Starting phenix.real_space_refine on Sun Feb 25 16:59:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8p_6709/02_2024/5x8p_6709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8p_6709/02_2024/5x8p_6709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8p_6709/02_2024/5x8p_6709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8p_6709/02_2024/5x8p_6709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8p_6709/02_2024/5x8p_6709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8p_6709/02_2024/5x8p_6709.pdb" } resolution = 3.4 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= 0.002 sd= 0.016 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 4508 5.49 5 S 191 5.16 5 C 74923 2.51 5 N 27512 2.21 5 O 39992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 20": "NH1" <-> "NH2" Residue "2 ARG 28": "NH1" <-> "NH2" Residue "2 ARG 32": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 112": "NH1" <-> "NH2" Residue "3 ARG 114": "NH1" <-> "NH2" Residue "3 ARG 121": "NH1" <-> "NH2" Residue "3 ARG 126": "NH1" <-> "NH2" Residue "3 ARG 127": "NH1" <-> "NH2" Residue "3 ARG 132": "NH1" <-> "NH2" Residue "3 ARG 146": "NH1" <-> "NH2" Residue "4 ARG 101": "NH1" <-> "NH2" Residue "4 ARG 103": "NH1" <-> "NH2" Residue "4 ARG 112": "NH1" <-> "NH2" Residue "4 ARG 113": "NH1" <-> "NH2" Residue "4 ARG 114": "NH1" <-> "NH2" Residue "4 ARG 128": "NH1" <-> "NH2" Residue "4 ARG 131": "NH1" <-> "NH2" Residue "5 ARG 4": "NH1" <-> "NH2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 18": "NH1" <-> "NH2" Residue "5 ARG 20": "NH1" <-> "NH2" Residue "5 ARG 22": "NH1" <-> "NH2" Residue "7 ARG 50": "NH1" <-> "NH2" Residue "7 ARG 63": "NH1" <-> "NH2" Residue "7 ARG 69": "NH1" <-> "NH2" Residue "7 ARG 74": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ARG 176": "NH1" <-> "NH2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G ARG 192": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 175": "NH1" <-> "NH2" Residue "K ARG 179": "NH1" <-> "NH2" Residue "K ARG 194": "NH1" <-> "NH2" Residue "K ARG 198": "NH1" <-> "NH2" Residue "K ARG 205": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 242": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 34": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 97": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 192": "NH1" <-> "NH2" Residue "M ARG 252": "NH1" <-> "NH2" Residue "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 14": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 52": "NH1" <-> "NH2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 101": "NH1" <-> "NH2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 116": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 27": "NH1" <-> "NH2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 43": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "O ARG 73": "NH1" <-> "NH2" Residue "O ARG 74": "NH1" <-> "NH2" Residue "O PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "O ARG 113": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "P ARG 49": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P ARG 143": "NH1" <-> "NH2" Residue "P ARG 151": "NH1" <-> "NH2" Residue "P ARG 160": "NH1" <-> "NH2" Residue "Q ARG 116": "NH1" <-> "NH2" Residue "Q ARG 138": "NH1" <-> "NH2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 152": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "Q ARG 161": "NH1" <-> "NH2" Residue "Q ARG 172": "NH1" <-> "NH2" Residue "Q ARG 182": "NH1" <-> "NH2" Residue "Q ARG 184": "NH1" <-> "NH2" Residue "Q ARG 185": "NH1" <-> "NH2" Residue "Q ARG 228": "NH1" <-> "NH2" Residue "Q PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 12": "NH1" <-> "NH2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 58": "NH1" <-> "NH2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 72": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 207": "NH1" <-> "NH2" Residue "S ARG 213": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "T ARG 35": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 48": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 119": "NH1" <-> "NH2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "T ARG 127": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "U ARG 106": "NH1" <-> "NH2" Residue "U ARG 148": "NH1" <-> "NH2" Residue "U ARG 160": "NH1" <-> "NH2" Residue "U ARG 167": "NH1" <-> "NH2" Residue "V ARG 146": "NH1" <-> "NH2" Residue "V ARG 156": "NH1" <-> "NH2" Residue "V ARG 159": "NH1" <-> "NH2" Residue "V ARG 173": "NH1" <-> "NH2" Residue "X ARG 70": "NH1" <-> "NH2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "Y ARG 73": "NH1" <-> "NH2" Residue "Y ARG 97": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Z ARG 69": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "Z ARG 111": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 86": "NH1" <-> "NH2" Residue "b ARG 90": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 119": "NH1" <-> "NH2" Residue "b ARG 122": "NH1" <-> "NH2" Residue "b ARG 129": "NH1" <-> "NH2" Residue "b ARG 132": "NH1" <-> "NH2" Residue "b ARG 136": "NH1" <-> "NH2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b ARG 178": "NH1" <-> "NH2" Residue "b ASP 209": "OD1" <-> "OD2" Residue "b ARG 215": "NH1" <-> "NH2" Residue "b ARG 229": "NH1" <-> "NH2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 40": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 108": "NH1" <-> "NH2" Residue "c ARG 116": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "c ARG 183": "NH1" <-> "NH2" Residue "c ARG 190": "NH1" <-> "NH2" Residue "c ARG 201": "NH1" <-> "NH2" Residue "e TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 226": "NH1" <-> "NH2" Residue "e ARG 280": "NH1" <-> "NH2" Residue "e ARG 290": "NH1" <-> "NH2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "f ARG 106": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 147": "NH1" <-> "NH2" Residue "f ARG 158": "NH1" <-> "NH2" Residue "f ARG 200": "NH1" <-> "NH2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 143": "NH1" <-> "NH2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 64": "NH1" <-> "NH2" Residue "h TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "i ARG 152": "NH1" <-> "NH2" Residue "i ARG 173": "NH1" <-> "NH2" Residue "i ARG 176": "NH1" <-> "NH2" Residue "i ARG 189": "NH1" <-> "NH2" Residue "j ARG 155": "NH1" <-> "NH2" Residue "k PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 137": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 31": "NH1" <-> "NH2" Residue "l ARG 36": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ARG 94": "NH1" <-> "NH2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ARG 110": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "m ARG 135": "NH1" <-> "NH2" Residue "o ARG 34": "NH1" <-> "NH2" Residue "o ARG 35": "NH1" <-> "NH2" Residue "o ARG 51": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 74": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 18": "NH1" <-> "NH2" Residue "p ARG 25": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p ARG 31": "NH1" <-> "NH2" Residue "p ARG 73": "NH1" <-> "NH2" Residue "r ARG 27": "NH1" <-> "NH2" Residue "r TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 38": "NH1" <-> "NH2" Residue "r ARG 49": "NH1" <-> "NH2" Residue "r ARG 50": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 60": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "s ARG 17": "NH1" <-> "NH2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "t ARG 84": "NH1" <-> "NH2" Residue "t ARG 103": "NH1" <-> "NH2" Residue "t ARG 105": "NH1" <-> "NH2" Residue "t ARG 150": "NH1" <-> "NH2" Residue "t ARG 162": "NH1" <-> "NH2" Residue "u ARG 104": "NH1" <-> "NH2" Residue "u ARG 109": "NH1" <-> "NH2" Residue "u ARG 120": "NH1" <-> "NH2" Residue "y ARG 91": "NH1" <-> "NH2" Residue "y ARG 110": "NH1" <-> "NH2" Residue "y ARG 115": "NH1" <-> "NH2" Residue "y ARG 130": "NH1" <-> "NH2" Residue "y ARG 131": "NH1" <-> "NH2" Residue "y ARG 140": "NH1" <-> "NH2" Residue "y ARG 166": "NH1" <-> "NH2" Residue "w ARG 98": "NH1" <-> "NH2" Residue "w GLU 107": "OE1" <-> "OE2" Residue "w ASP 115": "OD1" <-> "OD2" Residue "w ARG 134": "NH1" <-> "NH2" Residue "w ASP 136": "OD1" <-> "OD2" Residue "w GLU 140": "OE1" <-> "OE2" Residue "w GLU 146": "OE1" <-> "OE2" Residue "w ASP 165": "OD1" <-> "OD2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d ARG 47": "NH1" <-> "NH2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d ARG 108": "NH1" <-> "NH2" Residue "d ARG 114": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "d ARG 129": "NH1" <-> "NH2" Residue "d ARG 139": "NH1" <-> "NH2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "v ASP 17": "OD1" <-> "OD2" Residue "v ARG 22": "NH1" <-> "NH2" Residue "v ARG 23": "NH1" <-> "NH2" Residue "v ARG 31": "NH1" <-> "NH2" Residue "v ASP 36": "OD1" <-> "OD2" Residue "v ARG 39": "NH1" <-> "NH2" Residue "v GLU 44": "OE1" <-> "OE2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "v ARG 61": "NH1" <-> "NH2" Residue "v ARG 63": "NH1" <-> "NH2" Residue "v ARG 64": "NH1" <-> "NH2" Residue "v GLU 74": "OE1" <-> "OE2" Residue "v ASP 75": "OD1" <-> "OD2" Residue "v GLU 81": "OE1" <-> "OE2" Residue "v ASP 85": "OD1" <-> "OD2" Residue "v GLU 87": "OE1" <-> "OE2" Residue "v ARG 91": "NH1" <-> "NH2" Residue "v GLU 99": "OE1" <-> "OE2" Residue "v ASP 106": "OD1" <-> "OD2" Residue "v GLU 113": "OE1" <-> "OE2" Residue "v ASP 114": "OD1" <-> "OD2" Residue "v GLU 119": "OE1" <-> "OE2" Residue "v GLU 136": "OE1" <-> "OE2" Residue "v ASP 140": "OD1" <-> "OD2" Residue "v GLU 144": "OE1" <-> "OE2" Residue "v ARG 155": "NH1" <-> "NH2" Residue "v GLU 173": "OE1" <-> "OE2" Residue "v GLU 174": "OE1" <-> "OE2" Residue "v GLU 177": "OE1" <-> "OE2" Residue "v GLU 189": "OE1" <-> "OE2" Residue "v ARG 194": "NH1" <-> "NH2" Residue "n ARG 9": "NH1" <-> "NH2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 14": "NH1" <-> "NH2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 24": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" Residue "n ARG 62": "NH1" <-> "NH2" Residue "n ARG 70": "NH1" <-> "NH2" Residue "n ARG 74": "NH1" <-> "NH2" Residue "n ARG 84": "NH1" <-> "NH2" Residue "x ARG 75": "NH1" <-> "NH2" Residue "x PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 350": "OE1" <-> "OE2" Residue "8 PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 147126 Number of models: 1 Model: "" Number of chains: 58 Chain: "1" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 378 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "3" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "4" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "5" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "6" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 422 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "7" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 368 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 8, 'TRANS': 37} Chain: "B" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2500 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 49} Link IDs: {'rna2p': 9, 'rna3p': 107} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1904 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1655 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "F" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1351 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1353 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "K" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1568 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1342 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain: "N" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1067 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "O" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "P" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 947 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "Q" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 996 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "S" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 13, 'TRANS': 133} Chain: "T" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1149 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "U" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 740 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "W" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2187 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 36} Link IDs: {'rna2p': 13, 'rna3p': 88} Chain: "X" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 810 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "Y" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 605 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "Z" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "A" Number of atoms: 60324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2809, 60324 Classifications: {'RNA': 2809} Modifications used: {'rna2p_pur': 279, 'rna2p_pyr': 120, 'rna3p_pur': 1352, 'rna3p_pyr': 1058} Link IDs: {'rna2p': 399, 'rna3p': 2409} Chain: "0" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "b" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1787 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "c" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1719 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "e" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1292 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "f" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 886 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "g" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1161 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "h" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1088 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "i" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1020 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "j" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "k" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "m" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "o" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 525 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "p" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 664 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "q" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 635 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 62} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 832 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "u" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 393 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "y" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "a" Number of atoms: 31777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1480, 31777 Classifications: {'RNA': 1480} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 77, 'rna3p_pur': 730, 'rna3p_pyr': 555} Link IDs: {'rna2p': 195, 'rna3p': 1284} Chain breaks: 2 Chain: "w" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "d" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1633 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "v" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "n" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "x" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 289 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "8" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1201 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Time building chain proxies: 55.53, per 1000 atoms: 0.38 Number of scatterers: 147126 At special positions: 0 Unit cell: (283.5, 277.2, 225.75, 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 191 16.00 P 4508 15.00 O 39992 8.00 N 27512 7.00 C 74923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 11 " - pdb=" SG CYS 5 27 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM A0TV4 O5' G a1381 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.83 Conformation dependent library (CDL) restraints added in 6.9 seconds 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11654 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 72 sheets defined 33.1% alpha, 15.3% beta 1520 base pairs and 2501 stacking pairs defined. Time for finding SS restraints: 50.94 Creating SS restraints... Processing helix chain '1' and resid 9 through 26 Processing helix chain '1' and resid 28 through 38 Processing helix chain '3' and resid 101 through 109 removed outlier: 3.520A pdb=" N THR 3 108 " --> pdb=" O SER 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 110 through 116 Processing helix chain '3' and resid 117 through 131 Processing helix chain '4' and resid 95 through 100 Processing helix chain '4' and resid 125 through 132 Processing helix chain '4' and resid 140 through 145 Processing helix chain '5' and resid 29 through 33 removed outlier: 3.696A pdb=" N LYS 5 33 " --> pdb=" O PRO 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 95 through 128 Processing helix chain '6' and resid 132 through 138 Processing helix chain '7' and resid 68 through 73 removed outlier: 3.755A pdb=" N LYS 7 73 " --> pdb=" O ARG 7 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.885A pdb=" N VAL C 196 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 198 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 removed outlier: 3.609A pdb=" N TRP C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 210' Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.817A pdb=" N ALA D 160 " --> pdb=" O HIS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.800A pdb=" N HIS D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 95 removed outlier: 3.546A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.611A pdb=" N LEU E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 197 removed outlier: 3.670A pdb=" N ILE E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.645A pdb=" N GLU E 217 " --> pdb=" O VAL E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 259 Processing helix chain 'F' and resid 57 through 63 removed outlier: 4.023A pdb=" N GLU F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'F' and resid 99 through 114 Processing helix chain 'F' and resid 146 through 160 removed outlier: 3.700A pdb=" N TYR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'G' and resid 98 through 121 removed outlier: 3.604A pdb=" N ASN G 102 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 190 Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'K' and resid 55 through 73 Processing helix chain 'K' and resid 123 through 137 removed outlier: 3.825A pdb=" N HIS K 134 " --> pdb=" O THR K 130 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY K 137 " --> pdb=" O ILE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 161 removed outlier: 3.610A pdb=" N LYS K 160 " --> pdb=" O ASN K 157 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL K 161 " --> pdb=" O ALA K 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 157 through 161' Processing helix chain 'K' and resid 166 through 171 Processing helix chain 'K' and resid 187 through 195 Processing helix chain 'K' and resid 198 through 206 removed outlier: 3.618A pdb=" N ARG K 205 " --> pdb=" O GLU K 201 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY K 206 " --> pdb=" O HIS K 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 