final: 0.8236 (mp0) REVERT: e 16 MET cc_start: 0.8250 (tpt) cc_final: 0.7924 (tpt) REVERT: e 18 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8562 (mm-30) REVERT: e 25 MET cc_start: 0.8569 (tpt) cc_final: 0.8338 (tpp) REVERT: e 26 GLN cc_start: 0.8698 (tt0) cc_final: 0.8252 (tp40) REVERT: e 80 GLN cc_start: 0.8788 (tp40) cc_final: 0.8389 (tp-100) REVERT: e 82 TYR cc_start: 0.8686 (t80) cc_final: 0.7963 (t80) REVERT: e 142 TYR cc_start: 0.6624 (t80) cc_final: 0.6403 (t80) REVERT: e 176 PHE cc_start: 0.7421 (m-10) cc_final: 0.7056 (m-80) REVERT: f 25 ILE cc_start: 0.8174 (tp) cc_final: 0.7937 (tt) REVERT: f 32 LEU cc_start: 0.8753 (mt) cc_final: 0.8524 (mt) REVERT: f 63 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8316 (tp40) REVERT: f 72 ASN cc_start: 0.9225 (t0) cc_final: 0.8962 (t0) REVERT: f 76 ILE cc_start: 0.8616 (mm) cc_final: 0.8016 (pt) REVERT: f 93 TYR cc_start: 0.8541 (m-10) cc_final: 0.7867 (m-80) REVERT: f 103 ASN cc_start: 0.8422 (m110) cc_final: 0.7907 (p0) REVERT: f 106 LEU cc_start: 0.9266 (mt) cc_final: 0.8734 (mt) REVERT: f 114 HIS cc_start: 0.6817 (t70) cc_final: 0.6611 (t-90) REVERT: f 169 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7728 (mmm160) REVERT: g 22 LYS cc_start: 0.6779 (mmtm) cc_final: 0.6524 (mmmt) REVERT: i 135 MET cc_start: 0.1208 (mmp) cc_final: 0.0714 (tpt) REVERT: j 1 MET cc_start: 0.7729 (ptp) cc_final: 0.7488 (ptm) REVERT: j 34 ARG cc_start: 0.8525 (ttp-170) cc_final: 0.8272 (ttp80) REVERT: j 36 LEU cc_start: 0.9487 (mt) cc_final: 0.9268 (mp) REVERT: j 80 HIS cc_start: 0.7808 (m-70) cc_final: 0.7575 (m-70) REVERT: j 86 GLN cc_start: 0.8766 (pp30) cc_final: 0.8533 (pp30) REVERT: j 99 ARG cc_start: 0.8533 (mmm160) cc_final: 0.7830 (tpp80) REVERT: k 93 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8453 (mm-40) REVERT: l 23 ILE cc_start: 0.8903 (mp) cc_final: 0.8571 (tt) REVERT: m 47 GLU cc_start: 0.8854 (tp30) cc_final: 0.8622 (tp30) REVERT: m 100 LYS cc_start: 0.8537 (tptt) cc_final: 0.8053 (tttt) REVERT: m 106 ASP cc_start: 0.7751 (t70) cc_final: 0.7264 (t70) REVERT: m 110 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7817 (tm-30) REVERT: n 78 LYS cc_start: 0.8314 (tptm) cc_final: 0.8090 (tptm) REVERT: n 94 TYR cc_start: 0.8752 (m-80) cc_final: 0.8407 (m-10) REVERT: o 21 LEU cc_start: 0.8759 (tt) cc_final: 0.8429 (tt) REVERT: o 43 ASN cc_start: 0.8564 (p0) cc_final: 0.8289 (p0) REVERT: p 5 LYS cc_start: 0.8875 (tptt) cc_final: 0.8294 (tptp) REVERT: p 54 LEU cc_start: 0.9140 (tp) cc_final: 0.8903 (tp) REVERT: p 70 GLU cc_start: 0.7221 (mp0) cc_final: 0.6696 (mp0) REVERT: q 8 ILE cc_start: 0.8745 (pt) cc_final: 0.8478 (mm) REVERT: q 113 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8364 (ttmt) REVERT: r 94 THR cc_start: 0.8699 (m) cc_final: 0.8313 (p) REVERT: r 95 ASP cc_start: 0.8005 (t0) cc_final: 0.7782 (t0) REVERT: r 97 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8949 (ttmm) REVERT: s 52 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8046 (pt0) REVERT: s 66 ILE cc_start: 0.8820 (mm) cc_final: 0.8555 (mm) REVERT: s 68 ASP cc_start: 0.7669 (m-30) cc_final: 0.7440 (m-30) REVERT: s 108 SER cc_start: 0.7964 (p) cc_final: 0.7753 (m) REVERT: t 12 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7677 (mmm160) REVERT: t 79 ASP cc_start: 0.8479 (m-30) cc_final: 0.8265 (m-30) REVERT: u 5 ARG cc_start: 0.8617 (ptp-170) cc_final: 0.7722 (ptp-110) REVERT: u 20 LYS cc_start: 0.8005 (mttt) cc_final: 0.7626 (mptt) REVERT: v 12 GLN cc_start: 0.8059 (pp30) cc_final: 0.7434 (pp30) REVERT: v 19 ARG cc_start: 0.9001 (ttm110) cc_final: 0.8768 (mtm110) REVERT: v 55 GLU cc_start: 0.9134 (mp0) cc_final: 0.8823 (mp0) REVERT: v 77 VAL cc_start: 0.9033 (m) cc_final: 0.8139 (m) REVERT: v 91 PHE cc_start: 0.8730 (m-80) cc_final: 0.8487 (m-80) REVERT: w 20 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8707 (mmtt) REVERT: w 79 GLU cc_start: 0.8879 (mp0) cc_final: 0.8509 (mp0) REVERT: x 53 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8915 (ttmt) REVERT: y 29 ARG cc_start: 0.8593 (mtm110) cc_final: 0.8133 (ttp-170) REVERT: y 31 GLN cc_start: 0.9101 (tp40) cc_final: 0.8780 (tp-100) REVERT: z 15 ARG cc_start: 0.7663 (mmt-90) cc_final: 0.7409 (mmt-90) REVERT: z 20 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8969 (mtmm) REVERT: z 46 MET cc_start: 0.8509 (mtp) cc_final: 0.8280 (mtt) REVERT: A 35 ASP cc_start: 0.8366 (p0) cc_final: 0.7729 (p0) REVERT: B 30 ASP cc_start: 0.7526 (t70) cc_final: 0.7250 (t70) REVERT: C 20 TYR cc_start: 0.6934 (m-80) cc_final: 0.6727 (m-80) REVERT: C 47 ILE cc_start: 0.7805 (mm) cc_final: 0.7493 (tp) REVERT: D 6 GLN cc_start: 0.8596 (tp40) cc_final: 0.8348 (tp40) REVERT: D 9 VAL cc_start: 0.9415 (p) cc_final: 0.9091 (p) REVERT: D 13 ASN cc_start: 0.9108 (m-40) cc_final: 0.8814 (m110) REVERT: D 14 ARG cc_start: 0.8536 (mmt90) cc_final: 0.8164 (mtm-85) REVERT: D 26 ASN cc_start: 0.8901 (m-40) cc_final: 0.8593 (m-40) REVERT: E 39 ARG cc_start: 0.8957 (ptm160) cc_final: 0.8545 (ptm160) REVERT: F 8 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8430 (mppt) REVERT: H 2 GLN cc_start: 0.8415 (pm20) cc_final: 0.7992 (pt0) REVERT: H 30 ASP cc_start: 0.8967 (t0) cc_final: 0.8648 (t0) REVERT: H 44 LYS cc_start: 0.9253 (tppp) cc_final: 0.8889 (tptp) REVERT: H 66 THR cc_start: 0.8947 (m) cc_final: 0.8632 (p) REVERT: H 129 PHE cc_start: 0.8691 (p90) cc_final: 0.8474 (p90) REVERT: H 138 GLN cc_start: 0.8059 (pt0) cc_final: 0.7846 (pm20) REVERT: H 168 ARG cc_start: 0.8454 (ppt170) cc_final: 0.7801 (ptp-170) REVERT: L 27 ASN cc_start: 0.8190 (m110) cc_final: 0.7961 (m110) REVERT: L 41 ILE cc_start: 0.8975 (mm) cc_final: 0.8665 (tp) REVERT: L 52 ARG cc_start: 0.8089 (tpm170) cc_final: 0.7753 (ttp80) REVERT: L 102 TRP cc_start: 0.8848 (m-10) cc_final: 0.8557 (m-10) REVERT: L 105 GLU cc_start: 0.8759 (pp20) cc_final: 0.8437 (pp20) REVERT: L 108 ARG cc_start: 0.8798 (mtt90) cc_final: 0.8574 (mmt90) REVERT: L 115 MET cc_start: 0.8882 (tpp) cc_final: 0.8363 (tpp) REVERT: L 138 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8388 (mm-30) REVERT: N 24 ASN cc_start: 0.7846 (t0) cc_final: 0.7332 (t0) REVERT: N 55 ASP cc_start: 0.8312 (p0) cc_final: 0.8068 (p0) REVERT: N 125 GLN cc_start: 0.7488 (tm-30) cc_final: 0.6680 (pp30) REVERT: O 66 GLU cc_start: 0.8016 (pt0) cc_final: 0.7676 (pt0) REVERT: R 22 TYR cc_start: 0.8477 (t80) cc_final: 0.8171 (t80) REVERT: R 33 LEU cc_start: 0.9078 (tp) cc_final: 0.8778 (tt) REVERT: S 42 ASN cc_start: 0.8476 (m-40) cc_final: 0.8194 (t0) REVERT: X 54 ARG cc_start: 0.8355 (ptp90) cc_final: 0.7871 (ptp-110) REVERT: G 34 ARG cc_start: 0.7550 (mtp180) cc_final: 0.6531 (tpt90) REVERT: G 47 PRO cc_start: 0.7960 (OUTLIER) cc_final: 0.7742 (Cg_exo) REVERT: G 48 MET cc_start: 0.8825 (mtt) cc_final: 0.8598 (mtt) REVERT: G 94 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7004 (ttp80) REVERT: G 132 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8613 (tp30) REVERT: G 144 GLU cc_start: 0.8962 (tp30) cc_final: 0.8624 (tp30) REVERT: G 153 MET cc_start: 0.8580 (tmm) cc_final: 0.7974 (tmm) REVERT: G 207 ARG cc_start: 0.8436 (mtt180) cc_final: 0.7900 (mmt-90) REVERT: I 40 HIS cc_start: 0.7296 (m90) cc_final: 0.6980 (m90) REVERT: I 53 GLN cc_start: 0.9280 (mt0) cc_final: 0.8944 (mt0) REVERT: I 123 MET cc_start: 0.8631 (mtp) cc_final: 0.8421 (tpp) REVERT: I 199 ILE cc_start: 0.8568 (mp) cc_final: 0.8103 (mm) REVERT: J 70 MET cc_start: 0.7357 (mmm) cc_final: 0.7132 (mmm) REVERT: J 85 LYS cc_start: 0.9100 (mttt) cc_final: 0.8785 (mmmt) REVERT: K 63 ASN cc_start: 0.8176 (m-40) cc_final: 0.7851 (m110) REVERT: M 29 SER cc_start: 0.8887 (p) cc_final: 0.7893 (t) REVERT: P 14 GLN cc_start: 0.8768 (pt0) cc_final: 0.8147 (mp-120) REVERT: P 34 THR cc_start: 0.9239 (p) cc_final: 0.8986 (t) REVERT: P 67 GLU cc_start: 0.8913 (tp30) cc_final: 0.8702 (tp30) REVERT: P 82 GLU cc_start: 0.7544 (mp0) cc_final: 0.7147 (mp0) REVERT: P 84 MET cc_start: 0.7816 (mmm) cc_final: 0.7533 (mmt) REVERT: P 118 ASN cc_start: 0.7751 (m110) cc_final: 0.7407 (m110) REVERT: P 126 ARG cc_start: 0.8313 (mmp80) cc_final: 0.8080 (mmt180) REVERT: Q 40 THR cc_start: 0.9245 (t) cc_final: 0.8937 (p) REVERT: Q 76 HIS cc_start: 0.8147 (m90) cc_final: 0.7910 (m-70) REVERT: Q 107 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8487 (tppt) REVERT: T 34 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8577 (tp40) REVERT: T 48 ASP cc_start: 0.8063 (t0) cc_final: 0.7704 (t0) REVERT: T 64 LYS cc_start: 0.9208 (mttt) cc_final: 0.8874 (mtpp) REVERT: T 70 LYS cc_start: 0.9184 (ptmt) cc_final: 0.8905 (ptmm) REVERT: U 12 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8805 (mtpp) REVERT: U 13 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8349 (mmtp) REVERT: V 47 ASP cc_start: 0.7872 (p0) cc_final: 0.7361 (p0) REVERT: V 69 THR cc_start: 0.9085 (m) cc_final: 0.8827 (p) REVERT: W 52 ARG cc_start: 0.9077 (mtm-85) cc_final: 0.8864 (ttm110) REVERT: Y 23 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.8134 (mmm160) REVERT: Y 27 MET cc_start: 0.8778 (mmm) cc_final: 0.8524 (mmm) REVERT: Y 52 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8580 (tm-30) REVERT: Y 53 MET cc_start: 0.8697 (ppp) cc_final: 0.8069 (ptm) REVERT: Y 69 ASN cc_start: 0.9416 (t0) cc_final: 0.9128 (t0) REVERT: Z 20 ARG cc_start: 0.7654 (mtt180) cc_final: 0.6966 (mtt180) REVERT: Z 28 LEU cc_start: 0.9018 (mt) cc_final: 0.8736 (mt) REVERT: 8 39 LYS cc_start: 0.8072 (tptp) cc_final: 0.7852 (tttm) REVERT: 8 106 LEU cc_start: 0.7527 (pp) cc_final: 0.7191 (pp) REVERT: 8 122 GLN cc_start: 0.8047 (mm110) cc_final: 0.7725 (tp-100) REVERT: 8 144 MET cc_start: 0.8354 (mmm) cc_final: 0.7791 (mmm) REVERT: 8 176 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7730 (mm-30) REVERT: 8 184 ASP cc_start: 0.8841 (t0) cc_final: 0.8530 (t0) REVERT: 8 214 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8259 (tt) REVERT: 8 217 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8158 (mp0) REVERT: 8 271 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8965 (mmmm) REVERT: 8 446 ARG cc_start: 0.8625 (mpt-90) cc_final: 0.8075 (tpt170) REVERT: 8 461 MET cc_start: 0.7212 (mmt) cc_final: 0.6879 (tpp) REVERT: 8 505 HIS cc_start: 0.5281 (t70) cc_final: 0.5073 (t-170) REVERT: 8 574 MET cc_start: 0.6089 (tmm) cc_final: 0.5383 (mmt) REVERT: 8 641 MET cc_start: 0.7809 (tpt) cc_final: 0.7219 (tpt) REVERT: 8 657 GLU cc_start: 0.7868 (mp0) cc_final: 0.7504 (mp0) REVERT: 8 683 GLU cc_start: 0.8504 (tp30) cc_final: 0.8033 (mp0) outliers start: 55 outliers final: 24 residues processed: 2008 average time/residue: 1.4128 time to fit residues: 4822.8122 Evaluate side-chains 1509 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1483 time to evaluate : 6.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain G residue 47 PRO Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 519 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 938 optimal weight: 0.9990 chunk 842 optimal weight: 40.0000 chunk 467 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 568 optimal weight: 9.9990 chunk 449 optimal weight: 20.0000 chunk 870 optimal weight: 10.0000 chunk 336 optimal weight: 0.0870 chunk 529 optimal weight: 10.0000 chunk 648 optimal weight: 6.9990 chunk 1008 optimal weight: 30.0000 overall best weight: 5.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN b 152 GLN c 36 GLN c 42 ASN c 49 GLN d 97 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 62 GLN f 44 HIS f 47 ASN ** f 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN f 142 GLN g 11 ASN g 20 ASN a 24 ASN a 47 ASN a 57 GLN i 29 GLN i 110 GLN j 40 HIS j 128 ASN j 135 GLN k 3 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 13 HIS ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN n 81 ASN n 107 ASN p 11 GLN q 70 GLN q 71 ASN r 11 GLN s 57 ASN t 15 HIS u 39 ASN v 49 ASN v 78 GLN w 8 ASN w 46 ASN x 33 HIS x 35 HIS y 31 GLN ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 GLN A 41 HIS B 5 ASN E 27 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN H 139 ASN L 147 ASN O 15 HIS O 58 ASN S 3 GLN S 48 GLN S 65 GLN X 55 GLN G 93 HIS I 58 GLN I 151 GLN J 134 ASN ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 63 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS Q 95 HIS ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Y 67 HIS Y 74 HIS Z 63 ASN 8 44 HIS 8 272 ASN 8 310 HIS 8 365 GLN 8 465 HIS ** 8 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 517 HIS ** 8 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 166465 Z= 0.260 Angle : 0.676 14.322 248236 Z= 0.354 Chirality : 0.039 0.351 31605 Planarity : 0.006 0.081 13907 Dihedral : 23.179 179.599 81308 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.03 % Favored : 89.62 % Rotamer: Outliers : 4.51 % Allowed : 19.15 % Favored : 76.