Processing helix chain 'L' and resid 110 through 116 removed outlier: 3.798A pdb=" N VAL L 114 " --> pdb=" O PHE L 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 149 Processing helix chain 'M' and resid 162 through 167 removed outlier: 3.597A pdb=" N VAL M 167 " --> pdb=" O ARG M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 184 Processing helix chain 'M' and resid 218 through 228 Processing helix chain 'M' and resid 243 through 253 removed outlier: 3.565A pdb=" N ALA M 253 " --> pdb=" O ASN M 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 110 through 121 Processing helix chain 'N' and resid 122 through 124 No H-bonds generated for 'chain 'N' and resid 122 through 124' Processing helix chain 'O' and resid 23 through 42 Processing helix chain 'O' and resid 48 through 65 removed outlier: 3.918A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA O 65 " --> pdb=" O MET O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 removed outlier: 3.572A pdb=" N ARG O 73 " --> pdb=" O SER O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 removed outlier: 4.205A pdb=" N VAL O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 87' Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 100 through 104 Processing helix chain 'P' and resid 116 through 131 removed outlier: 3.906A pdb=" N CYS P 131 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 161 removed outlier: 4.373A pdb=" N ALA P 154 " --> pdb=" O GLY P 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 138 Processing helix chain 'Q' and resid 175 through 178 Processing helix chain 'Q' and resid 226 through 230 Processing helix chain 'R' and resid 8 through 21 removed outlier: 3.606A pdb=" N ARG R 12 " --> pdb=" O TYR R 8 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE R 17 " --> pdb=" O ARG R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 70 removed outlier: 4.872A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 77 through 87 removed outlier: 3.668A pdb=" N PHE R 81 " --> pdb=" O ASN R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 104 Processing helix chain 'R' and resid 104 through 117 removed outlier: 3.893A pdb=" N LYS R 117 " --> pdb=" O ASN R 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 111 Processing helix chain 'T' and resid 42 through 53 removed outlier: 3.601A pdb=" N ALA T 46 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE T 53 " --> pdb=" O VAL T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 65 Processing helix chain 'T' and resid 72 through 90 removed outlier: 3.931A pdb=" N ILE T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 161 removed outlier: 4.642A pdb=" N ALA T 159 " --> pdb=" O LYS T 155 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU T 161 " --> pdb=" O LEU T 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 113 Processing helix chain 'U' and resid 121 through 132 removed outlier: 3.517A pdb=" N ILE U 125 " --> pdb=" O THR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 150 removed outlier: 3.563A pdb=" N GLU U 149 " --> pdb=" O LYS U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 189 removed outlier: 3.514A pdb=" N LEU U 187 " --> pdb=" O ASN U 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 54 removed outlier: 3.745A pdb=" N LYS V 54 " --> pdb=" O TRP V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 61 removed outlier: 3.857A pdb=" N SER V 60 " --> pdb=" O LYS V 57 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU V 61 " --> pdb=" O PRO V 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 57 through 61' Processing helix chain 'X' and resid 149 through 165 removed outlier: 3.527A pdb=" N ARG X 153 " --> pdb=" O SER X 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS X 165 " --> pdb=" O GLN X 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 132 Processing helix chain 'Y' and resid 133 through 142 removed outlier: 3.601A pdb=" N VAL Y 137 " --> pdb=" O GLY Y 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 70 removed outlier: 3.842A pdb=" N LEU Z 68 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Z 69 " --> pdb=" O LYS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 96 Processing helix chain 'Z' and resid 101 through 125 removed outlier: 3.506A pdb=" N PHE Z 105 " --> pdb=" O LYS Z 101 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG Z 109 " --> pdb=" O PHE Z 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Z 114 " --> pdb=" O LYS Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 129 through 142 removed outlier: 3.538A pdb=" N ARG Z 142 " --> pdb=" O LYS Z 138 " (cutoff:3.500A) Processing helix chain '0' and resid 81 through 86 Processing helix chain '0' and resid 94 through 99 removed outlier: 3.571A pdb=" N LYS 0 99 " --> pdb=" O GLU 0 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 16 removed outlier: 3.859A pdb=" N MET b 13 " --> pdb=" O ASN b 9 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA b 16 " --> pdb=" O GLU b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 46 through 68 removed outlier: 3.696A pdb=" N ALA b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 90 removed outlier: 3.888A pdb=" N VAL b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA b 85 " --> pdb=" O ALA b 81 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG b 90 " --> pdb=" O ARG b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 127 removed outlier: 3.518A pdb=" N THR b 111 " --> pdb=" O ASN b 107 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 152 Processing helix chain 'b' and resid 173 through 184 Processing helix chain 'b' and resid 210 through 230 Processing helix chain 'c' and resid 6 through 11 Processing helix chain 'c' and resid 25 through 53 Processing helix chain 'c' and resid 80 through 84 Processing helix chain 'c' and resid 89 through 101 removed outlier: 3.608A pdb=" N GLU c 93 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 140 through 154 Processing helix chain 'c' and resid 188 through 191 Processing helix chain 'e' and resid 196 through 209 Processing helix chain 'e' and resid 250 through 259 Processing helix chain 'e' and resid 275 through 288 removed outlier: 3.715A pdb=" N THR e 288 " --> pdb=" O VAL e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 292 through 300 Processing helix chain 'f' and resid 124 through 137 Processing helix chain 'f' and resid 185 through 195 removed outlier: 3.722A pdb=" N ASP f 195 " --> pdb=" O