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.30 % 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: -3.80 (0.09), residues: 6542 helix: -2.28 (0.09), residues: 2013 sheet: -2.28 (0.14), residues: 1087 loop : -2.78 (0.09), residues: 3442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 212 HIS 0.009 0.001 HIS a 172 PHE 0.048 0.002 PHE Z 36 TYR 0.025 0.002 TYR a 163 ARG 0.008 0.001 ARG W 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1862 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1617 time to evaluate : 6.884 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: b 95 TYR cc_start: 0.9078 (m-80) cc_final: 0.8572 (m-10) REVERT: b 113 ASP cc_start: 0.7580 (m-30) cc_final: 0.7327 (m-30) REVERT: b 131 MET cc_start: 0.9167 (mpp) cc_final: 0.8634 (mpp) REVERT: b 152 GLN cc_start: 0.8205 (mp-120) cc_final: 0.7859 (mp10) REVERT: c 133 THR cc_start: 0.8802 (m) cc_final: 0.8484 (m) REVERT: d 108 ILE cc_start: 0.9137 (tt) cc_final: 0.8836 (tt) REVERT: e 16 MET cc_start: 0.8193 (tpt) cc_final: 0.7904 (tpt) REVERT: e 21 TYR cc_start: 0.6462 (m-80) cc_final: 0.5523 (m-80) REVERT: e 26 GLN cc_start: 0.8734 (tt0) cc_final: 0.8433 (tt0) REVERT: e 80 GLN cc_start: 0.8753 (tp40) cc_final: 0.8547 (tp40) REVERT: e 82 TYR cc_start: 0.8621 (t80) cc_final: 0.7898 (t80) REVERT: f 25 ILE cc_start: 0.7975 (tp) cc_final: 0.7388 (tt) REVERT: f 93 TYR cc_start: 0.8433 (m-10) cc_final: 0.8068 (m-80) REVERT: f 103 ASN cc_start: 0.8492 (m-40) cc_final: 0.7694 (p0) REVERT: f 154 GLU cc_start: 0.7723 (pm20) cc_final: 0.7442 (pm20) REVERT: i 116 MET cc_start: -0.1645 (ppp) cc_final: -0.1925 (ppp) REVERT: i 135 MET cc_start: 0.1786 (mmp) cc_final: 0.1302 (tpt) REVERT: j 1 MET cc_start: 0.7677 (ptp) cc_final: 0.7447 (ptm) REVERT: j 16 TYR cc_start: 0.8805 (m-80) cc_final: 0.8367 (m-80) REVERT: j 86 GLN cc_start: 0.8716 (pp30) cc_final: 0.8456 (pp30) REVERT: k 2 ILE cc_start: 0.8791 (mt) cc_final: 0.8547 (mm) REVERT: k 93 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8205 (mm-40) REVERT: l 23 ILE cc_start: 0.8875 (mp) cc_final: 0.8605 (tt) REVERT: m 47 GLU cc_start: 0.8937 (tp30) cc_final: 0.8687 (tp30) REVERT: m 100 LYS cc_start: 0.8520 (tptt) cc_final: 0.8071 (tttt) REVERT: m 106 ASP cc_start: 0.7725 (t70) cc_final: 0.7492 (t70) REVERT: m 110 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7872 (tm-30) REVERT: n 82 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7913 (mt-10) REVERT: o 19 GLN cc_start: 0.9018 (tp40) cc_final: 0.8605 (tm-30) REVERT: o 21 LEU cc_start: 0.8613 (tt) cc_final: 0.8253 (tt) REVERT: o 46 GLU cc_start: 0.8332 (pm20) cc_final: 0.7590 (pm20) REVERT: p 5 LYS cc_start: 0.8821 (tptt) cc_final: 0.8575 (tppt) REVERT: q 87 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9244 (m) REVERT: s 66 ILE cc_start: 0.9046 (mm) cc_final: 0.8737 (tt) REVERT: s 68 ASP cc_start: 0.7885 (m-30) cc_final: 0.7467 (m-30) REVERT: t 12 ARG cc_start: 0.8194 (mmm160) cc_final: 0.7613 (mmm160) REVERT: t 42 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7563 (mm-30) REVERT: t 56 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7313 (tm-30) REVERT: u 5 ARG cc_start: 0.8643 (ptp-170) cc_final: 0.7990 (ptp-110) REVERT: u 20 LYS cc_start: 0.7886 (mttt) cc_final: 0.7636 (mptt) REVERT: u 39 ASN cc_start: 0.7649 (t0) cc_final: 0.7053 (t0) REVERT: u 40 LEU cc_start: 0.8008 (mt) cc_final: 0.7687 (mp) REVERT: u 61 GLU cc_start: 0.8245 (tp30) cc_final: 0.7438 (mm-30) REVERT: v 12 GLN cc_start: 0.8139 (pp30) cc_final: 0.7588 (pp30) REVERT: v 19 ARG cc_start: 0.9008 (ttm110) cc_final: 0.8648 (mtm110) REVERT: v 55 GLU cc_start: 0.9112 (mp0) cc_final: 0.8865 (mp0) REVERT: w 13 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7285 (tm-30) REVERT: w 20 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8693 (mmtt) REVERT: x 53 LYS cc_start: 0.9205 (mtpt) cc_final: 0.8958 (ttmt) REVERT: x 71 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7651 (mtt180) REVERT: y 9 LYS cc_start: 0.8713 (tptp) cc_final: 0.8397 (tptp) REVERT: y 29 ARG cc_start: 0.8729 (mtm110) cc_final: 0.8384 (ttp-170) REVERT: y 49 ASP cc_start: 0.8847 (t0) cc_final: 0.8630 (t0) REVERT: y 52 ARG cc_start: 0.8860 (mtt90) cc_final: 0.8290 (mmm-85) REVERT: z 15 ARG cc_start: 0.7965 (mmt-90) cc_final: 0.7695 (mmt180) REVERT: z 20 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8950 (mtmm) REVERT: A 35 ASP cc_start: 0.8366 (p0) cc_final: 0.7659 (p0) REVERT: B 30 ASP cc_start: 0.7526 (t70) cc_final: 0.7303 (t70) REVERT: C 47 ILE cc_start: 0.7743 (mm) cc_final: 0.7454 (mm) REVERT: D 9 VAL cc_start: 0.9454 (p) cc_final: 0.9238 (p) REVERT: D 13 ASN cc_start: 0.9148 (m-40) cc_final: 0.8883 (m110) REVERT: F 8 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8440 (mppt) REVERT: H 42 LEU cc_start: 0.8544 (tp) cc_final: 0.8325 (tp) REVERT: H 44 LYS cc_start: 0.9251 (tppp) cc_final: 0.8812 (tptp) REVERT: H 46 LEU cc_start: 0.8545 (mp) cc_final: 0.8318 (mp) REVERT: H 129 PHE cc_start: 0.8841 (p90) cc_final: 0.8619 (p90) REVERT: H 138 GLN cc_start: 0.8170 (pt0) cc_final: 0.7874 (pt0) REVERT: H 168 ARG cc_start: 0.8282 (ppt170) cc_final: 0.7763 (ptp-170) REVERT: L 52 ARG cc_start: 0.8259 (tpm170) cc_final: 0.7811 (ttp80) REVERT: L 108 ARG cc_start: 0.8618 (mtt90) cc_final: 0.7685 (ttt90) REVERT: L 115 MET cc_start: 0.8674 (tpp) cc_final: 0.8372 (tpt) REVERT: N 18 VAL cc_start: 0.7301 (t) cc_final: 0.7096 (p) REVERT: N 24 ASN cc_start: 0.7779 (t0) cc_final: 0.7061 (t0) REVERT: N 26 LYS cc_start: 0.8224 (ptpp) cc_final: 0.7948 (pttm) REVERT: N 49 GLN cc_start: 0.8336 (pt0) cc_final: 0.8069 (pp30) REVERT: N 109 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7884 (mt0) REVERT: N 125 GLN cc_start: 0.7543 (tm-30) cc_final: 0.6958 (pp30) REVERT: O 66 GLU cc_start: 0.7977 (pt0) cc_final: 0.7641 (pt0) REVERT: R 30 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8865 (mtmm) REVERT: R 33 LEU cc_start: 0.8980 (tp) cc_final: 0.8317 (tt) REVERT: R 40 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8202 (mm-30) REVERT: R 80 MET cc_start: 0.8269 (mmm) cc_final: 0.8028 (mmm) REVERT: X 2 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7472 (mtp85) REVERT: X 16 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8449 (mmpt) REVERT: X 28 LYS cc_start: 0.8657 (tptt) cc_final: 0.8441 (tmtt) REVERT: X 60 PHE cc_start: 0.8467 (t80) cc_final: 0.8105 (t80) REVERT: G 34 ARG cc_start: 0.7462 (mtp180) cc_final: 0.6597 (tpt90) REVERT: G 94 ARG cc_start: 0.7763 (mmt180) cc_final: 0.7215 (ptt90) REVERT: G 153 MET cc_start: 0.8417 (tmm) cc_final: 0.8025 (tmm) REVERT: G 207 ARG cc_start: 0.8453 (mtt180) cc_final: 0.7969 (mmt-90) REVERT: I 40 HIS cc_start: 0.7294 (m90) cc_final: 0.7036 (m90) REVERT: I 50 TYR cc_start: 0.7727 (t80) cc_final: 0.7169 (t80) REVERT: I 53 GLN cc_start: 0.9312 (mt0) cc_final: 0.8876 (mt0) REVERT: I 123 MET cc_start: 0.8584 (mtp) cc_final: 0.8348 (tpp) REVERT: J 61 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8802 (mtmt) REVERT: J 69 ASN cc_start: 0.8074 (t0) cc_final: 0.6994 (t0) REVERT: J 70 MET cc_start: 0.7308 (mmm) cc_final: 0.6862 (mmm) REVERT: J 96 GLN cc_start: 0.8927 (tt0) cc_final: 0.8606 (mt0) REVERT: K 94 HIS cc_start: 0.9001 (m-70) cc_final: 0.8554 (m-70) REVERT: M 59 GLU cc_start: 0.7125 (pp20) cc_final: 0.6857 (pp20) REVERT: P 14 GLN cc_start: 0.8790 (pt0) cc_final: 0.8178 (mp10) REVERT: P 75 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7873 (mp0) REVERT: P 84 MET cc_start: 0.7573 (mmm) cc_final: 0.7323 (mmt) REVERT: P 118 ASN cc_start: 0.7876 (m110) cc_final: 0.7472 (m110) REVERT: Q 76 HIS cc_start: 0.8149 (m-70) cc_final: 0.7781 (m170) REVERT: Q 77 SER cc_start: 0.7988 (m) cc_final: 0.7188 (m) REVERT: T 48 ASP cc_start: 0.7936 (t0) cc_final: 0.7691 (t70) REVERT: U 13 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8295 (mmtp) REVERT: U 51 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7649 (ttp80) REVERT: V 48 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: V 51 GLU cc_start: 0.6810 (pm20) cc_final: 0.6565 (pm20) REVERT: V 59 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7764 (mm-30) REVERT: V 69 THR cc_start: 0.9140 (m) cc_final: 0.8893 (p) REVERT: W 49 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8401 (tttp) REVERT: W 52 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8231 (ttm-80) REVERT: Y 26 MET cc_start: 0.8550 (tmm) cc_final: 0.8294 (tmm) REVERT: Y 27 MET cc_start: 0.8608 (mmm) cc_final: 0.8393 (mmm) REVERT: Z 20 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7062 (mtt180) REVERT: Z 38 GLU cc_start: 0.7624 (tp30) cc_final: 0.7169 (tp30) REVERT: 8 39 LYS cc_start: 0.8017 (tptp) cc_final: 0.7793 (mmmm) REVERT: 8 106 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7533 (pp) REVERT: 8 144 MET cc_start: 0.8506 (mmm) cc_final: 0.8137 (mmm) REVERT: 8 176 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7826 (mm-30) REVERT: 8 184 ASP cc_start: 0.8657 (t0) cc_final: 0.8457 (t0) REVERT: 8 195 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.8000 (p0) REVERT: 8 198 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.5989 (pm20) REVERT: 8 214 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8046 (tp) REVERT: 8 217 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8193 (mp0) REVERT: 8 271 LYS cc_start: 0.9213 (mmmt) cc_final: 0.9012 (mmmm) REVERT: 8 360 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: 8 446 ARG cc_start: 0.8434 (mpt-90) cc_final: 0.7964 (tpt170) REVERT: 8 461 MET cc_start: 0.7375 (mmt) cc_final: 0.7149 (tpp) REVERT: 8 574 MET cc_start: 0.6074 (tmm) cc_final: 0.5576 (mmt) REVERT: 8 641 MET cc_start: 0.7807 (tpt) cc_final: 0.7595 (tpp) REVERT: 8 683 GLU cc_start: 0.8394 (tp30) cc_final: 0.8122 (mp0) outliers start: 245 outliers final: 154 residues processed: 1728 average time/residue: 1.3051 time to fit residues: 3936.1219 Evaluate side-chains 1603 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1441 time to evaluate : 6.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 181 ASP Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 43 ASP Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 60 LYS Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 116 VAL Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 195 ASP Chi-restraints excluded: chain 8 residue 198 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 360 PHE Chi-restraints excluded: chain 8 residue 448 TRP Chi-restraints excluded: chain 8 residue 464 LEU Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 560 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 839 optimal weight: 20.0000 chunk 687 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 1010 optimal weight: 2.9990 chunk 1091 optimal weight: 9.9990 chunk 900 optimal weight: 6.9990 chunk 1002 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 810 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 42 ASN c 58 ASN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 97 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN q 58 GLN q 70 GLN q 71 ASN ** x 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS S 59 GLN S 65 GLN G 57 ASN I 70 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 129 GLN ** 8 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 560 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 166465 Z= 0.290 Angle : 0.646 14.424 248236 Z= 0.339 Chirality : 0.038 0.354 31605 Planarity : 0.005 0.072 13907 Dihedral : 23.389 178.529 81300 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.20 % Favored : 88.44 % Rotamer: Outliers : 6.14 % Allowed : 21.72 % Favored : 72.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.17 (0.09), residues: 6542 helix: -1.39 (0.11), residues: 2024 sheet: -1.97 (0.15), residues: 1088 loop : -2.64 (0.10), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 102 HIS 0.051 0.001 HIS O 15 PHE 0.047 0.002 PHE Z 36 TYR 0.026 0.002 TYR e 142 ARG 0.009 0.001 ARG b 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1873 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1539 time to evaluate : 6.783 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: b 95 TYR cc_start: 0.9016 (m-80) cc_final: 0.8532 (m-80) REVERT: b 99 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6791 (tm-30) REVERT: b 152 GLN cc_start: 0.8200 (mp-120) cc_final: 0.7885 (mp10) REVERT: b 196 ASN cc_start: 0.8621 (t0) cc_final: 0.8195 (t0) REVERT: e 16 MET cc_start: 0.8294 (tpt) cc_final: 0.7885 (tpt) REVERT: e 25 MET cc_start: 0.8533 (mmm) cc_final: 0.8048 (tpp) REVERT: e 26 GLN cc_start: 0.8767 (tt0) cc_final: 0.8443 (tt0) REVERT: e 80 GLN cc_start: 0.8735 (tp40) cc_final: 0.8359 (tp40) REVERT: e 82 TYR cc_start: 0.8710 (t80) cc_final: 0.7943 (t80) REVERT: e 174 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6744 (t80) REVERT: f 93 TYR cc_start: 0.8462 (m-10) cc_final: 0.8136 (m-80) REVERT: f 103 ASN cc_start: 0.8573 (m-40) cc_final: 0.7807 (p0) REVERT: f 123 GLU cc_start: 0.7265 (tp30) cc_final: 0.7055 (tp30) REVERT: i 135 MET cc_start: 0.1685 (mmp) cc_final: 0.1219 (tpt) REVERT: j 1 MET cc_start: 0.7766 (ptp) cc_final: 0.7525 (ptm) REVERT: j 16 TYR cc_start: 0.8815 (m-80) cc_final: 0.8360 (m-80) REVERT: j 86 GLN cc_start: 0.8736 (pp30) cc_final: 0.8476 (pp30) REVERT: k 2 ILE cc_start: 0.8737 (mt) cc_final: 0.8524 (mm) REVERT: k 93 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8171 (mm-40) REVERT: m 47 GLU cc_start: 0.8847 (tp30) cc_final: 0.8598 (tp30) REVERT: m 100 LYS cc_start: 0.8534 (tptt) cc_final: 0.8052 (ttmt) REVERT: m 110 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7899 (tm-30) REVERT: n 94 TYR cc_start: 0.8703 (m-80) cc_final: 0.8345 (m-80) REVERT: o 19 GLN cc_start: 0.9027 (tp40) cc_final: 0.8634 (tm-30) REVERT: o 21 LEU cc_start: 0.8635 (tt) cc_final: 0.8269 (tt) REVERT: p 5 LYS cc_start: 0.8913 (tptt) cc_final: 0.8681 (tppt) REVERT: p 38 ARG cc_start: 0.8841 (ptm160) cc_final: 0.8556 (ptm160) REVERT: t 12 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7613 (mmm160) REVERT: t 42 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7526 (mm-30) REVERT: t 56 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7510 (tm-30) REVERT: t 79 ASP cc_start: 0.8513 (m-30) cc_final: 0.8274 (m-30) REVERT: u 5 ARG cc_start: 0.8537 (ptp-170) cc_final: 0.7991 (ptp-110) REVERT: u 6 ARG cc_start: 0.7972 (ptm160) cc_final: 0.7598 (ptm160) REVERT: u 20 LYS cc_start: 0.7999 (mttt) cc_final: 0.7775 (mptt) REVERT: u 39 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7332 (t0) REVERT: v 48 MET cc_start: 0.8629 (ttm) cc_final: 0.8362 (mmm) REVERT: v 51 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: v 60 VAL cc_start: 0.7329 (m) cc_final: 0.6905 (p) REVERT: w 20 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8816 (mmtt) REVERT: w 64 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8164 (ttpp) REVERT: y 9 LYS cc_start: 0.8659 (tptp) cc_final: 0.8301 (tptt) REVERT: y 13 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: y 16 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8955 (t) REVERT: y 29 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8396 (ttm170) REVERT: y 52 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8602 (mmm-85) REVERT: z 20 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8987 (mtmm) REVERT: A 35 ASP cc_start: 0.8354 (p0) cc_final: 0.7737 (p0) REVERT: C 39 ASP cc_start: 0.8662 (t70) cc_final: 0.8246 (t0) REVERT: C 44 GLN cc_start: 0.8495 (mp10) cc_final: 0.8069 (tp40) REVERT: C 47 ILE cc_start: 0.7568 (mm) cc_final: 0.7358 (mm) REVERT: D 9 VAL cc_start: 0.9465 (p) cc_final: 0.9237 (p) REVERT: D 13 ASN cc_start: 0.9124 (m-40) cc_final: 0.8837 (m110) REVERT: E 61 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9272 (pp) REVERT: F 8 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8475 (mppt) REVERT: H 44 LYS cc_start: 0.9274 (tppp) cc_final: 0.8924 (tptp) REVERT: H 138 GLN cc_start: 0.8061 (pt0) cc_final: 0.7819 (pt0) REVERT: H 168 ARG cc_start: 0.8355 (ppt170) cc_final: 0.7785 (ptm160) REVERT: L 52 ARG cc_start: 0.8229 (tpm170) cc_final: 0.7855 (ttp80) REVERT: L 108 ARG cc_start: 0.8565 (mtt90) cc_final: 0.7738 (ttt90) REVERT: L 115 MET cc_start: 0.8740 (tpp) cc_final: 0.8446 (tpt) REVERT: N 18 VAL cc_start: 0.7191 (t) cc_final: 0.6952 (p) REVERT: N 24 ASN cc_start: 0.7965 (t0) cc_final: 0.7387 (t0) REVERT: N 109 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8076 (mt0) REVERT: N 125 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7161 (pp30) REVERT: O 66 GLU cc_start: 0.8002 (pt0) cc_final: 0.7683 (pt0) REVERT: R 80 MET cc_start: 0.8253 (mmm) cc_final: 0.8002 (mmm) REVERT: S 78 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8534 (pp) REVERT: S 91 GLU cc_start: 0.7895 (mp0) cc_final: 0.7574 (mp0) REVERT: X 2 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7363 (mtp85) REVERT: X 60 PHE cc_start: 0.8552 (t80) cc_final: 0.8211 (t80) REVERT: G 92 ASN cc_start: 0.8490 (m110) cc_final: 0.8245 (t0) REVERT: G 94 ARG cc_start: 0.7701 (mmt180) cc_final: 0.7186 (ptt90) REVERT: G 153 MET cc_start: 0.8433 (tmm) cc_final: 0.7992 (tmm) REVERT: G 207 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8023 (mmt-90) REVERT: G 221 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7371 (mtt180) REVERT: I 50 TYR cc_start: 0.7821 (t80) cc_final: 0.7366 (t80) REVERT: I 123 MET cc_start: 0.8584 (mtp) cc_final: 0.8365 (tpp) REVERT: I 199 ILE cc_start: 0.8506 (mp) cc_final: 0.8066 (mm) REVERT: J 69 ASN cc_start: 0.8143 (t0) cc_final: 0.7174 (t0) REVERT: J 70 MET cc_start: 0.7330 (mmm) cc_final: 0.6913 (mmm) REVERT: J 96 GLN cc_start: 0.8935 (tt0) cc_final: 0.8533 (mt0) REVERT: K 56 LYS cc_start: 0.8288 (ptmm) cc_final: 0.7943 (ptmm) REVERT: M 6 ILE cc_start: 0.9373 (mm) cc_final: 0.9163 (mm) REVERT: M 59 GLU cc_start: 0.7243 (pp20) cc_final: 0.6921 (pp20) REVERT: M 73 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8613 (t) REVERT: M 95 MET cc_start: 0.7963 (mtt) cc_final: 0.7679 (mtt) REVERT: P 14 GLN cc_start: 0.8819 (pt0) cc_final: 0.8197 (mp10) REVERT: P 67 GLU cc_start: 0.9039 (tp30) cc_final: 0.8771 (tp30) REVERT: P 75 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7843 (mp0) REVERT: P 80 ASN cc_start: 0.8610 (p0) cc_final: 0.8054 (p0) REVERT: P 84 MET cc_start: 0.7625 (mmm) cc_final: 0.7324 (mmt) REVERT: P 118 ASN cc_start: 0.7893 (m110) cc_final: 0.7512 (m110) REVERT: P 126 ARG cc_start: 0.8278 (mmm160) cc_final: 0.8063 (mmt180) REVERT: Q 76 HIS cc_start: 0.8268 (m-70) cc_final: 0.7985 (m-70) REVERT: T 48 ASP cc_start: 0.7916 (t0) cc_final: 0.7571 (t70) REVERT: U 13 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8437 (mmtp) REVERT: U 51 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7367 (ttp80) REVERT: U 63 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7706 (mp10) REVERT: V 59 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7838 (mm-30) REVERT: V 69 THR cc_start: 0.9205 (m) cc_final: 0.8944 (p) REVERT: W 52 ARG cc_start: 0.9004 (mtm-85) cc_final: 0.8737 (ttm110) REVERT: Y 26 MET cc_start: 0.8829 (tmm) cc_final: 0.8447 (tmm) REVERT: Z 20 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7064 (mtt180) REVERT: Z 65 ARG cc_start: 0.7061 (mmp80) cc_final: 0.6860 (mmp80) REVERT: 8 144 MET cc_start: 0.8461 (mmm) cc_final: 0.8172 (mmm) REVERT: 8 170 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: 8 184 ASP cc_start: 0.8641 (t0) cc_final: 0.8391 (t0) REVERT: 8 195 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7966 (p0) REVERT: 8 198 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6137 (pm20) REVERT: 8 214 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8203 (tp) REVERT: 8 217 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8124 (mt-10) REVERT: 8 446 ARG cc_start: 0.8427 (mpt-90) cc_final: 0.7954 (tpt170) REVERT: 8 461 MET cc_start: 0.7475 (mmt) cc_final: 0.7221 (tpp) REVERT: 8 473 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7425 (tmt) REVERT: 8 574 MET cc_start: 0.6105 (tmm) cc_final: 0.5587 (mmt) REVERT: 8 683 GLU cc_start: 0.8403 (tp30) cc_final: 0.8091 (mp0) outliers start: 334 outliers final: 235 residues processed: 1707 average time/residue: 1.2949 time to fit residues: 3873.9496 Evaluate side-chains 1678 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1429 time to evaluate : 6.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 181 ASP Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 72 ILE Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 43 ASP Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 29 ARG Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain P residue 15 VAL 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 45 THR Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 72 LYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 15 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 54 GLU Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 116 VAL Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 195 ASP Chi-restraints excluded: chain 8 residue 198 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 252 LEU Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 343 VAL Chi-restraints excluded: chain 8 residue 381 ASP Chi-restraints excluded: chain 8 residue 464 LEU Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 525 LEU Chi-restraints excluded: chain 8 residue 566 LEU Chi-restraints excluded: chain 8 residue 585 ASP Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Chi-restraints excluded: chain 8 residue 694 VAL Chi-restraints excluded: chain h residue 3 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 998 optimal weight: 3.9990 chunk 759 optimal weight: 20.0000 chunk 524 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 482 optimal weight: 5.9990 chunk 678 optimal weight: 0.6980 chunk 1014 optimal weight: 5.9990 chunk 1073 optimal weight: 9.9990 chunk 529 optimal weight: 8.9990 chunk 961 optimal weight: 7.9990 chunk 289 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN b 114 GLN ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 GLN q 70 GLN y 39 GLN ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS S 3 GLN X 55 GLN I 35 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN K 17 GLN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 ASN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS U 9 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 508 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 166465 Z= 0.217 Angle : 0.591 15.039 248236 Z= 0.310 Chirality : 0.036 0.316 31605 Planarity : 0.005 0.070 13907 Dihedral : 23.422 179.905 81297 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.06 % Favored : 89.62 % Rotamer: Outliers : 6.07 % Allowed : 24.06 % Favored : 69.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 6542 helix: -0.90 (0.11), residues: 2040 sheet: -1.74 (0.15), residues: 1089 loop : -2.51 (0.10), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 102 HIS 0.022 0.001 HIS O 15 PHE 0.045 0.002 PHE Z 36 TYR 0.026 0.002 TYR N 5 ARG 0.008 0.000 ARG Y 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1858 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1528 time to evaluate : 6.835 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: c 129 THR cc_start: 0.8976 (m) cc_final: 0.8713 (p) REVERT: d 73 ILE cc_start: 0.9147 (mp) cc_final: 0.8926 (mm) REVERT: e 16 MET cc_start: 0.8291 (tpt) cc_final: 0.7828 (tpt) REVERT: e 25 MET cc_start: 0.8486 (mmm) cc_final: 0.8004 (tpp) REVERT: e 26 GLN cc_start: 0.8809 (tt0) cc_final: 0.8488 (tt0) REVERT: e 80 GLN cc_start: 0.8661 (tp40) cc_final: 0.8261 (tp40) REVERT: e 82 TYR cc_start: 0.8730 (t80) cc_final: 0.8368 (t80) REVERT: e 163 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8705 (mp0) REVERT: e 174 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6638 (t80) REVERT: f 19 ASN cc_start: 0.7395 (m110) cc_final: 0.7155 (m110) REVERT: f 59 ASP cc_start: 0.5983 (OUTLIER) cc_final: 0.5662 (p0) REVERT: f 93 TYR cc_start: 0.8366 (m-10) cc_final: 0.8085 (m-80) REVERT: f 103 ASN cc_start: 0.8613 (m-40) cc_final: 0.7888 (p0) REVERT: f 129 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6841 (tm-30) REVERT: f 169 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7894 (mmm160) REVERT: i 116 MET cc_start: -0.1949 (OUTLIER) cc_final: -0.2381 (ppp) REVERT: i 135 MET cc_start: 0.1672 (mmp) cc_final: 0.1206 (tpt) REVERT: j 1 MET cc_start: 0.7794 (ptp) cc_final: 0.7530 (ptm) REVERT: j 16 TYR cc_start: 0.8764 (m-80) cc_final: 0.8289 (m-80) REVERT: j 86 GLN cc_start: 0.8708 (pp30) cc_final: 0.8461 (pp30) REVERT: j 108 MET cc_start: 0.8669 (mtt) cc_final: 0.8442 (mtt) REVERT: k 93 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8204 (mm-40) REVERT: l 111 ILE cc_start: 0.8882 (mm) cc_final: 0.8482 (mm) REVERT: m 47 GLU cc_start: 0.8878 (tp30) cc_final: 0.8375 (tp30) REVERT: m 100 LYS cc_start: 0.8488 (tptt) cc_final: 0.8029 (tttt) REVERT: m 110 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7934 (tm-30) REVERT: n 94 TYR cc_start: 0.8680 (m-80) cc_final: 0.8386 (m-80) REVERT: o 19 GLN cc_start: 0.9032 (tp40) cc_final: 0.8827 (tm-30) REVERT: o 20 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7743 (pp20) REVERT: o 21 LEU cc_start: 0.8544 (tt) cc_final: 0.8225 (tt) REVERT: p 5 LYS cc_start: 0.8843 (tptt) cc_final: 0.8637 (tppt) REVERT: q 8 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8535 (mm) REVERT: t 12 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7617 (mmm160) REVERT: t 42 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7645 (mm-30) REVERT: t 56 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7697 (tm-30) REVERT: u 39 ASN cc_start: 0.7768 (t0) cc_final: 0.6938 (t0) REVERT: v 38 LEU cc_start: 0.8528 (mm) cc_final: 0.8282 (mm) REVERT: v 60 VAL cc_start: 0.7389 (m) cc_final: 0.7042 (p) REVERT: w 13 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7370 (tm-30) REVERT: w 20 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8857 (mmtt) REVERT: w 64 LYS cc_start: 0.8492 (ttpp) cc_final: 0.7869 (ttpp) REVERT: w 66 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7126 (mt-10) REVERT: x 43 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8304 (pptt) REVERT: y 13 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: y 29 ARG cc_start: 0.8728 (mtm110) cc_final: 0.8457 (ttm170) REVERT: y 31 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8833 (tp-100) REVERT: A 16 CYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5804 (t) REVERT: A 35 ASP cc_start: 0.8355 (p0) cc_final: 0.7682 (p0) REVERT: F 8 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8417 (mppt) REVERT: H 44 LYS cc_start: 0.9231 (tppp) cc_final: 0.8922 (tptp) REVERT: H 129 PHE cc_start: 0.8755 (p90) cc_final: 0.8528 (p90) REVERT: H 138 GLN cc_start: 0.8125 (pt0) cc_final: 0.7870 (pt0) REVERT: H 139 ASN cc_start: 0.9238 (m-40) cc_final: 0.9034 (m-40) REVERT: H 168 ARG cc_start: 0.8366 (ppt170) cc_final: 0.7798 (ptm160) REVERT: L 20 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: L 52 ARG cc_start: 0.8128 (tpm170) cc_final: 0.7876 (ttp80) REVERT: L 102 TRP cc_start: 0.8672 (m-10) cc_final: 0.8403 (m-10) REVERT: L 108 ARG cc_start: 0.8483 (mtt90) cc_final: 0.7709 (ttt90) REVERT: L 115 MET cc_start: 0.8658 (tpp) cc_final: 0.8333 (tpt) REVERT: N 24 ASN cc_start: 0.7900 (t0) cc_final: 0.7396 (t0) REVERT: N 47 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8672 (p) REVERT: N 125 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7032 (pp30) REVERT: R 30 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8713 (mmmm) REVERT: R 40 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7617 (mm-30) REVERT: R 80 MET cc_start: 0.8215 (mmm) cc_final: 0.7966 (mmm) REVERT: S 78 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (pp) REVERT: X 2 ARG cc_start: 0.7567 (mtm180) cc_final: 0.7310 (mtp85) REVERT: X 12 LEU cc_start: 0.8748 (pt) cc_final: 0.8361 (pt) REVERT: X 16 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8334 (mmpt) REVERT: X 20 LYS cc_start: 0.4793 (ptpp) cc_final: 0.3701 (ptpt) REVERT: X 43 MET cc_start: 0.8871 (tpp) cc_final: 0.8321 (tpp) REVERT: X 60 PHE cc_start: 0.8501 (t80) cc_final: 0.8211 (t80) REVERT: G 92 ASN cc_start: 0.8464 (m110) cc_final: 0.8229 (m-40) REVERT: G 94 ARG cc_start: 0.7568 (mmt180) cc_final: 0.7087 (ptt90) REVERT: G 153 MET cc_start: 0.8455 (tmm) cc_final: 0.8029 (tmm) REVERT: G 207 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8088 (mmt-90) REVERT: G 221 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7437 (mtt180) REVERT: I 50 TYR cc_start: 0.7801 (t80) cc_final: 0.7363 (t80) REVERT: I 123 MET cc_start: 0.8624 (mtp) cc_final: 0.8421 (tpp) REVERT: I 199 ILE cc_start: 0.8543 (mp) cc_final: 0.8072 (mm) REVERT: J 25 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8310 (tptp) REVERT: J 53 ARG cc_start: 0.7434 (mtp-110) cc_final: 0.6469 (tpt-90) REVERT: J 69 ASN cc_start: 0.8174 (t0) cc_final: 0.7292 (t0) REVERT: J 70 MET cc_start: 0.7322 (mmm) cc_final: 0.6898 (mmm) REVERT: J 96 GLN cc_start: 0.8984 (tt0) cc_final: 0.8637 (mt0) REVERT: J 110 MET cc_start: 0.8550 (ttm) cc_final: 0.8201 (mtt) REVERT: M 59 GLU cc_start: 0.7378 (pp20) cc_final: 0.6866 (pp20) REVERT: M 73 SER cc_start: 0.8684 (t) cc_final: 0.8484 (p) REVERT: M 95 MET cc_start: 0.7949 (mtt) cc_final: 0.7719 (mtt) REVERT: P 14 GLN cc_start: 0.8845 (pt0) cc_final: 0.8293 (mp-120) REVERT: P 67 GLU cc_start: 0.8987 (tp30) cc_final: 0.8642 (tp30) REVERT: P 75 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7858 (mp0) REVERT: P 84 MET cc_start: 0.7598 (mmm) cc_final: 0.7291 (mmt) REVERT: P 118 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7535 (m110) REVERT: Q 65 TYR cc_start: 0.8748 (t80) cc_final: 0.8513 (t80) REVERT: Q 72 ASN cc_start: 0.8851 (p0) cc_final: 0.8446 (p0) REVERT: T 48 ASP cc_start: 0.7921 (t0) cc_final: 0.7556 (t70) REVERT: U 13 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8419 (mmtp) REVERT: V 17 GLU cc_start: 0.7624 (pp20) cc_final: 0.7227 (pp20) REVERT: V 59 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7706 (mm-30) REVERT: V 69 THR cc_start: 0.9244 (m) cc_final: 0.8987 (p) REVERT: W 22 TYR cc_start: 0.8765 (p90) cc_final: 0.8544 (p90) REVERT: W 23 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7977 (pttt) REVERT: W 52 ARG cc_start: 0.8907 (mtm-85) cc_final: 0.8696 (ttm110) REVERT: Y 26 MET cc_start: 0.8869 (tmm) cc_final: 0.8500 (tmm) REVERT: Y 27 MET cc_start: 0.8649 (mmm) cc_final: 0.8337 (mmm) REVERT: Z 20 ARG cc_start: 0.7781 (mtt180) cc_final: 0.6762 (mtt90) REVERT: Z 38 GLU cc_start: 0.7372 (tp30) cc_final: 0.6953 (tp30) REVERT: 8 144 MET cc_start: 0.8468 (mmm) cc_final: 0.8190 (mmm) REVERT: 8 157 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8453 (pp30) REVERT: 8 170 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: 8 184 ASP cc_start: 0.8686 (t0) cc_final: 0.8469 (t0) REVERT: 8 195 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7990 (p0) REVERT: 8 198 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6143 (pm20) REVERT: 8 214 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8218 (tp) REVERT: 8 217 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8075 (mt-10) REVERT: 8 446 ARG cc_start: 0.8399 (mpt-90) cc_final: 0.7932 (tpt170) REVERT: 8 461 MET cc_start: 0.7514 (mmt) cc_final: 0.7122 (tpp) REVERT: 8 579 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6397 (t70) REVERT: 8 683 GLU cc_start: 0.8397 (tp30) cc_final: 0.8063 (mp0) outliers start: 330 outliers final: 226 residues processed: 1706 average time/residue: 1.2815 time to fit residues: 3837.6379 Evaluate side-chains 1667 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1424 time to evaluate : 6.