ALA f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.611A pdb=" N MET g 25 " --> pdb=" O ARG g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.658A pdb=" N GLN g 52 " --> pdb=" O LYS g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 68 removed outlier: 3.744A pdb=" N GLY g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 133 through 146 removed outlier: 4.003A pdb=" N MET g 144 " --> pdb=" O GLU g 140 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 18 removed outlier: 3.876A pdb=" N ILE h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 41 removed outlier: 4.019A pdb=" N ARG h 41 " --> pdb=" O LYS h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 103 removed outlier: 3.964A pdb=" N MET h 103 " --> pdb=" O LEU h 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 116 through 122 Processing helix chain 'i' and resid 101 through 105 Processing helix chain 'i' and resid 109 through 123 removed outlier: 3.988A pdb=" N GLN i 113 " --> pdb=" O PRO i 109 " (cutoff:3.500A) Proline residue: i 118 - end of helix removed outlier: 3.529A pdb=" N LEU i 122 " --> pdb=" O PRO i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 138 through 156 removed outlier: 3.576A pdb=" N LYS i 156 " --> pdb=" O ARG i 152 " (cutoff:3.500A) Processing helix chain 'i' and resid 157 through 160 removed outlier: 6.583A pdb=" N SER i 160 " --> pdb=" O VAL i 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 157 through 160' Processing helix chain 'i' and resid 161 through 168 removed outlier: 3.609A pdb=" N GLN i 167 " --> pdb=" O ALA i 163 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU i 168 " --> pdb=" O PRO i 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 107 through 126 Processing helix chain 'j' and resid 173 through 181 Processing helix chain 'k' and resid 68 through 81 Processing helix chain 'k' and resid 82 through 84 No H-bonds generated for 'chain 'k' and resid 82 through 84' Processing helix chain 'k' and resid 101 through 113 removed outlier: 3.745A pdb=" N ALA k 105 " --> pdb=" O GLY k 101 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 51 Processing helix chain 'm' and resid 56 through 64 Processing helix chain 'm' and resid 79 through 93 removed outlier: 3.780A pdb=" N SER m 93 " --> pdb=" O THR m 89 " (cutoff:3.500A) Processing helix chain 'm' and resid 95 through 113 removed outlier: 4.116A pdb=" N LEU m 100 " --> pdb=" O GLU m 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG m 113 " --> pdb=" O VAL m 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 115 through 123 removed outlier: 3.605A pdb=" N ILE m 123 " --> pdb=" O CYS m 119 " (cutoff:3.500A) Processing helix chain 'o' and resid 22 through 41 Processing helix chain 'o' and resid 48 through 71 removed outlier: 3.961A pdb=" N GLY o 52 " --> pdb=" O SER o 48 " (cutoff:3.500A) Processing helix chain 'o' and resid 72 through 82 removed outlier: 3.725A pdb=" N LEU o 82 " --> pdb=" O LEU o 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 60 Processing helix chain 'p' and resid 64 through 74 removed outlier: 3.504A pdb=" N ALA p 74 " --> pdb=" O ILE p 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 53 Processing helix chain 'r' and resid 55 through 72 Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.591A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 3.553A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 120 Processing helix chain 't' and resid 127 through 148 removed outlier: 3.983A pdb=" N LEU t 131 " --> pdb=" O PRO t 127 " (cutoff:3.500A) Processing helix chain 't' and resid 155 through 171 Processing helix chain 'u' and resid 100 through 106 Processing helix chain 'u' and resid 107 through 113 removed outlier: 7.595A pdb=" N ALA u 110 " --> pdb=" O VAL u 107 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY u 111 " --> pdb=" O MET u 108 " (cutoff:3.500A) Processing helix chain 'u' and resid 122 through 137 removed outlier: 3.688A pdb=" N ALA u 137 " --> pdb=" O HIS u 133 " (cutoff:3.500A) Processing helix chain 'y' and resid 87 through 102 removed outlier: 3.869A pdb=" N ARG y 91 " --> pdb=" O SER y 87 " (cutoff:3.500A) Processing helix chain 'y' and resid 152 through 175 Processing helix chain 'w' and resid 137 through 148 Processing helix chain 'w' and resid 152 through 176 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 42 through 59 removed outlier: 3.791A pdb=" N HIS d 57 " --> pdb=" O LYS d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 75 Processing helix chain 'd' and resid 78 through 87 removed outlier: 4.167A pdb=" N LEU d 84 " --> pdb=" O GLY d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 98 Processing helix chain 'd' and resid 103 through 113 Processing helix chain 'd' and resid 139 through 144 removed outlier: 3.716A pdb=" N LYS d 143 " --> pdb=" O ASP d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 155 Processing helix chain 'd' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) Processing helix chain 'v' and resid 10 through 20 Processing helix chain 'v' and resid 34 through 44 removed outlier: 3.853A pdb=" N GLU v 44 " --> pdb=" O THR v 40 " (cutoff:3.500A) Processing helix chain 'v' and resid 72 through 84 removed outlier: 3.869A pdb=" N ASN v 84 " --> pdb=" O ILE v 80 " (cutoff:3.500A) Processing helix chain 'v' and resid 105 through 116 Processing helix chain 'v' and resid 134 through 145 Processing helix chain 'v' and resid 172 through 184 Processing helix chain 'n' and resid 3 through 32 removed outlier: 3.877A pdb=" N ILE n 7 " --> pdb=" O ARG n 3 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR n 20 " --> pdb=" O LEU n 16 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU n 30 " --> pdb=" O SER n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 49 Processing helix chain 'n' and resid 80 through 86 removed outlier: 3.866A pdb=" N ARG n 84 " --> pdb=" O GLY n 80 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU n 85 " --> pdb=" O HIS n 81 " (cutoff:3.500A) Processing helix chain 'x' and resid 61 through 69 removed outlier: 3.751A pdb=" N LYS x 65 " --> pdb=" O THR x 61 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 66 Processing helix chain '8' and resid 250 through 257 Processing helix chain '8' and resid 289 through 292 Processing helix chain '8' and resid 319 through 323 removed outlier: 4.123A pdb=" N ARG 8 323 " --> pdb=" O GLU 8 320 " (cutoff:3.500A) Processing helix chain '8' and resid 341 through 359 removed outlier: 3.670A pdb=" N GLU 8 347 " --> pdb=" O LYS 8 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain '4' and resid 102 through 104 Processing sheet with id=AA3, first strand: chain '5' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain '7' and resid 90 through 91 removed outlier: 7.007A pdb=" N ALA S 181 " --> pdb=" O ILE S 224 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE S 224 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS S 183 " --> pdb=" O THR S 222 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG S 218 " --> pdb=" O GLU S 187 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN S 189 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE S 216 " --> pdb=" O GLN S 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 78 removed outlier: 3.776A pdb=" N THR C 76 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.801A pdb=" N ASN C 139 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 159 through 163 removed outlier: 4.390A pdb=" N THR C 169 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS C 163 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 258 through 264 removed outlier: 5.620A pdb=" N LYS D 260 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLY D 201 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG D 262 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE D 199 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR D 202 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU D 289 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 114 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET D 99 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 112 " --> pdb=" O MET D 99 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 101 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL D 110 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 275 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 268 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS D 279 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 266 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 165 through 172 removed outlier: 6.847A pdb=" N GLU D 142 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 168 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY D 140 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU D 170 " --> pdb=" O GLN D 138 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN D 138 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG D 172 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA D 136 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA D 136 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL D 126 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN D 138 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 122 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 123 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS D 184 " --> pdb=" O VAL D 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AB2, first strand: chain 'E' and resid 228 through 229 removed outlier: 7.373A pdb=" N PHE E 207 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 246 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE E 208 " --> pdb=" O VAL E 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 119 through 120 removed outlier: 3.577A pdb=" N LEU F 144 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 87 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 48 through 49 removed outlier: 3.754A pdb=" N LEU G 90 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 55 through 59 Processing sheet with id=AB6, first strand: chain 'G' and resid 161 through 164 Processing sheet with id=AB7, first strand: chain 'G' and resid 135 through 139 Processing sheet with id=AB8, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AB9, first strand: chain 'K' and resid 221 through 223 removed outlier: 6.163A pdb=" N TYR K 115 " --> pdb=" O ILE K 154 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL K 156 " --> pdb=" O TYR K 115 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL K 117 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TRP K 114 " --> pdb=" O ILE K 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 7 through 10 removed outlier: 7.370A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS L 44 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA L 84 " --> pdb=" O HIS L 7 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 76 through 78 removed outlier: 3.609A pdb=" N ILE L 76 " --> pdb=" O VAL Q 195 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG Q 182 " --> pdb=" O ILE Q 170 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU Q 153 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP Q 147 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE Q 148 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL Q 208 " --> pdb=" O ILE Q 148 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN Q 150 " --> pdb=" O ILE Q 206 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE Q 206 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG Q 152 " --> pdb=" O LYS Q 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AC4, first strand: chain 'M' and resid 175 through 176 Processing sheet with id=AC5, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.391A pdb=" N ILE N 102 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA N 36 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR N 104 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 40 through 43 removed outlier: 3.696A pdb=" N LYS N 72 " --> pdb=" O VAL N 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 44 through 47 Processing sheet with id=AC8, first strand: chain 'P' and resid 93 through 99 removed outlier: 6.542A pdb=" N VAL P 86 " --> pdb=" O LEU P 95 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA P 97 " --> pdb=" O VAL P 84 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL P 84 " --> pdb=" O ALA P 97 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER P 99 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU P 82 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU P 73 " --> pdb=" O ALA P 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 132 through 136 Processing sheet with id=AD1, first strand: chain 'S' and resid 164 through 165 Processing sheet with id=AD2, first strand: chain 'S' and resid 197 through 200 Processing sheet with id=AD3, first