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 181 ASP Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 72 ILE Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 224 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 32 GLU Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 40 MET Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 43 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 38 GLN Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain P residue 15 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 80 ASN Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 72 LYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 107 ASP Chi-restraints excluded: chain 8 residue 156 ASN Chi-restraints excluded: chain 8 residue 157 GLN Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 195 ASP Chi-restraints excluded: chain 8 residue 198 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 252 LEU Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 343 VAL Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 525 LEU Chi-restraints excluded: chain 8 residue 566 LEU Chi-restraints excluded: chain 8 residue 572 VAL Chi-restraints excluded: chain 8 residue 579 HIS Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Chi-restraints excluded: chain 8 residue 694 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 894 optimal weight: 30.0000 chunk 609 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 799 optimal weight: 20.0000 chunk 443 optimal weight: 50.0000 chunk 916 optimal weight: 0.6980 chunk 742 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 548 optimal weight: 20.0000 chunk 963 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 overall best weight: 7.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 58 ASN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 ASN ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN l 4 ASN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** x 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN C 25 ASN N 74 GLN N 109 GLN S 3 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN K 14 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 166465 Z= 0.317 Angle : 0.656 14.951 248236 Z= 0.339 Chirality : 0.038 0.397 31605 Planarity : 0.005 0.069 13907 Dihedral : 23.498 179.711 81297 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.79 % Favored : 87.89 % Rotamer: Outliers : 6.79 % Allowed : 25.38 % Favored : 67.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.10), residues: 6542 helix: -0.77 (0.11), residues: 2038 sheet: -1.66 (0.15), residues: 1109 loop : -2.50 (0.10), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 41 HIS 0.007 0.001 HIS C 18 PHE 0.041 0.002 PHE Z 36 TYR 0.029 0.002 TYR a 163 ARG 0.014 0.001 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1808 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 1439 time to evaluate : 6.690 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: b 152 GLN cc_start: 0.8240 (mp10) cc_final: 0.7946 (mp10) REVERT: c 133 THR cc_start: 0.8836 (t) cc_final: 0.8544 (t) REVERT: d 73 ILE cc_start: 0.9139 (mp) cc_final: 0.8914 (mm) REVERT: e 16 MET cc_start: 0.8337 (tpt) cc_final: 0.7791 (tpt) REVERT: e 25 MET cc_start: 0.8524 (mmm) cc_final: 0.8009 (tpp) REVERT: e 26 GLN cc_start: 0.8850 (tt0) cc_final: 0.8320 (tp40) REVERT: e 80 GLN cc_start: 0.8661 (tp40) cc_final: 0.8443 (tp40) REVERT: e 82 TYR cc_start: 0.8765 (t80) cc_final: 0.8380 (t80) REVERT: e 163 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8687 (mp0) REVERT: e 174 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6638 (t80) REVERT: f 19 ASN cc_start: 0.7510 (m110) cc_final: 0.7251 (m110) REVERT: f 59 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5949 (p0) REVERT: f 93 TYR cc_start: 0.8387 (m-10) cc_final: 0.8091 (m-80) REVERT: f 103 ASN cc_start: 0.8676 (m-40) cc_final: 0.7976 (p0) REVERT: f 169 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7867 (mmm160) REVERT: g 127 GLU cc_start: 0.3526 (OUTLIER) cc_final: 0.3254 (pp20) REVERT: a 172 HIS cc_start: 0.3944 (OUTLIER) cc_final: 0.3264 (t-90) REVERT: i 41 PHE cc_start: -0.1093 (OUTLIER) cc_final: -0.1489 (m-10) REVERT: i 116 MET cc_start: -0.2072 (OUTLIER) cc_final: -0.2526 (ppp) REVERT: i 135 MET cc_start: 0.1861 (mmp) cc_final: 0.1412 (mmm) REVERT: j 1 MET cc_start: 0.7761 (ptp) cc_final: 0.7528 (ptm) REVERT: j 16 TYR cc_start: 0.8770 (m-80) cc_final: 0.8277 (m-80) REVERT: j 86 GLN cc_start: 0.8744 (pp30) cc_final: 0.8500 (pp30) REVERT: j 102 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7731 (mt-10) REVERT: k 93 GLN cc_start: 0.8735 (mm110) cc_final: 0.8257 (mm-40) REVERT: m 47 GLU cc_start: 0.8852 (tp30) cc_final: 0.8275 (tp30) REVERT: m 100 LYS cc_start: 0.8544 (tptt) cc_final: 0.8018 (ttmt) REVERT: m 103 TYR cc_start: 0.8262 (m-80) cc_final: 0.7850 (m-80) REVERT: m 110 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7926 (tm-30) REVERT: n 94 TYR cc_start: 0.8723 (m-80) cc_final: 0.8335 (m-80) REVERT: o 20 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7625 (pp20) REVERT: o 21 LEU cc_start: 0.8609 (tt) cc_final: 0.8272 (tt) REVERT: o 61 GLN cc_start: 0.7969 (mm110) cc_final: 0.7570 (tm-30) REVERT: p 5 LYS cc_start: 0.8872 (tptt) cc_final: 0.8657 (tppt) REVERT: p 70 GLU cc_start: 0.7426 (mp0) cc_final: 0.7210 (tp30) REVERT: q 8 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8604 (mm) REVERT: r 16 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7119 (mm-30) REVERT: t 12 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7829 (mmm160) REVERT: t 42 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7673 (mm-30) REVERT: t 56 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7743 (tm-30) REVERT: t 68 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8753 (mmmm) REVERT: u 39 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.6967 (t0) REVERT: v 38 LEU cc_start: 0.8551 (mm) cc_final: 0.8303 (mm) REVERT: v 60 VAL cc_start: 0.7478 (m) cc_final: 0.7090 (p) REVERT: w 20 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8905 (mmtt) REVERT: y 13 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: y 29 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8531 (ttm170) REVERT: y 52 ARG cc_start: 0.8808 (mtt90) cc_final: 0.8493 (mmm-85) REVERT: A 8 LYS cc_start: 0.8822 (tppt) cc_final: 0.8560 (tppt) REVERT: A 35 ASP cc_start: 0.8255 (p0) cc_final: 0.7614 (p0) REVERT: F 8 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8420 (mppt) REVERT: H 44 LYS cc_start: 0.9245 (tppp) cc_final: 0.8902 (tptp) REVERT: H 138 GLN cc_start: 0.8163 (pt0) cc_final: 0.7930 (pt0) REVERT: H 139 ASN cc_start: 0.9225 (m-40) cc_final: 0.8556 (m-40) REVERT: H 168 ARG cc_start: 0.8439 (ppt170) cc_final: 0.7848 (ptp-170) REVERT: L 20 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: L 52 ARG cc_start: 0.8157 (tpm170) cc_final: 0.7878 (ttp80) REVERT: L 108 ARG cc_start: 0.8527 (mtt90) cc_final: 0.7702 (ttt90) REVERT: L 115 MET cc_start: 0.8673 (tpp) cc_final: 0.8323 (tpt) REVERT: N 24 ASN cc_start: 0.8101 (t0) cc_final: 0.7606 (t0) REVERT: R 80 MET cc_start: 0.8260 (mmm) cc_final: 0.7962 (mmm) REVERT: R 91 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8571 (mtp85) REVERT: S 78 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8485 (pp) REVERT: S 91 GLU cc_start: 0.8078 (mp0) cc_final: 0.7606 (mp0) REVERT: X 2 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7360 (mtp85) REVERT: X 43 MET cc_start: 0.8870 (tpp) cc_final: 0.8327 (tpp) REVERT: X 60 PHE cc_start: 0.8339 (t80) cc_final: 0.8033 (t80) REVERT: G 94 ARG cc_start: 0.7527 (mmt180) cc_final: 0.7115 (ptt90) REVERT: G 153 MET cc_start: 0.8339 (tmm) cc_final: 0.7831 (tmm) REVERT: G 207 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8118 (mmt-90) REVERT: I 123 MET cc_start: 0.8636 (mtp) cc_final: 0.8299 (tpp) REVERT: I 199 ILE cc_start: 0.8611 (mp) cc_final: 0.8080 (mm) REVERT: J 25 LYS cc_start: 0.8657 (tmtt) cc_final: 0.8350 (tptp) REVERT: J 53 ARG cc_start: 0.7463 (mtp-110) cc_final: 0.6590 (tpt-90) REVERT: J 69 ASN cc_start: 0.8165 (t0) cc_final: 0.7254 (t0) REVERT: J 70 MET cc_start: 0.7363 (mmm) cc_final: 0.7062 (mmm) REVERT: J 96 GLN cc_start: 0.8965 (tt0) cc_final: 0.8579 (mt0) REVERT: K 49 TYR cc_start: 0.7920 (p90) cc_final: 0.7443 (p90) REVERT: K 86 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.6895 (mtp85) REVERT: K 97 THR cc_start: 0.6495 (OUTLIER) cc_final: 0.5913 (m) REVERT: M 42 GLU cc_start: 0.8743 (tp30) cc_final: 0.8273 (tp30) REVERT: M 46 GLU cc_start: 0.8413 (mp0) cc_final: 0.8123 (pm20) REVERT: M 51 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8381 (pp20) REVERT: M 59 GLU cc_start: 0.7466 (pp20) cc_final: 0.7079 (pp20) REVERT: M 61 THR cc_start: 0.8315 (p) cc_final: 0.7845 (p) REVERT: M 73 SER cc_start: 0.8740 (t) cc_final: 0.8534 (p) REVERT: M 95 MET cc_start: 0.7978 (mtt) cc_final: 0.7743 (mtt) REVERT: P 14 GLN cc_start: 0.8849 (pt0) cc_final: 0.8302 (mp-120) REVERT: P 67 GLU cc_start: 0.9037 (tp30) cc_final: 0.8670 (tp30) REVERT: P 75 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7960 (mp0) REVERT: P 84 MET cc_start: 0.7680 (mmm) cc_final: 0.7334 (mmt) REVERT: P 118 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7580 (m110) REVERT: Q 72 ASN cc_start: 0.8802 (p0) cc_final: 0.8439 (p0) REVERT: T 17 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7913 (p0) REVERT: T 48 ASP cc_start: 0.7895 (t0) cc_final: 0.7518 (t70) REVERT: U 13 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8461 (mmtp) REVERT: U 51 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7782 (ttp80) REVERT: V 59 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7778 (mm-30) REVERT: V 69 THR cc_start: 0.9251 (m) cc_final: 0.8977 (p) REVERT: W 22 TYR cc_start: 0.8838 (p90) cc_final: 0.8637 (p90) REVERT: W 23 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8033 (pttt) REVERT: W 52 ARG cc_start: 0.8957 (mtm-85) cc_final: 0.8697 (ttm110) REVERT: W 65 SER cc_start: 0.8970 (p) cc_final: 0.8696 (t) REVERT: Y 26 MET cc_start: 0.8817 (tmm) cc_final: 0.8563 (tmm) REVERT: Z 38 GLU cc_start: 0.7383 (tp30) cc_final: 0.7099 (tp30) REVERT: 8 144 MET cc_start: 0.8474 (mmm) cc_final: 0.8202 (mmm) REVERT: 8 170 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: 8 184 ASP cc_start: 0.8749 (t0) cc_final: 0.8537 (t0) REVERT: 8 195 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7982 (p0) REVERT: 8 214 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8357 (tp) REVERT: 8 217 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8233 (mt-10) REVERT: 8 446 ARG cc_start: 0.8354 (mpt-90) cc_final: 0.7931 (tpt170) REVERT: 8 461 MET cc_start: 0.7545 (mmt) cc_final: 0.7287 (tpp) REVERT: 8 473 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7427 (tmt) REVERT: 8 579 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6336 (t70) REVERT: 8 683 GLU cc_start: 0.8445 (tp30) cc_final: 0.8003 (mp0) outliers start: 369 outliers final: 276 residues processed: 1658 average time/residue: 1.3011 time to fit residues: 3783.7256 Evaluate side-chains 1681 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1382 time to evaluate : 8.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 181 ASP Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain i residue 41 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 32 GLU Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 98 LYS Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 43 ASP Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 29 ARG Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain P residue 15 VAL 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 107 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 72 LYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 15 LYS Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain 8 residue 16 SER Chi-restraints excluded: chain 8 residue 36 VAL Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 106 LEU Chi-restraints excluded: chain 8 residue 107 ASP Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 156 ASN Chi-restraints excluded: chain 8 residue 157 GLN Chi-restraints excluded: chain 8 residue 160 THR Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 195 ASP Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 252 LEU Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 343 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 525 LEU Chi-restraints excluded: chain 8 residue 566 LEU Chi-restraints excluded: chain 8 residue 572 VAL Chi-restraints excluded: chain 8 residue 579 HIS Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Chi-restraints excluded: chain 8 residue 694 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 361 optimal weight: 7.9990 chunk 967 optimal weight: 0.0470 chunk 212 optimal weight: 50.0000 chunk 630 optimal weight: 1.9990 chunk 265 optimal weight: 20.0000 chunk 1074 optimal weight: 0.7980 chunk 892 optimal weight: 6.9990 chunk 497 optimal weight: 9.9990 chunk 89 optimal weight: 50.0000 chunk 355 optimal weight: 0.9980 chunk 564 optimal weight: 0.0770 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN b 57 HIS b 116 GLN ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 97 ASN d 163 ASN ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN p 40 GLN ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN L 67 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN K 14 GLN K 17 GLN P 80 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN V 30 HIS V 46 HIS Y 60 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 166465 Z= 0.133 Angle : 0.559 15.714 248236 Z= 0.288 Chirality : 0.033 0.245 31605 Planarity : 0.004 0.060 13907 Dihedral : 23.377 177.056 81297 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.20 % Favored : 90.55 % Rotamer: Outliers : 4.43 % Allowed : 28.55 % Favored : 67.02 % Cbeta Deviations : 0.03 % 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: -2.23 (0.10), residues: 6542 helix: -0.33 (0.12), residues: 2024 sheet: -1.39 (0.16), residues: 1100 loop : -2.28 (0.10), residues: 3418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 102 HIS 0.007 0.001 HIS I 197 PHE 0.045 0.001 PHE Z 36 TYR 0.022 0.002 TYR H 183 ARG 0.026 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1856 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1615 time to evaluate : 6.715 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: b 53 ILE cc_start: 0.9290 (mm) cc_final: 0.9083 (tp) REVERT: b 110 LYS cc_start: 0.8889 (pttm) cc_final: 0.8461 (mtpt) REVERT: b 131 MET cc_start: 0.8980 (mpp) cc_final: 0.8611 (mpp) REVERT: b 145 MET cc_start: 0.8541 (mmm) cc_final: 0.8211 (tpp) REVERT: b 196 ASN cc_start: 0.8402 (t0) cc_final: 0.8080 (t0) REVERT: d 73 ILE cc_start: 0.9093 (mp) cc_final: 0.8872 (mm) REVERT: d 195 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8292 (tm-30) REVERT: e 16 MET cc_start: 0.8279 (tpt) cc_final: 0.7831 (tpt) REVERT: e 25 MET cc_start: 0.8385 (mmm) cc_final: 0.7909 (tpp) REVERT: e 26 GLN cc_start: 0.8730 (tt0) cc_final: 0.8177 (tp40) REVERT: e 82 TYR cc_start: 0.8690 (t80) cc_final: 0.8345 (t80) REVERT: e 126 ASN cc_start: 0.7708 (m110) cc_final: 0.7323 (m110) REVERT: e 174 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6714 (t80) REVERT: f 103 ASN cc_start: 0.8640 (m-40) cc_final: 0.7878 (p0) REVERT: f 114 HIS cc_start: 0.6810 (t-90) cc_final: 0.6221 (t70) REVERT: g 127 GLU cc_start: 0.3433 (OUTLIER) cc_final: 0.3195 (pp20) REVERT: a 172 HIS cc_start: 0.2100 (OUTLIER) cc_final: 0.1862 (t-90) REVERT: i 41 PHE cc_start: -0.1170 (OUTLIER) cc_final: -0.1603 (m-10) REVERT: i 116 MET cc_start: -0.2426 (OUTLIER) cc_final: -0.3071 (ppp) REVERT: i 135 MET cc_start: 0.1590 (mmp) cc_final: 0.1107 (tpt) REVERT: j 1 MET cc_start: 0.7633 (ptp) cc_final: 0.7390 (ptm) REVERT: j 16 TYR cc_start: 0.8653 (m-80) cc_final: 0.8275 (m-80) REVERT: j 86 GLN cc_start: 0.8505 (pp30) cc_final: 0.8257 (pp30) REVERT: j 96 ARG cc_start: 0.8466 (mmp80) cc_final: 0.7794 (mtm180) REVERT: j 102 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7674 (mt-10) REVERT: k 93 GLN cc_start: 0.8541 (mm110) cc_final: 0.8226 (mm-40) REVERT: l 111 ILE cc_start: 0.8650 (mm) cc_final: 0.8371 (mm) REVERT: m 47 GLU cc_start: 0.8835 (tp30) cc_final: 0.8566 (tp30) REVERT: m 65 ILE cc_start: 0.9130 (mm) cc_final: 0.8841 (mm) REVERT: m 100 LYS cc_start: 0.8461 (tptt) cc_final: 0.7989 (tttt) REVERT: m 110 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7894 (tm-30) REVERT: m 129 THR cc_start: 0.9217 (t) cc_final: 0.8973 (p) REVERT: n 94 TYR cc_start: 0.8383 (m-80) cc_final: 0.8115 (m-10) REVERT: o 21 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8087 (tt) REVERT: p 5 LYS cc_start: 0.8889 (tptt) cc_final: 0.8568 (tppt) REVERT: p 30 TRP cc_start: 0.8620 (m100) cc_final: 0.8349 (m100) REVERT: p 37 LYS cc_start: 0.8862 (tppt) cc_final: 0.8568 (tppt) REVERT: s 52 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8323 (mm-30) REVERT: s 78 GLU cc_start: 0.8476 (pm20) cc_final: 0.8017 (pm20) REVERT: t 12 ARG cc_start: 0.8094 (mmm160) cc_final: 0.7662 (mmm160) REVERT: t 42 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7626 (mm-30) REVERT: t 44 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8086 (tttt) REVERT: t 68 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8758 (mmtm) REVERT: u 20 LYS cc_start: 0.8093 (mttt) cc_final: 0.7739 (mptt) REVERT: v 19 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8346 (ptt90) REVERT: v 60 VAL cc_start: 0.7492 (m) cc_final: 0.7096 (p) REVERT: w 13 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7542 (tm-30) REVERT: w 20 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8888 (mmtt) REVERT: w 33 ILE cc_start: 0.9234 (mp) cc_final: 0.8964 (mp) REVERT: w 71 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8240 (mttm) REVERT: w 77 SER cc_start: 0.9020 (m) cc_final: 0.8600 (t) REVERT: y 13 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: y 16 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8983 (t) REVERT: y 52 ARG cc_start: 0.8724 (mtt90) cc_final: 0.8485 (mmm-85) REVERT: y 60 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8510 (tptm) REVERT: z 40 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.8024 (p) REVERT: A 9 TYR cc_start: 0.7379 (t80) cc_final: 0.7059 (t80) REVERT: A 11 GLU cc_start: 0.7705 (pp20) cc_final: 0.7201 (pp20) REVERT: A 12 ILE cc_start: 0.7935 (mt) cc_final: 0.7386 (mp) REVERT: A 16 CYS cc_start: 0.5411 (OUTLIER) cc_final: 0.5113 (t) REVERT: A 35 ASP cc_start: 0.8438 (p0) cc_final: 0.7814 (p0) REVERT: C 42 VAL cc_start: 0.7830 (p) cc_final: 0.7431 (m) REVERT: C 44 GLN cc_start: 0.8662 (pm20) cc_final: 0.7915 (tp40) REVERT: D 1 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5235 (ppp) REVERT: D 25 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8650 (tmtt) REVERT: E 53 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: H 44 LYS cc_start: 0.9198 (tppp) cc_final: 0.8928 (tptp) REVERT: H 138 GLN cc_start: 0.8073 (pt0) cc_final: 0.7861 (pt0) REVERT: H 139 ASN cc_start: 0.9151 (m-40) cc_final: 0.8514 (m-40) REVERT: H 141 MET cc_start: 0.8498 (tpp) cc_final: 0.8259 (tpp) REVERT: H 143 LEU cc_start: 0.8329 (mm) cc_final: 0.8096 (mm) REVERT: H 168 ARG cc_start: 0.8324 (ppt170) cc_final: 0.7720 (ptp-170) REVERT: L 104 VAL cc_start: 0.8418 (t) cc_final: 0.8056 (t) REVERT: L 105 GLU cc_start: 0.8725 (pp20) cc_final: 0.8470 (pp20) REVERT: L 108 ARG cc_start: 0.8422 (mtt90) cc_final: 0.7927 (tmt170) REVERT: L 115 MET cc_start: 0.8495 (tpp) cc_final: 0.8213 (tpt) REVERT: N 24 ASN cc_start: 0.7893 (t0) cc_final: 0.7132 (t0) REVERT: N 26 LYS cc_start: 0.7551 (ptpp) cc_final: 0.7223 (pttt) REVERT: N 55 ASP cc_start: 0.8297 (p0) cc_final: 0.7863 (p0) REVERT: N 125 GLN cc_start: 0.7742 (tm-30) cc_final: 0.6783 (pp30) REVERT: O 63 ASP cc_start: 0.7944 (p0) cc_final: 0.7372 (p0) REVERT: R 67 ASP cc_start: 0.9022 (p0) cc_final: 0.8423 (m-30) REVERT: R 80 MET cc_start: 0.8309 (mmm) cc_final: 0.7959 (mmm) REVERT: S 48 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8857 (tm-30) REVERT: S 91 GLU cc_start: 0.7829 (mp0) cc_final: 0.7569 (mp0) REVERT: X 2 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7256 (mtp85) REVERT: X 60 PHE cc_start: 0.8470 (t80) cc_final: 0.8177 (t80) REVERT: G 92 ASN cc_start: 0.8394 (m-40) cc_final: 0.7822 (t0) REVERT: G 94 ARG cc_start: 0.7348 (mmt180) cc_final: 0.7064 (ptt90) REVERT: G 99 MET cc_start: 0.8208 (ptm) cc_final: 0.7830 (ptp) REVERT: G 153 MET cc_start: 0.8163 (tmm) cc_final: 0.7770 (tmm) REVERT: G 207 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8092 (mmt-90) REVERT: G 221 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7625 (mtt180) REVERT: I 50 TYR cc_start: 0.7621 (t80) cc_final: 0.7316 (t80) REVERT: I 123 MET cc_start: 0.8621 (mtp) cc_final: 0.8368 (tpp) REVERT: I 199 ILE cc_start: 0.8479 (mp) cc_final: 0.8171 (mm) REVERT: J 22 LYS cc_start: 0.8842 (tttm) cc_final: 0.8585 (tptp) REVERT: J 30 PHE cc_start: 0.8054 (m-80) cc_final: 0.7854 (m-80) REVERT: J 53 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.6554 (tpp80) REVERT: J 69 ASN cc_start: 0.8157 (t0) cc_final: 0.7291 (t0) REVERT: J 70 MET cc_start: 0.7252 (mmm) cc_final: 0.6827 (mmm) REVERT: J 96 GLN cc_start: 0.8882 (tt0) cc_final: 0.8608 (mt0) REVERT: K 23 GLU cc_start: 0.8721 (mp0) cc_final: 0.8418 (mp0) REVERT: K 49 TYR cc_start: 0.7762 (p90) cc_final: 0.7423 (p90) REVERT: M 2 MET cc_start: 0.8597 (tpp) cc_final: 0.8213 (tpp) REVERT: M 46 GLU cc_start: 0.8261 (mp0) cc_final: 0.7611 (pm20) REVERT: M 47 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: M 59 GLU cc_start: 0.7303 (pp20) cc_final: 0.6702 (pp20) REVERT: M 61 THR cc_start: 0.8137 (p) cc_final: 0.7039 (p) REVERT: M 127 TYR cc_start: 0.8383 (m-10) cc_final: 0.8169 (m-10) REVERT: P 13 LYS cc_start: 0.8287 (tppt) cc_final: 0.7855 (tptt) REVERT: P 14 GLN cc_start: 0.8809 (pt0) cc_final: 0.8282 (mp-120) REVERT: P 75 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7845 (mp0) REVERT: P 84 MET cc_start: 0.7550 (mmm) cc_final: 0.7192 (mmt) REVERT: P 93 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6896 (tm-30) REVERT: P 118 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7479 (m110) REVERT: P 126 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7421 (mpt180) REVERT: Q 26 CYS cc_start: 0.7787 (t) cc_final: 0.7335 (p) REVERT: Q 65 TYR cc_start: 0.8708 (t80) cc_final: 0.8405 (t80) REVERT: Q 72 ASN cc_start: 0.8812 (p0) cc_final: 0.8394 (p0) REVERT: T 48 ASP cc_start: 0.7717 (t0) cc_final: 0.7369 (t70) REVERT: U 13 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8284 (mmtp) REVERT: U 51 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7807 (ttp80) REVERT: U 63 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7794 (mm110) REVERT: V 59 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7253 (mm-30) REVERT: V 69 THR cc_start: 0.9208 (m) cc_final: 0.8990 (p) REVERT: W 22 TYR cc_start: 0.8537 (p90) cc_final: 0.8253 (p90) REVERT: W 23 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8132 (pttt) REVERT: W 30 ASN cc_start: 0.8550 (m-40) cc_final: 0.8018 (p0) REVERT: W 52 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8164 (ttp-110) REVERT: Y 12 GLN cc_start: 0.7786 (mt0) cc_final: 0.7109 (mp10) REVERT: Y 26 MET cc_start: 0.8663 (tmm) cc_final: 0.8402 (tmm) REVERT: Y 27 MET cc_start: 0.8591 (mmm) cc_final: 0.8287 (mmm) REVERT: Z 20 ARG cc_start: 0.7741 (mtt180) cc_final: 0.6879 (mtt90) REVERT: 8 144 MET cc_start: 0.8431 (mmm) cc_final: 0.8080 (mmm) REVERT: 8 157 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8480 (pp30) REVERT: 8 170 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: 8 184 ASP cc_start: 0.8712 (t0) cc_final: 0.8510 (t0) REVERT: 8 217 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7983 (mt-10) REVERT: 8 446 ARG cc_start: 0.8394 (mpt-90) cc_final: 0.7887 (tpt170) REVERT: 8 473 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7373 (tmt) REVERT: 8 579 HIS cc_start: 0.7083 (t-90) cc_final: 0.6474 (t70) REVERT: 8 630 ASP cc_start: 0.8632 (t70) cc_final: 0.8414 (t70) REVERT: 8 666 TYR cc_start: 0.7989 (t80) cc_final: 0.7551 (t80) REVERT: 8 683 GLU cc_start: 0.8313 (tp30) cc_final: 0.7978 (mp0) outliers start: 241 outliers final: 150 residues processed: 1742 average time/residue: 1.2957 time to fit residues: 3930.0737 Evaluate side-chains 1612 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1444 time to evaluate : 6.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain i residue 41 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 38 ILE Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 38 GLN Chi-restraints excluded: chain y residue 60 LYS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 TRP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 62 GLU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 97 ILE Chi-restraints excluded: chain 8 residue 111 MET Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 157 GLN Chi-restraints excluded: chain 8 residue 160 THR Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 367 HIS Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 1036 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 612 optimal weight: 8.9990 chunk 784 optimal weight: 10.0000 chunk 608 optimal weight: 20.0000 chunk 904 optimal weight: 30.0000 chunk 600 optimal weight: 7.9990 chunk 1070 optimal weight: 9.9990 chunk 670 optimal weight: 5.9990 chunk 652 optimal weight: 20.0000 chunk 494 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 58 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS f 114 HIS ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 GLN o 29 HIS ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN u 39 ASN v 24 ASN v 51 GLN ** x 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN L 85 GLN ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN J 134 ASN K 17 GLN Q 45 ASN Y 60 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 166465 Z= 0.363 Angle : 0.689 15.128 248236 Z= 0.352 Chirality : 0.039 0.291 31605 Planarity : 0.005 0.071 13907 Dihedral : 23.489 179.855 81293 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.43 % Favored : 88.26 % Rotamer: Outliers : 5.90 % Allowed : 28.10 % Favored : 65.99 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.10), residues: 6542 helix: -0.45 (0.12), residues: 2024 sheet: -1.42 (0.16), residues: 1102 loop : -2.35 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP p 30 HIS 0.011 0.002 HIS o 34 PHE 0.042 0.002 PHE Z 36 TYR 0.032 0.003 TYR e 142 ARG 0.015 0.001 ARG Z 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1752 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1431 time to evaluate : 9.221 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: b 196 ASN cc_start: 0.8639 (t0) cc_final: 0.8403 (t0) REVERT: d 73 ILE cc_start: 0.9128 (mp) cc_final: 0.8902 (mm) REVERT: e 16 MET cc_start: 0.8339 (tpt) cc_final: 0.7780 (tpt) REVERT: e 26 GLN cc_start: 0.8840 (tt0) cc_final: 0.8348 (tp40) REVERT: e 80 GLN cc_start: 0.8854 (tp40) cc_final: 0.8558 (tp40) REVERT: e 82 TYR cc_start: 0.8772 (t80) cc_final: 0.8392 (t80) REVERT: e 174 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6683 (t80) REVERT: f 19 ASN cc_start: 0.7591 (m110) cc_final: 0.7337 (m110) REVERT: f 93 TYR cc_start: 0.8418 (m-80) cc_final: 0.8155 (m-80) REVERT: f 103 ASN cc_start: 0.8706 (m-40) cc_final: 0.8034 (p0) REVERT: f 126 THR cc_start: 0.8746 (m) cc_final: 0.8463 (p) REVERT: g 127 GLU cc_start: 0.3563 (OUTLIER) cc_final: 0.3283 (pp20) REVERT: a 172 HIS cc_start: 0.3483 (OUTLIER) cc_final: 0.2972 (t-90) REVERT: i 41 PHE cc_start: -0.0716 (OUTLIER) cc_final: -0.1161 (m-10) REVERT: i 116 MET cc_start: -0.2656 (OUTLIER) cc_final: -0.3251 (ppp) REVERT: i 135 MET cc_start: 0.1952 (mmp) cc_final: 0.1489 (mmm) REVERT: j 1 MET cc_start: 0.7893 (ptp) cc_final: 0.7643 (ptm) REVERT: j 16 TYR cc_start: 0.8789 (m-80) cc_final: 0.8275 (m-80) REVERT: j 86 GLN cc_start: 0.8732 (pp30) cc_final: 0.8482 (pp30) REVERT: j 118 MET cc_start: 0.7988 (mtt) cc_final: 0.7760 (ttm) REVERT: k 2 ILE cc_start: 0.8811 (mt) cc_final: 0.8493 (mm) REVERT: k 93 GLN cc_start: 0.8690 (mm110) cc_final: 0.8232 (mm-40) REVERT: k 118 LEU cc_start: 0.9063 (tp) cc_final: 0.8850 (tt) REVERT: m 47 GLU cc_start: 0.8820 (tp30) cc_final: 0.8223 (tp30) REVERT: m 100 LYS cc_start: 0.8550 (tptt) cc_final: 0.8040 (tttt) REVERT: m 103 TYR cc_start: 0.8255 (m-80) cc_final: 0.7861 (m-80) REVERT: m 110 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7787 (tm-30) REVERT: m 111 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8317 (pp20) REVERT: n 94 TYR cc_start: 0.8728 (m-80) cc_final: 0.8177 (m-80) REVERT: o 21 LEU cc_start: 0.8552 (tt) cc_final: 0.8173 (tt) REVERT: o 61 GLN cc_start: 0.8001 (mm110) cc_final: 0.7637 (tm-30) REVERT: r 1 MET cc_start: 0.7743 (tpp) cc_final: 0.7223 (tpp) REVERT: r 37 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7063 (mm-30) REVERT: s 52 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8276 (mm-30) REVERT: s 78 GLU cc_start: 0.8598 (pm20) cc_final: 0.8028 (pm20) REVERT: t 1 MET cc_start: 0.3536 (mpp) cc_final: 0.2643 (mmm) REVERT: t 7 LEU cc_start: 0.9331 (mt) cc_final: 0.9097 (tp) REVERT: t 42 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7897 (mt-10) REVERT: t 56 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7729 (tm-30) REVERT: t 68 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8759 (mmtm) REVERT: u 17 ASP cc_start: 0.7397 (m-30) cc_final: 0.6524 (m-30) REVERT: u 20 LYS cc_start: 0.8233 (mttt) cc_final: 0.7898 (mttt) REVERT: u 39 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.6790 (t0) REVERT: v 19 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.8327 (ptt90) REVERT: v 60 VAL cc_start: 0.7592 (m) cc_final: 0.7190 (p) REVERT: w 13 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7434 (tm-30) REVERT: w 20 LYS cc_start: 0.9133 (mmtt) cc_final: 0.8931 (mmtt) REVERT: w 56 PHE cc_start: 0.8875 (p90) cc_final: 0.8566 (p90) REVERT: y 13 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: y 52 ARG cc_start: 0.8813 (mtt90) cc_final: 0.8613 (mmm-85) REVERT: z 40 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8117 (p) REVERT: A 12 ILE cc_start: 0.7710 (mt) cc_final: 0.7385 (mp) REVERT: A 35 ASP cc_start: 0.8229 (p0) cc_final: 0.7546 (p0) REVERT: H 7 ASN cc_start: 0.8937 (t0) cc_final: 0.8737 (t0) REVERT: H 44 LYS cc_start: 0.9228 (tppp) cc_final: 0.8890 (tptp) REVERT: H 138 GLN cc_start: 0.7972 (pt0) cc_final: 0.7746 (pt0) REVERT: H 139 ASN cc_start: 0.9152 (m-40) cc_final: 0.8828 (m-40) REVERT: H 141 MET cc_start: 0.8460 (tpp) cc_final: 0.8167 (tpp) REVERT: H 168 ARG cc_start: 0.8461 (ppt170) cc_final: 0.7852 (ptp-170) REVERT: L 20 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: L 41 ILE cc_start: 0.8887 (mm) cc_final: 0.8642 (tp) REVERT: L 85 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7064 (pp30) REVERT: L 102 TRP cc_start: 0.8564 (m-10) cc_final: 0.8250 (m-10) REVERT: L 104 VAL cc_start: 0.8454 (t) cc_final: 0.8088 (t) REVERT: L 108 ARG cc_start: 0.8483 (mtt90) cc_final: 0.7669 (ttt90) REVERT: L 115 MET cc_start: 0.8655 (tpp) cc_final: 0.8253 (tpt) REVERT: N 5 TYR cc_start: 0.7874 (m-10) cc_final: 0.7546 (m-10) REVERT: N 24 ASN cc_start: 0.8062 (t0) cc_final: 0.7531 (t0) REVERT: N 45 MET cc_start: 0.7628 (ppp) cc_final: 0.7315 (ppp) REVERT: N 98 ARG cc_start: 0.7851 (tpt170) cc_final: 0.6364 (ptm160) REVERT: O 63 ASP cc_start: 0.8308 (p0) cc_final: 0.8025 (p0) REVERT: R 80 MET cc_start: 0.8241 (mmm) cc_final: 0.7936 (mmm) REVERT: R 91 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8482 (mtp85) REVERT: S 45 LEU cc_start: 0.7372 (mm) cc_final: 0.6558 (pp) REVERT: S 48 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8863 (tm-30) REVERT: X 2 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7406 (mtp85) REVERT: X 60 PHE cc_start: 0.8372 (t80) cc_final: 0.8082 (t80) REVERT: G 8 MET cc_start: 0.4245 (tmm) cc_final: 0.3921 (tmm) REVERT: G 92 ASN cc_start: 0.8485 (m-40) cc_final: 0.8131 (t0) REVERT: G 94 ARG cc_start: 0.7469 (mmt180) cc_final: 0.7187 (ptt90) REVERT: G 153 MET cc_start: 0.8315 (tmm) cc_final: 0.7933 (tmm) REVERT: G 207 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8150 (mmt-90) REVERT: G 221 ARG cc_start: 0.7973 (mtp-110) cc_final: 0.7667 (mtt180) REVERT: I 50 TYR cc_start: 0.7777 (t80) cc_final: 0.7441 (t80) REVERT: I 123 MET cc_start: 0.8629 (mtp) cc_final: 0.8286 (tpp) REVERT: I 150 LYS cc_start: 0.7470 (mmtp) cc_final: 0.6464 (pttm) REVERT: I 199 ILE cc_start: 0.8599 (mp) cc_final: 0.8159 (mm) REVERT: J 53 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.6762 (tpt-90) REVERT: J 69 ASN cc_start: 0.8215 (t0) cc_final: 0.7317 (t0) REVERT: J 70 MET cc_start: 0.7447 (mmm) cc_final: 0.7125 (mmm) REVERT: J 96 GLN cc_start: 0.8981 (tt0) cc_final: 0.8655 (mt0) REVERT: K 23 GLU cc_start: 0.8685 (mp0) cc_final: 0.8380 (mp0) REVERT: K 49 TYR cc_start: 0.7982 (p90) cc_final: 0.7433 (p90) REVERT: K 74 LEU cc_start: 0.9262 (mm) cc_final: 0.9006 (mm) REVERT: M 2 MET cc_start: 0.8833 (tpp) cc_final: 0.8580 (tpp) REVERT: M 59 GLU cc_start: 0.7507 (pp20) cc_final: 0.6641 (pp20) REVERT: P 14 GLN cc_start: 0.8808 (pt0) cc_final: 0.8268 (mp-120) REVERT: P 67 GLU cc_start: 0.9063 (tp30) cc_final: 0.8761 (tp30) REVERT: P 75 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8068 (mp0) REVERT: P 84 MET cc_start: 0.7593 (mmm) cc_final: 0.7214 (mmt) REVERT: P 118 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7614 (m110) REVERT: Q 65 TYR cc_start: 0.8805 (t80) cc_final: 0.8498 (t80) REVERT: Q 72 ASN cc_start: 0.8804 (p0) cc_final: 0.8442 (p0) REVERT: T 17 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8020 (p0) REVERT: T 27 GLN cc_start: 0.8586 (mt0) cc_final: 0.8021 (mp10) REVERT: T 48 ASP cc_start: 0.7936 (t0) cc_final: 0.7539 (t70) REVERT: U 13 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8454 (mmtp) REVERT: U 51 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7975 (ttp80) REVERT: V 69 THR cc_start: 0.9268 (m) cc_final: 0.8988 (p) REVERT: W 52 ARG cc_start: 0.8950 (mtm-85) cc_final: 0.8173 (ttm-80) REVERT: Y 26 MET cc_start: 0.8839 (tmm) cc_final: 0.8533 (tmm) REVERT: Y 27 MET cc_start: 0.8683 (mmm) cc_final: 0.8325 (mmm) REVERT: Z 38 GLU cc_start: 0.7404 (tp30) cc_final: 0.7090 (tp30) REVERT: Z 66 ARG cc_start: 0.6586 (mmt180) cc_final: 0.5469 (mmt180) REVERT: 8 50 MET cc_start: 0.8634 (mmt) cc_final: 0.8355 (mmt) REVERT: 8 144 MET cc_start: 0.8492 (mmm) cc_final: 0.8213 (mmm) REVERT: 8 157 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8479 (pp30) REVERT: 8 170 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: 8 360 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: 8 405 ILE cc_start: 0.6252 (OUTLIER) cc_final: 0.5820 (mm) REVERT: 8 473 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7458 (tmt) REVERT: 8 579 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6266 (t70) REVERT: 8 683 GLU cc_start: 0.8435 (tp30) cc_final: 0.7939 (mp0) outliers start: 321 outliers final: 224 residues processed: 1616 average time/residue: 1.3257 time to fit residues: 3773.2823 Evaluate side-chains 1612 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1368 time to evaluate : 6.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain a residue 224 VAL Chi-restraints excluded: chain i residue 41 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 38 GLN Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 55 GLN Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 72 LYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain 8 residue 16 SER Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 107 ASP Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 157 GLN Chi-restraints excluded: chain 8 residue 160 THR Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 343 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 360 PHE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 405 ILE Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 566 LEU Chi-restraints excluded: chain 8 residue 579 HIS Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Chi-restraints excluded: chain 8 residue 681 THR Chi-restraints excluded: chain 8 residue 694 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 662 optimal weight: 6.9990 chunk 427 optimal weight: 30.0000 chunk 639 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 210 optimal weight: 30.0000 chunk 207 optimal weight: 10.0000 chunk 680 optimal weight: 20.0000 chunk 729 optimal weight: 20.0000 chunk 529 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 841 optimal weight: 40.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 36 GLN e 126 ASN f 44 HIS ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN u 39 ASN v 87 GLN ** x 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN H 184 ASN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 166465 Z= 0.267 Angle : 0.629 15.134 248236 Z= 0.325 Chirality : 0.037 0.277 31605 Planarity : 0.005 0.100 13907 Dihedral : 23.514 179.683 81291 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.87 % Favored : 88.84 % Rotamer: Outliers : 5.39 % Allowed : 29.12 % Favored : 65.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 6542 helix: -0.40 (0.11), residues: 2029 sheet: -1.39 (0.16), residues: 1110 loop : -2.33 (0.10), residues: 3403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 102 HIS 0.015 0.001 HIS j 80 PHE 0.044 0.002 PHE Z 36 TYR 0.031 0.002 TYR e 142 ARG 0.011 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1426 time to evaluate : 9.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 145 MET cc_start: 0.8437 (mmm) cc_final: 0.8176 (tpp) REVERT: b 196 ASN cc_start: 0.8647 (t0) cc_final: 0.8367 (t0) REVERT: d 73 ILE cc_start: 0.9113 (mp) cc_final: 0.8898 (mm) REVERT: e 21 TYR cc_start: 0.6524 (m-80) cc_final: 0.6266 (m-80) REVERT: e 25 MET cc_start: 0.8690 (tpp) cc_final: 0.8155 (tpp) REVERT: e 26 GLN cc_start: 0.8877 (tt0) cc_final: 0.8562 (tt0) REVERT: e 80 GLN cc_start: 0.8843 (tp40) cc_final: 0.8513 (tp40) REVERT: e 82 TYR cc_start: 0.8720 (t80) cc_final: 0.8349 (t80) REVERT: e 174 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6678 (t80) REVERT: f 93 TYR cc_start: 0.8460 (m-80) cc_final: 0.8196 (m-80) REVERT: f 103 ASN cc_start: 0.8736 (m-40) cc_final: 0.8016 (p0) REVERT: f 126 THR cc_start: 0.8710 (m) cc_final: 0.8442 (p) REVERT: g 127 GLU cc_start: 0.3611 (OUTLIER) cc_final: 0.3345 (pp20) REVERT: a 172 HIS cc_start: 0.3512 (OUTLIER) cc_final: 0.2960 (t-90) REVERT: i 41 PHE cc_start: -0.0734 (OUTLIER) cc_final: -0.1207 (m-10) REVERT: i 116 MET cc_start: -0.2817 (OUTLIER) cc_final: -0.3313 (ppp) REVERT: i 135 MET cc_start: 0.1699 (mmp) cc_final: 0.1338 (tpt) REVERT: j 1 MET cc_start: 0.7804 (ptp) cc_final: 0.7541 (ptm) REVERT: j 16 TYR cc_start: 0.8770 (m-80) cc_final: 0.8313 (m-80) REVERT: j 86 GLN cc_start: 0.8723 (pp30) cc_final: 0.8475 (pp30) REVERT: j 108 MET cc_start: 0.8701 (mtt) cc_final: 0.8220 (mtt) REVERT: j 118 MET cc_start: 0.7965 (mtt) cc_final: 0.7761 (ttm) REVERT: k 2 ILE cc_start: 0.8822 (mt) cc_final: 0.8515 (mm) REVERT: k 93 GLN cc_start: 0.8675 (mm110) cc_final: 0.8293 (mm-40) REVERT: k 118 LEU cc_start: 0.8998 (tp) cc_final: 0.8792 (tt) REVERT: m 47 GLU cc_start: 0.8823 (tp30) cc_final: 0.8249 (tp30) REVERT: m 100 LYS cc_start: 0.8517 (tptt) cc_final: 0.8009 (tttt) REVERT: m 103 TYR cc_start: 0.8231 (m-80) cc_final: 0.7931 (m-80) REVERT: m 104 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: m 110 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7825 (tm-30) REVERT: n 94 TYR cc_start: 0.8661 (m-80) cc_final: 0.8181 (m-80) REVERT: o 21 LEU cc_start: 0.8489 (tt) cc_final: 0.8145 (tt) REVERT: r 37 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7063 (mt-10) REVERT: s 52 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8303 (mm-30) REVERT: t 1 MET cc_start: 0.3472 (mpp) cc_final: 0.2936 (mpp) REVERT: t 12 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7919 (mmm160) REVERT: t 56 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7685 (tm-30) REVERT: t 68 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8642 (mmmm) REVERT: u 20 LYS cc_start: 0.8194 (mttt) cc_final: 0.7889 (mttp) REVERT: u 65 GLN cc_start: 0.8795 (mt0) cc_final: 0.8230 (mt0) REVERT: v 19 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8305 (ptt90) REVERT: v 60 VAL cc_start: 0.7525 (m) cc_final: 0.7135 (p) REVERT: w 13 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7409 (tm-30) REVERT: w 20 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8909 (mmtt) REVERT: y 13 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: y 16 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8955 (t) REVERT: y 52 ARG cc_start: 0.8806 (mtt90) cc_final: 0.8580 (mmm-85) REVERT: z 40 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 35 ASP cc_start: 0.8285 (p0) cc_final: 0.7638 (p0) REVERT: D 1 MET cc_start: 0.6225 (ppp) cc_final: 0.5263 (ppp) REVERT: H 44 LYS cc_start: 0.9228 (tppp) cc_final: 0.8876 (tptp) REVERT: H 141 MET cc_start: 0.8457 (tpp) cc_final: 0.8139 (tpp) REVERT: H 168 ARG cc_start: 0.8478 (ppt170) cc_final: 0.7839 (ptp-170) REVERT: L 20 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: L 85 GLN cc_start: 0.7074 (pp30) cc_final: 0.6744 (pp30) REVERT: L 102 TRP cc_start: 0.8578 (m-10) cc_final: 0.8325 (m-10) REVERT: L 104 VAL cc_start: 0.8463 (t) cc_final: 0.8095 (t) REVERT: L 108 ARG cc_start: 0.8474 (mtt90) cc_final: 0.7700 (ttt90) REVERT: L 115 MET cc_start: 0.8625 (tpp) cc_final: 0.8289 (tpt) REVERT: N 5 TYR cc_start: 0.7930 (m-10) cc_final: 0.7630 (m-10) REVERT: N 24 ASN cc_start: 0.8053 (t0) cc_final: 0.7541 (t0) REVERT: N 98 ARG cc_start: 0.7829 (tpt170) cc_final: 0.6380 (ptm160) REVERT: O 63 ASP cc_start: 0.8359 (p0) cc_final: 0.8137 (p0) REVERT: R 40 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7902 (mm-30) REVERT: R 80 MET cc_start: 0.8335 (mmm) cc_final: 0.8011 (mmm) REVERT: R 91 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8477 (mtp85) REVERT: S 45 LEU cc_start: 0.7431 (mm) cc_final: 0.6633 (pp) REVERT: S 48 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8853 (tm-30) REVERT: X 2 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7369 (mtp85) REVERT: X 60 PHE cc_start: 0.8394 (t80) cc_final: 0.8094 (t80) REVERT: G 8 MET cc_start: 0.4262 (tmm) cc_final: 0.3859 (tmm) REVERT: G 92 ASN cc_start: 0.8543 (m-40) cc_final: 0.8196 (t0) REVERT: G 94 ARG cc_start: 0.7451 (mmt180) cc_final: 0.7175 (ptt90) REVERT: G 153 MET cc_start: 0.8335 (tmm) cc_final: 0.7956 (tmm) REVERT: G 207 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8160 (mmt-90) REVERT: G 221 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7647 (mtt180) REVERT: I 50 TYR cc_start: 0.7723 (t80) cc_final: 0.7382 (t80) REVERT: I 123 MET cc_start: 0.8639 (mtp) cc_final: 0.8303 (tpp) REVERT: I 150 LYS cc_start: 0.7545 (mmtp) cc_final: 0.6334 (ptpp) REVERT: I 199 ILE cc_start: 0.8557 (mp) cc_final: 0.8185 (mm) REVERT: J 53 ARG cc_start: 0.7518 (mtp-110) cc_final: 0.6825 (ttm-80) REVERT: J 69 ASN cc_start: 0.8217 (t0) cc_final: 0.7299 (t0) REVERT: J 96 GLN cc_start: 0.8931 (tt0) cc_final: 0.8581 (mt0) REVERT: K 23 GLU cc_start: 0.8725 (mp0) cc_final: 0.8449 (mp0) REVERT: M 2 MET cc_start: 0.8806 (tpp) cc_final: 0.8514 (tpp) REVERT: M 42 GLU cc_start: 0.8677 (tp30) cc_final: 0.8455 (tp30) REVERT: M 46 GLU cc_start: 0.8402 (mp0) cc_final: 0.8003 (pm20) REVERT: M 59 GLU cc_start: 0.7471 (pp20) cc_final: 0.6961 (pp20) REVERT: M 61 THR cc_start: 0.8201 (p) cc_final: 0.7621 (p) REVERT: P 13 LYS cc_start: 0.8332 (tppt) cc_final: 0.7878 (tptt) REVERT: P 14 GLN cc_start: 0.8793 (pt0) cc_final: 0.8289 (mp-120) REVERT: P 17 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8493 (m-30) REVERT: P 67 GLU cc_start: 0.8934 (tp30) cc_final: 0.8580 (tp30) REVERT: P 75 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8007 (mp0) REVERT: P 84 MET cc_start: 0.7586 (mmm) cc_final: 0.7238 (mmt) REVERT: P 118 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7554 (m110) REVERT: Q 65 TYR cc_start: 0.8780 (t80) cc_final: 0.8448 (t80) REVERT: Q 72 ASN cc_start: 0.8834 (p0) cc_final: 0.8461 (p0) REVERT: Q 111 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8680 (mm-40) REVERT: T 17 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7961 (p0) REVERT: T 48 ASP cc_start: 0.7986 (t0) cc_final: 0.7568 (t70) REVERT: U 13 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8464 (mmtp) REVERT: U 31 ARG cc_start: 0.8929 (ttp-170) cc_final: 0.8642 (ptm160) REVERT: U 51 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7804 (ttp80) REVERT: V 69 THR cc_start: 0.9306 (m) cc_final: 0.9047 (p) REVERT: W 50 TYR cc_start: 0.8262 (m-80) cc_final: 0.7900 (m-80) REVERT: W 52 ARG cc_start: 0.8936 (mtm-85) cc_final: 0.8166 (ttm-80) REVERT: Y 26 MET cc_start: 0.8794 (tmm) cc_final: 0.8515 (tmm) REVERT: Y 27 MET cc_start: 0.8669 (mmm) cc_final: 0.8309 (mmm) REVERT: Z 38 GLU cc_start: 0.7319 (tp30) cc_final: 0.6980 (tp30) REVERT: 8 144 MET cc_start: 0.8518 (mmm) cc_final: 0.8249 (mmm) REVERT: 8 170 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: 8 405 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5748 (mm) REVERT: 8 446 ARG cc_start: 0.8349 (mpt-90) cc_final: 0.7919 (tpt170) REVERT: 8 473 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7436 (tmt) REVERT: 8 579 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.6026 (t-90) REVERT: 8 625 GLU cc_start: 0.6523 (mm-30) cc_final: 0.6038 (mm-30) REVERT: 8 683 GLU cc_start: 0.8432 (tp30) cc_final: 0.7833 (mp0) outliers start: 293 outliers final: 237 residues processed: 1590 average time/residue: 1.2771 time to fit residues: 3575.5181 Evaluate side-chains 1643 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1388 time to evaluate : 6.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain a residue 224 VAL Chi-restraints excluded: chain i residue 41 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 38 GLN Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 55 GLN Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain P residue 15 VAL 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 39 ASN Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 72 LYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 157 GLN Chi-restraints excluded: chain 8 residue 160 THR Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 343 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 405 ILE Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 579 HIS Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Chi-restraints excluded: chain 8 residue 681 THR Chi-restraints excluded: chain 8 residue 694 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 974 optimal weight: 8.9990 chunk 1025 optimal weight: 8.9990 chunk 935 optimal weight: 6.9990 chunk 997 optimal weight: 20.0000 chunk 600 optimal weight: 8.9990 chunk 434 optimal weight: 30.0000 chunk 783 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 901 optimal weight: 5.9990 chunk 943 optimal weight: 40.0000 chunk 994 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 36 GLN c 58 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN s 15 GLN ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 94 HIS ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 166465 Z= 0.304 Angle : 0.657 15.097 248236 Z= 0.338 Chirality : 0.038 0.404 31605 Planarity : 0.005 0.094 13907 Dihedral : 23.543 179.891 81291 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.75 % Favored : 87.99 % Rotamer: Outliers : 5.81 % Allowed : 29.00 % Favored : 65.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.34 (0.10), residues: 6542 helix: -0.43 (0.11), residues: 2021 sheet: -1.46 (0.16), residues: 1116 loop : -2.33 (0.10), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 96 HIS 0.014 0.001 HIS j 80 PHE 0.045 0.002 PHE w 56 TYR 0.027 0.002 TYR I 64 ARG 0.011 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1724 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1408 time to evaluate : 6.959 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: b 196 ASN cc_start: 0.8665 (t0) cc_final: 0.8434 (t0) REVERT: d 73 ILE cc_start: 0.9141 (mp) cc_final: 0.8919 (mm) REVERT: e 16 MET cc_start: 0.8347 (tpt) cc_final: 0.7835 (tpt) REVERT: e 21 TYR cc_start: 0.6546 (m-80) cc_final: 0.5912 (m-80) REVERT: e 25 MET cc_start: 0.8707 (tpp) cc_final: 0.8204 (tpp) REVERT: e 26 GLN cc_start: 0.8910 (tt0) cc_final: 0.8600 (tt0) REVERT: e 80 GLN cc_start: 0.8855 (tp40) cc_final: 0.8501 (tp40) REVERT: e 82 TYR cc_start: 0.8735 (t80) cc_final: 0.8351 (t80) REVERT: e 174 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6723 (t80) REVERT: f 19 ASN cc_start: 0.7533 (m110) cc_final: 0.7277 (m110) REVERT: f 93 TYR cc_start: 0.8474 (m-80) cc_final: 0.8235 (m-80) REVERT: f 103 ASN cc_start: 0.8728 (m-40) cc_final: 0.8046 (p0) REVERT: f 126 THR cc_start: 0.8743 (m) cc_final: 0.8478 (p) REVERT: g 127 GLU cc_start: 0.3677 (OUTLIER) cc_final: 0.3411 (pp20) REVERT: a 172 HIS cc_start: 0.4060 (OUTLIER) cc_final: 0.3397 (t-90) REVERT: i 41 PHE cc_start: -0.0741 (OUTLIER) cc_final: -0.1215 (m-10) REVERT: i 116 MET cc_start: -0.2880 (OUTLIER) cc_final: -0.3415 (ppp) REVERT: i 135 MET cc_start: 0.1493 (mmp) cc_final: 0.1136 (tpt) REVERT: j 1 MET cc_start: 0.7796 (ptp) cc_final: 0.7550 (ptm) REVERT: j 86 GLN cc_start: 0.8735 (pp30) cc_final: 0.8487 (pp30) REVERT: j 108 MET cc_start: 0.8682 (mtt) cc_final: 0.8360 (mtt) REVERT: j 118 MET cc_start: 0.7932 (mtt) cc_final: 0.7640 (ttm) REVERT: k 2 ILE cc_start: 0.8851 (mt) cc_final: 0.8558 (mm) REVERT: k 93 GLN cc_start: 0.8690 (mm110) cc_final: 0.8279 (mm-40) REVERT: k 118 LEU cc_start: 0.8973 (tp) cc_final: 0.8773 (tt) REVERT: m 47 GLU cc_start: 0.8825 (tp30) cc_final: 0.8253 (tp30) REVERT: m 100 LYS cc_start: 0.8539 (tptt) cc_final: 0.8028 (tttt) REVERT: m 103 TYR cc_start: 0.8242 (m-80) cc_final: 0.7927 (m-80) REVERT: m 104 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6174 (tm-30) REVERT: m 110 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7861 (tm-30) REVERT: n 94 TYR cc_start: 0.8696 (m-80) cc_final: 0.8154 (m-80) REVERT: o 21 LEU cc_start: 0.8437 (tt) cc_final: 0.8121 (tt) REVERT: o 61 GLN cc_start: 0.8040 (mm110) cc_final: 0.7478 (tm-30) REVERT: p 37 LYS cc_start: 0.8912 (tppt) cc_final: 0.8641 (tppt) REVERT: r 37 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7031 (mt-10) REVERT: s 52 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8288 (mm-30) REVERT: t 1 MET cc_start: 0.3465 (mpp) cc_final: 0.2945 (mpp) REVERT: t 12 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7795 (mmm160) REVERT: t 42 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7708 (mm-30) REVERT: t 56 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7630 (tm-30) REVERT: t 68 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8652 (mmmm) REVERT: u 20 LYS cc_start: 0.8271 (mttt) cc_final: 0.7907 (mttt) REVERT: u 65 GLN cc_start: 0.8770 (mt0) cc_final: 0.8278 (mt0) REVERT: v 19 ARG cc_start: 0.8750 (ttp-110) cc_final: 0.8306 (ptt90) REVERT: v 60 VAL cc_start: 0.7502 (m) cc_final: 0.7118 (p) REVERT: w 13 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7462 (tm-30) REVERT: y 16 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8951 (t) REVERT: y 52 ARG cc_start: 0.8841 (mtt90) cc_final: 0.8616 (mmm-85) REVERT: z 18 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8353 (mmmt) REVERT: z 40 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 35 ASP cc_start: 0.8248 (p0) cc_final: 0.7602 (p0) REVERT: B 14 MET cc_start: 0.8546 (ptp) cc_final: 0.8344 (mtm) REVERT: F 30 GLU cc_start: 0.8201 (tp30) cc_final: 0.7547 (tm-30) REVERT: H 44 LYS cc_start: 0.9228 (tppp) cc_final: 0.8864 (tptp) REVERT: H 141 MET cc_start: 0.8466 (tpp) cc_final: 0.8122 (tpp) REVERT: H 168 ARG cc_start: 0.8487 (ppt170) cc_final: 0.7873 (ptp-170) REVERT: L 20 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: L 25 PHE cc_start: 0.9104 (t80) cc_final: 0.8904 (t80) REVERT: L 85 GLN cc_start: 0.7079 (pp30) cc_final: 0.6876 (pp30) REVERT: L 102 TRP cc_start: 0.8644 (m-10) cc_final: 0.8434 (m-10) REVERT: L 104 VAL cc_start: 0.8422 (t) cc_final: 0.8057 (t) REVERT: L 108 ARG cc_start: 0.8487 (mtt90) cc_final: 0.7671 (ttt90) REVERT: L 115 MET cc_start: 0.8623 (tpp) cc_final: 0.8278 (tpt) REVERT: N 5 TYR cc_start: 0.7923 (m-10) cc_final: 0.7632 (m-10) REVERT: N 24 ASN cc_start: 0.8104 (t0) cc_final: 0.7621 (t0) REVERT: N 55 ASP cc_start: 0.8384 (p0) cc_final: 0.7973 (p0) REVERT: N 98 ARG cc_start: 0.7839 (tpt170) cc_final: 0.6405 (ptm160) REVERT: O 63 ASP cc_start: 0.8349 (p0) cc_final: 0.8086 (p0) REVERT: R 40 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7989 (mm-30) REVERT: R 80 MET cc_start: 0.8331 (mmm) cc_final: 0.8009 (mmm) REVERT: R 91 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8498 (mtp85) REVERT: R 109 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8074 (ttpp) REVERT: S 45 LEU cc_start: 0.7412 (mm) cc_final: 0.6622 (pp) REVERT: S 48 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8844 (tm-30) REVERT: X 2 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7385 (mtp85) REVERT: G 8 MET cc_start: 0.4288 (tmm) cc_final: 0.3822 (tmm) REVERT: G 50 ASN cc_start: 0.6922 (m-40) cc_final: 0.6529 (m110) REVERT: G 92 ASN cc_start: 0.8505 (m-40) cc_final: 0.8188 (t0) REVERT: G 94 ARG cc_start: 0.7468 (mmt180) cc_final: 0.7164 (ptt90) REVERT: G 153 MET cc_start: 0.8352 (tmm) cc_final: 0.7961 (tmm) REVERT: G 207 ARG cc_start: 0.8414 (mtt180) cc_final: 0.8141 (mmt-90) REVERT: G 221 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7653 (mtt180) REVERT: I 123 MET cc_start: 0.8620 (mtp) cc_final: 0.8297 (tpp) REVERT: I 150 LYS cc_start: 0.7607 (mmtp) cc_final: 0.6460 (ptpp) REVERT: I 199 ILE cc_start: 0.8660 (mp) cc_final: 0.8233 (mm) REVERT: J 53 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.6810 (ttm-80) REVERT: J 69 ASN cc_start: 0.8140 (t0) cc_final: 0.7262 (t0) REVERT: J 70 MET cc_start: 0.7236 (mmm) cc_final: 0.6938 (mmm) REVERT: J 96 GLN cc_start: 0.8916 (tt0) cc_final: 0.8586 (mt0) REVERT: K 23 GLU cc_start: 0.8763 (mp0) cc_final: 0.8499 (mp0) REVERT: M 2 MET cc_start: 0.8822 (tpp) cc_final: 0.8596 (tpp) REVERT: M 46 GLU cc_start: 0.8416 (mp0) cc_final: 0.8015 (pm20) REVERT: M 59 GLU cc_start: 0.7516 (pp20) cc_final: 0.6989 (pp20) REVERT: M 61 THR cc_start: 0.8099 (p) cc_final: 0.7470 (p) REVERT: M 82 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9319 (tt) REVERT: P 14 GLN cc_start: 0.8804 (pt0) cc_final: 0.8272 (mp-120) REVERT: P 17 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8565 (m-30) REVERT: P 34 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8795 (t) REVERT: P 67 GLU cc_start: 0.8958 (tp30) cc_final: 0.8594 (tp30) REVERT: P 75 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8041 (mp0) REVERT: P 84 MET cc_start: 0.7583 (mmm) cc_final: 0.7206 (mmt) REVERT: P 118 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7585 (m110) REVERT: Q 65 TYR cc_start: 0.8792 (t80) cc_final: 0.8485 (t80) REVERT: Q 72 ASN cc_start: 0.8791 (p0) cc_final: 0.8408 (p0) REVERT: Q 111 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8710 (mm-40) REVERT: T 17 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7923 (p0) REVERT: T 27 GLN cc_start: 0.8569 (mt0) cc_final: 0.8011 (mp10) REVERT: T 48 ASP cc_start: 0.8021 (t0) cc_final: 0.7600 (t70) REVERT: U 13 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8489 (mmtp) REVERT: U 31 ARG cc_start: 0.8921 (ttp-170) cc_final: 0.8672 (ptm160) REVERT: U 51 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8063 (ttp80) REVERT: V 69 THR cc_start: 0.9290 (m) cc_final: 0.9058 (p) REVERT: W 52 ARG cc_start: 0.8951 (mtm-85) cc_final: 0.8743 (ttm110) REVERT: Y 26 MET cc_start: 0.8797 (tmm) cc_final: 0.8595 (tmm) REVERT: Z 38 GLU cc_start: 0.7364 (tp30) cc_final: 0.6996 (tp30) REVERT: 8 144 MET cc_start: 0.8496 (mmm) cc_final: 0.8219 (mmm) REVERT: 8 157 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8503 (pp30) REVERT: 8 170 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: 8 405 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5851 (mm) REVERT: 8 446 ARG cc_start: 0.8330 (mpt-90) cc_final: 0.7923 (tpt170) REVERT: 8 473 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7441 (tmt) REVERT: 8 534 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.4572 (t80) REVERT: 8 579 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6092 (t-90) REVERT: 8 625 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6056 (mm-30) REVERT: 8 683 GLU cc_start: 0.8411 (tp30) cc_final: 0.7760 (mp0) outliers start: 316 outliers final: 272 residues processed: 1591 average time/residue: 1.3025 time to fit residues: 3647.3063 Evaluate side-chains 1668 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1375 time to evaluate : 6.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain a residue 224 VAL Chi-restraints excluded: chain i residue 41 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 15 GLN Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 38 GLN Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain P residue 15 VAL 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 57 SER Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 72 LYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain 8 residue 16 SER Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 107 ASP Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 157 GLN Chi-restraints excluded: chain 8 residue 160 THR Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 343 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 405 ILE Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 534 TYR Chi-restraints excluded: chain 8 residue 579 HIS Chi-restraints excluded: chain 8 residue 587 ASP Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Chi-restraints excluded: chain 8 residue 681 THR Chi-restraints excluded: chain 8 residue 694 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 655 optimal weight: 40.0000 chunk 1055 optimal weight: 0.9990 chunk 644 optimal weight: 9.9990 chunk 500 optimal weight: 7.9990 chunk 733 optimal weight: 20.0000 chunk 1106 optimal weight: 30.0000 chunk 1018 optimal weight: 20.0000 chunk 881 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 680 optimal weight: 30.0000 chunk 540 optimal weight: 8.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 36 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 166465 Z= 0.319 Angle : 0.673 15.164 248236 Z= 0.346 Chirality : 0.039 0.411 31605 Planarity : 0.005 0.119 13907 Dihedral : 23.593 179.707 81291 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.43 % Favored : 88.29 % Rotamer: Outliers : 5.55 % Allowed : 29.39 % Favored : 65.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.10), residues: 6542 helix: -0.48 (0.11), residues: 2019 sheet: -1.50 (0.15), residues: 1122 loop : -2.36 (0.10), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 102 HIS 0.015 0.001 HIS j 80 PHE 0.043 0.002 PHE Z 36 TYR 0.037 0.002 TYR I 64 ARG 0.011 0.001 ARG H 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13084 Ramachandran restraints generated. 6542 Oldfield, 0 Emsley, 6542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1683 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1381 time to evaluate : 6.803 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: b 145 MET cc_start: 0.8454 (mmm) cc_final: 0.8191 (tpp) REVERT: b 196 ASN cc_start: 0.8663 (t0) cc_final: 0.8453 (t0) REVERT: d 73 ILE cc_start: 0.9145 (mp) cc_final: 0.8925 (mm) REVERT: e 21 TYR cc_start: 0.6627 (m-80) cc_final: 0.6285 (m-80) REVERT: e 25 MET cc_start: 0.8695 (tpp) cc_final: 0.8252 (tpp) REVERT: e 26 GLN cc_start: 0.8911 (tt0) cc_final: 0.8608 (tt0) REVERT: e 80 GLN cc_start: 0.8841 (tp40) cc_final: 0.8490 (tp40) REVERT: e 82 TYR cc_start: 0.8719 (t80) cc_final: 0.8312 (t80) REVERT: e 174 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6698 (t80) REVERT: f 19 ASN cc_start: 0.7545 (m110) cc_final: 0.7272 (m110) REVERT: f 93 TYR cc_start: 0.8442 (m-80) cc_final: 0.8194 (m-80) REVERT: f 103 ASN cc_start: 0.8715 (m-40) cc_final: 0.8036 (p0) REVERT: f 126 THR cc_start: 0.8742 (m) cc_final: 0.8473 (p) REVERT: g 127 GLU cc_start: 0.3642 (OUTLIER) cc_final: 0.3364 (pp20) REVERT: a 172 HIS cc_start: 0.4122 (OUTLIER) cc_final: 0.3403 (t-90) REVERT: i 41 PHE cc_start: -0.0698 (OUTLIER) cc_final: -0.1179 (m-10) REVERT: i 116 MET cc_start: -0.2387 (OUTLIER) cc_final: -0.3031 (ppp) REVERT: i 135 MET cc_start: 0.1562 (mmp) cc_final: 0.1223 (tpt) REVERT: j 1 MET cc_start: 0.7799 (ptp) cc_final: 0.7558 (ptm) REVERT: j 16 TYR cc_start: 0.8876 (m-80) cc_final: 0.8559 (m-80) REVERT: j 86 GLN cc_start: 0.8743 (pp30) cc_final: 0.8498 (pp30) REVERT: j 118 MET cc_start: 0.7821 (mtt) cc_final: 0.7565 (ttm) REVERT: k 2 ILE cc_start: 0.8862 (mt) cc_final: 0.8529 (mm) REVERT: k 93 GLN cc_start: 0.8706 (mm110) cc_final: 0.8330 (mm-40) REVERT: m 47 GLU cc_start: 0.8812 (tp30) cc_final: 0.8259 (tp30) REVERT: m 100 LYS cc_start: 0.8551 (tptt) cc_final: 0.8077 (tttt) REVERT: m 103 TYR cc_start: 0.8248 (m-80) cc_final: 0.7935 (m-80) REVERT: m 110 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7802 (tm-30) REVERT: n 43 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8324 (mp0) REVERT: n 94 TYR cc_start: 0.8671 (m-80) cc_final: 0.8129 (m-80) REVERT: o 21 LEU cc_start: 0.8467 (tt) cc_final: 0.8159 (tt) REVERT: o 61 GLN cc_start: 0.8052 (mm110) cc_final: 0.7480 (tm-30) REVERT: p 37 LYS cc_start: 0.8889 (tppt) cc_final: 0.8615 (tppt) REVERT: r 37 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7018 (mt-10) REVERT: t 1 MET cc_start: 0.3350 (mpp) cc_final: 0.2849 (mpp) REVERT: t 12 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7814 (mmm160) REVERT: t 42 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7687 (mm-30) REVERT: t 56 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7631 (tm-30) REVERT: t 68 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8648 (mmmm) REVERT: u 20 LYS cc_start: 0.8227 (mttt) cc_final: 0.7837 (mttt) REVERT: u 65 GLN cc_start: 0.8793 (mt0) cc_final: 0.8329 (mt0) REVERT: v 19 ARG cc_start: 0.8765 (ttp-110) cc_final: 0.8307 (ptt90) REVERT: v 60 VAL cc_start: 0.7584 (m) cc_final: 0.7217 (p) REVERT: w 13 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7414 (tm-30) REVERT: y 16 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8933 (t) REVERT: y 52 ARG cc_start: 0.8846 (mtt90) cc_final: 0.8629 (mmm-85) REVERT: z 18 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8294 (mmmt) REVERT: z 40 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.7992 (p) REVERT: A 35 ASP cc_start: 0.8279 (p0) cc_final: 0.7634 (p0) REVERT: B 14 MET cc_start: 0.8511 (ptp) cc_final: 0.8215 (mtm) REVERT: D 1 MET cc_start: 0.6393 (ppp) cc_final: 0.6186 (ppp) REVERT: H 44 LYS cc_start: 0.9229 (tppp) cc_final: 0.8849 (tptp) REVERT: H 141 MET cc_start: 0.8412 (tpp) cc_final: 0.8089 (tpp) REVERT: H 168 ARG cc_start: 0.8499 (ppt170) cc_final: 0.7864 (ptp-170) REVERT: L 20 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: L 41 ILE cc_start: 0.8902 (mm) cc_final: 0.8619 (tp) REVERT: L 102 TRP cc_start: 0.8638 (m-10) cc_final: 0.8427 (m-10) REVERT: L 104 VAL cc_start: 0.8437 (t) cc_final: 0.8080 (t) REVERT: L 108 ARG cc_start: 0.8521 (mtt90) cc_final: 0.7696 (ttt90) REVERT: L 115 MET cc_start: 0.8608 (tpp) cc_final: 0.8203 (tpt) REVERT: N 5 TYR cc_start: 0.7936 (m-10) cc_final: 0.7657 (m-10) REVERT: N 24 ASN cc_start: 0.8148 (t0) cc_final: 0.7664 (t0) REVERT: N 98 ARG cc_start: 0.7835 (tpt170) cc_final: 0.6444 (ptm160) REVERT: O 63 ASP cc_start: 0.8386 (p0) cc_final: 0.8151 (p0) REVERT: R 40 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8078 (mm-30) REVERT: R 71 GLU cc_start: 0.9221 (pp20) cc_final: 0.8945 (pp20) REVERT: R 80 MET cc_start: 0.8332 (mmm) cc_final: 0.8055 (mmm) REVERT: R 91 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8512 (mtp85) REVERT: R 109 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8068 (ttpp) REVERT: S 45 LEU cc_start: 0.7388 (mm) cc_final: 0.6622 (pp) REVERT: S 48 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8912 (tm-30) REVERT: X 2 ARG cc_start: 0.7791 (mtm180) cc_final: 0.7556 (mtp85) REVERT: X 16 LYS cc_start: 0.8613 (mmtm) cc_final: 0.7998 (mtpp) REVERT: G 50 ASN cc_start: 0.6833 (m-40) cc_final: 0.6443 (m110) REVERT: G 92 ASN cc_start: 0.8578 (m-40) cc_final: 0.8252 (t0) REVERT: G 94 ARG cc_start: 0.7498 (mmt180) cc_final: 0.6985 (tmm160) REVERT: G 153 MET cc_start: 0.8359 (tmm) cc_final: 0.7980 (tmm) REVERT: G 207 ARG cc_start: 0.8417 (mtt180) cc_final: 0.8150 (mmt-90) REVERT: G 221 ARG cc_start: 0.7915 (mtp-110) cc_final: 0.7628 (mtt180) REVERT: I 123 MET cc_start: 0.8627 (mtp) cc_final: 0.8297 (tpp) REVERT: I 150 LYS cc_start: 0.7579 (mmtp) cc_final: 0.6453 (ptpp) REVERT: I 199 ILE cc_start: 0.8691 (mp) cc_final: 0.8271 (mm) REVERT: J 53 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.6783 (ttm-80) REVERT: J 69 ASN cc_start: 0.8169 (t0) cc_final: 0.7270 (t0) REVERT: J 70 MET cc_start: 0.7193 (mmm) cc_final: 0.6976 (mmm) REVERT: J 96 GLN cc_start: 0.8872 (tt0) cc_final: 0.8667 (mt0) REVERT: K 23 GLU cc_start: 0.8730 (mp0) cc_final: 0.8450 (mp0) REVERT: K 49 TYR cc_start: 0.7978 (p90) cc_final: 0.7514 (p90) REVERT: K 74 LEU cc_start: 0.9272 (mm) cc_final: 0.8999 (mm) REVERT: M 46 GLU cc_start: 0.8405 (mp0) cc_final: 0.8013 (pm20) REVERT: M 59 GLU cc_start: 0.7528 (pp20) cc_final: 0.7050 (pp20) REVERT: M 61 THR cc_start: 0.8093 (p) cc_final: 0.7446 (p) REVERT: M 82 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9350 (tt) REVERT: P 13 LYS cc_start: 0.8288 (tppt) cc_final: 0.7857 (tptt) REVERT: P 14 GLN cc_start: 0.8814 (pt0) cc_final: 0.8309 (mp-120) REVERT: P 17 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8577 (m-30) REVERT: P 67 GLU cc_start: 0.8922 (tp30) cc_final: 0.8556 (tp30) REVERT: P 75 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8045 (mp0) REVERT: P 76 TYR cc_start: 0.8282 (m-10) cc_final: 0.8031 (m-10) REVERT: P 84 MET cc_start: 0.7614 (mmm) cc_final: 0.7237 (mmt) REVERT: P 118 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7581 (m110) REVERT: Q 65 TYR cc_start: 0.8805 (t80) cc_final: 0.8516 (t80) REVERT: Q 72 ASN cc_start: 0.8792 (p0) cc_final: 0.8431 (p0) REVERT: Q 111 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8722 (mm-40) REVERT: T 17 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7986 (p0) REVERT: T 27 GLN cc_start: 0.8565 (mt0) cc_final: 0.8018 (mp10) REVERT: T 48 ASP cc_start: 0.7922 (t0) cc_final: 0.7509 (t70) REVERT: U 13 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8479 (mmtp) REVERT: U 31 ARG cc_start: 0.8898 (ttp-170) cc_final: 0.8670 (ptm160) REVERT: U 51 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8074 (ttp80) REVERT: V 69 THR cc_start: 0.9301 (m) cc_final: 0.9039 (p) REVERT: W 52 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8721 (ttm110) REVERT: Z 38 GLU cc_start: 0.7579 (tp30) cc_final: 0.7339 (tp30) REVERT: 8 144 MET cc_start: 0.8501 (mmm) cc_final: 0.8227 (mmm) REVERT: 8 157 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8502 (pp30) REVERT: 8 170 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7798 (pt0) REVERT: 8 405 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.5951 (mm) REVERT: 8 446 ARG cc_start: 0.8325 (mpt-90) cc_final: 0.7901 (tpt170) REVERT: 8 473 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7535 (tmt) REVERT: 8 579 HIS cc_start: 0.6613 (OUTLIER) cc_final: 0.6015 (t-90) REVERT: 8 625 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6049 (mm-30) REVERT: 8 683 GLU cc_start: 0.8465 (tp30) cc_final: 0.7781 (mp0) outliers start: 302 outliers final: 263 residues processed: 1565 average time/residue: 1.3338 time to fit residues: 3674.5688 Evaluate side-chains 1648 residues out of total 5437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1367 time to evaluate : 6.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 127 GLU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 172 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain a residue 224 VAL Chi-restraints excluded: chain i residue 41 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 128 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 55 MET Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 9 GLN Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 25 LEU Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 38 GLN Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 55 GLN Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 197 HIS Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain P residue 15 VAL 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 39 ASN Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 72 LYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain 8 residue 16 SER Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 107 ASP Chi-restraints excluded: chain 8 residue 119 VAL Chi-restraints excluded: chain 8 residue 154 VAL Chi-restraints excluded: chain 8 residue 157 GLN Chi-restraints excluded: chain 8 residue 160 THR Chi-restraints excluded: chain 8 residue 170 GLN Chi-restraints excluded: chain 8 residue 200 VAL Chi-restraints excluded: chain 8 residue 262 ILE Chi-restraints excluded: chain 8 residue 272 ASN Chi-restraints excluded: chain 8 residue 296 ASN Chi-restraints excluded: chain 8 residue 343 VAL Chi-restraints excluded: chain 8 residue 344 ASN Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 381 ASP Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 405 ILE Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 473 MET Chi-restraints excluded: chain 8 residue 519 VAL Chi-restraints excluded: chain 8 residue 579 HIS Chi-restraints excluded: chain 8 residue 650 THR Chi-restraints excluded: chain 8 residue 652 VAL Chi-restraints excluded: chain 8 residue 681 THR Chi-restraints excluded: chain 8 residue 694 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 700 optimal weight: 30.0000 chunk 938 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 812 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 882 optimal weight: 50.0000 chunk 369 optimal weight: 4.9990 chunk 906 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 overall best weight: 8.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 36 GLN c 58 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 13 HIS ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN s 15 GLN ** u 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS 8 579 HIS 8 584 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.082336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063676 restraints weight = 575684.030| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.05 r_work: 0.3114 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 166465 Z= 0.372 Angle : 0.717 15.119 248236 Z= 0.367 Chirality : 0.041 0.362 31605 Planarity : 0.006 0.115 13907 Dihedral : 23.685 179.774 81291 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.40 % Favored : 87.33 % Rotamer: Outliers : 5.89 % Allowed : 29.37 % Favored : 64.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.47 (0.10), residues: 6542 helix: -0.55 (0.11), residues: 1990 sheet: -1.60 (0.15), residues: 1122 loop : -2.36 (0.10), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 96 HIS 0.015 0.002 HIS j 80 PHE 0.042 0.002 PHE Z 36 TYR 0.047 0.003 TYR I 64 ARG 0.012 0.001 ARG H 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52508.99 seconds wall clock time: 913 minutes 54.86 seconds (54834.86 seconds total)