strand: chain 'T' and resid 31 through 34 Processing sheet with id=AD4, first strand: chain 'T' and resid 31 through 34 Processing sheet with id=AD5, first strand: chain 'T' and resid 111 through 117 Processing sheet with id=AD6, first strand: chain 'U' and resid 115 through 118 Processing sheet with id=AD7, first strand: chain 'V' and resid 129 through 130 removed outlier: 7.595A pdb=" N THR V 98 " --> pdb=" O ILE V 92 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE V 92 " --> pdb=" O THR V 98 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE V 100 " --> pdb=" O SER V 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 107 through 110 Processing sheet with id=AD9, first strand: chain 'V' and resid 149 through 151 Processing sheet with id=AE1, first strand: chain 'X' and resid 78 through 79 removed outlier: 6.430A pdb=" N ILE X 92 " --> pdb=" O ALA X 117 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA X 117 " --> pdb=" O ILE X 92 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 122 through 124 Processing sheet with id=AE3, first strand: chain 'Y' and resid 83 through 84 Processing sheet with id=AE4, first strand: chain 'Y' and resid 87 through 88 removed outlier: 3.787A pdb=" N ARG Y 87 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR Y 95 " --> pdb=" O ARG Y 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'Y' and resid 104 through 110 Processing sheet with id=AE6, first strand: chain '0' and resid 58 through 63 removed outlier: 4.893A pdb=" N GLY 0 63 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU 0 47 " --> pdb=" O GLY 0 63 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR 0 68 " --> pdb=" O ASP 0 48 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS 0 50 " --> pdb=" O TYR 0 68 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL 0 70 " --> pdb=" O LYS 0 50 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR 0 52 " --> pdb=" O VAL 0 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 37 through 39 Processing sheet with id=AE8, first strand: chain 'b' and resid 94 through 95 removed outlier: 3.507A pdb=" N ILE b 73 " --> pdb=" O HIS b 94 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU b 72 " --> pdb=" O ILE b 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'b' and resid 190 through 191 Processing sheet with id=AF1, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.698A pdb=" N LYS c 67 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG c 62 " --> pdb=" O HIS c 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.698A pdb=" N LYS c 67 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG c 62 " --> pdb=" O HIS c 77 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR c 115 " --> pdb=" O VAL c 74 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE c 76 " --> pdb=" O THR c 115 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 177 through 181 Processing sheet with id=AF4, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.517A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN e 158 " --> pdb=" O ILE e 177 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.517A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN e 158 " --> pdb=" O ILE e 177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN e 186 " --> pdb=" O ASP e 182 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'e' and resid 227 through 228 removed outlier: 6.767A pdb=" N ILE e 248 " --> pdb=" O GLY e 267 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN e 269 " --> pdb=" O ILE e 248 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 106 through 107 Processing sheet with id=AF8, first strand: chain 'f' and resid 146 through 155 removed outlier: 5.392A pdb=" N ASN f 146 " --> pdb=" O LEU f 175 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU f 175 " --> pdb=" O ASN f 146 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY f 148 " --> pdb=" O TYR f 173 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR f 173 " --> pdb=" O GLY f 148 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE f 150 " --> pdb=" O GLY f 171 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY f 171 " --> pdb=" O ILE f 150 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU f 169 " --> pdb=" O LEU f 152 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE f 172 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL f 113 " --> pdb=" O ARG f 200 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG f 200 " --> pdb=" O VAL f 113 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 74 through 75 removed outlier: 3.755A pdb=" N ALA g 74 " --> pdb=" O ILE g 89 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 78 through 80 Processing sheet with id=AG2, first strand: chain 'h' and resid 24 through 27 removed outlier: 6.240A pdb=" N PHE h 58 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS h 50 " --> pdb=" O PHE h 58 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL h 60 " --> pdb=" O ALA h 48 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA h 48 " --> pdb=" O VAL h 60 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR h 62 " --> pdb=" O GLU h 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 114 through 115 removed outlier: 3.562A pdb=" N LEU h 108 " --> pdb=" O MET h 115 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE h 105 " --> pdb=" O TYR h 132 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR h 132 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE h 107 " --> pdb=" O LEU h 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 128 " --> pdb=" O SER h 109 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'i' and resid 73 through 78 removed outlier: 3.551A pdb=" N HIS i 135 " --> pdb=" O ILE i 82 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 95 through 96 Processing sheet with id=AG6, first strand: chain 'j' and resid 130 through 134 removed outlier: 4.871A pdb=" N GLY j 131 " --> pdb=" O ASP j 168 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP j 168 " --> pdb=" O GLY j 131 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'j' and resid 130 through 134 removed outlier: 4.871A pdb=" N GLY j 131 " --> pdb=" O ASP j 168 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP j 168 " --> pdb=" O GLY j 131 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 50 through 55 removed outlier: 6.235A pdb=" N GLY k 28 " --> pdb=" O GLU k 92 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET k 94 " --> pdb=" O GLY k 28 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE k 30 " --> pdb=" O MET k 94 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS k 96 " --> pdb=" O ILE k 30 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL k 32 " --> pdb=" O LYS k 96 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA k 91 " --> pdb=" O SER k 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL k 119 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL k 93 " --> pdb=" O VAL k 119 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP k 121 " --> pdb=" O VAL k 93 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE k 95 " --> pdb=" O ASP k 121 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 39 through 40 removed outlier: 4.390A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'p' and resid 2 through 8 removed outlier: 4.042A pdb=" N ILE p 22 " --> pdb=" O LYS p 3 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'q' and resid 61 through 64 removed outlier: 3.793A pdb=" N ASP q 115 " --> pdb=" O LEU q 127 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU q 127 " --> pdb=" O ASP q 115 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE q 126 " --> pdb=" O GLN q 98 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 's' and resid 48 through 52 Processing sheet with id=AH4, first strand: chain 'y' and resid 76 through 82 removed outlier: 6.109A pdb=" N LYS y 76 " --> pdb=" O VAL y 112 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL y 114 " --> pdb=" O LYS y 76 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE y 78 " --> pdb=" O VAL y 114 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU y 116 " --> pdb=" O ILE y 78 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN y 80 " --> pdb=" O LEU y 116 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA y 118 " --> pdb=" O GLN y 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG y 82 " --> pdb=" O ALA y 118 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'w' and resid 100 through 106 Processing sheet with id=AH6, first strand: chain 'd' and resid 117 through 118 Processing sheet with id=AH7, first strand: chain 'v' and resid 48 through 53 removed outlier: 3.714A pdb=" N THR v 86 " --> pdb=" O ILE v 93 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'v' and resid 148 through 154 removed outlier: 3.923A pdb=" N PHE v 165 " --> pdb=" O GLN v 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS v 123 " --> pdb=" O ALA v 198 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '8' and resid 309 through 310 removed outlier: 7.097A pdb=" N PHE 8 277 " --> pdb=" O GLN 8 269 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU 8 271 " --> pdb=" O GLY 8 275 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY 8 275 " --> pdb=" O LEU 8 271 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU 8 326 " --> pdb=" O ASN 8 284 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU 8 286 " --> pdb=" O LEU 8 326 " (cutoff:3.500A) 1834 hydrogen bonds defined for protein. 5184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3829 hydrogen bonds 5966 hydrogen bond angles 0 basepair planarities 1520 basepair parallelities 2501 stacking parallelities Total time for adding SS restraints: 253.59 Time building geometry restraints manager: 64.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 13 1.17 - 1.34: 33384 1.34 - 1.50: 80583 1.50 - 1.67: 45251 1.67 - 1.84: 321 Bond restraints: 159552 Sorted by residual: bond pdb=" CZ ARG h 67 " pdb=" NH2 ARG h 67 " ideal model delta sigma weight residual 1.330 1.127 0.203 1.30e-02 5.92e+03 2.45e+02 bond pdb=" CB ARG h 67 " pdb=" CG ARG h 67 " ideal model delta sigma weight residual 1.520 1.127 0.393 3.00e-02 1.11e+03 1.72e+02 bond pdb=" CE1 PHE v 142 " pdb=" CZ PHE v 142 " ideal model delta sigma weight residual 1.382 1.008 0.374 3.00e-02 1.11e+03 1.55e+02 bond pdb=" CE2 PHE v 142 " pdb=" CZ PHE v 142 " ideal model delta sigma weight residual 1.382 1.030 0.352 3.00e-02 1.11e+03 1.38e+02 bond pdb=" CG ASN b 7 " pdb=" ND2 ASN b 7 " ideal model delta sigma weight residual 1.328 1.084 0.244 2.10e-02 2.27e+03 1.35e+02 ... (remaining 159547 not shown) Histogram of bond angle deviations from ideal: 85.27 - 97.33: 10 97.33 - 109.39: 63694 109.39 - 121.45: 134070 121.45 - 133.51: 39821 133.51 - 145.57: 112 Bond angle restraints: 237707 Sorted by residual: angle pdb=" NE ARG h 67 " pdb=" CZ ARG h 67 " pdb=" NH1 ARG h 67 " ideal model delta sigma weight residual 121.50 145.57 -24.07 1.00e+00 1.00e+00 5.79e+02 angle pdb=" CA ASP b 201 " pdb=" CB ASP b 201 " pdb=" CG ASP b 201 " ideal model delta sigma weight residual 112.60 126.79 -14.19 1.00e+00 1.00e+00 2.01e+02 angle pdb=" NH1 ARG h 67 " pdb=" CZ ARG h 67 " pdb=" NH2 ARG h 67 " ideal model delta sigma weight residual 119.30 101.21 18.09 1.30e+00 5.92e-01 1.94e+02 angle pdb=" CD ARG h 67 " pdb=" NE ARG h 67 " pdb=" CZ ARG h 67 " ideal model delta sigma weight residual 124.40 143.78 -19.38 1.40e+00 5.10e-01 1.92e+02 angle pdb=" CB ARG h 67 " pdb=" CG ARG h 67 " pdb=" CD ARG h 67 " ideal model delta sigma weight residual 111.30 143.04 -31.74 2.30e+00 1.89e-01 1.90e+02 ... (remaining 237702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 90279 35.78 - 71.55: 10456 71.55 - 107.33: 1309 107.33 - 143.10: 19 143.10 - 178.88: 17 Dihedral angle restraints: 102080 sinusoidal: 83983 harmonic: 18097 Sorted by residual: dihedral pdb=" CA THR 8 302 " pdb=" C THR 8 302 " pdb=" N VAL 8 303 " pdb=" CA VAL 8 303 " ideal model delta harmonic sigma weight residual -180.00 -103.83 -76.17 0 5.00e+00 4.00e-02 2.32e+02 dihedral pdb=" CA MET 8 72 " pdb=" C MET 8 72 " pdb=" N GLU 8 73 " pdb=" CA GLU 8 73 " ideal model delta harmonic sigma weight residual 180.00 110.70 69.30 0 5.00e+00 4.00e-02 1.92e+02 dihedral pdb=" CA THR S 174 " pdb=" C THR S 174 " pdb=" N PRO S 175 " pdb=" CA PRO S 175 " ideal model delta harmonic sigma weight residual -180.00 -117.75 -62.25 0 5.00e+00 4.00e-02 1.55e+02 ... (remaining 102077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 30037 0.238 - 0.477: 79 0.477 - 0.715: 9 0.715 - 0.953: 2 0.953 - 1.192: 1 Chirality restraints: 30128 Sorted by residual: chirality pdb=" CB ILE 8 280 " pdb=" CA ILE 8 280 " pdb=" CG1 ILE 8 280 " pdb=" CG2 ILE 8 280 " both_signs ideal model delta sigma weight residual False 2.64 1.45 1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" CG LEU 8 315 " pdb=" CB LEU 8 315 " pdb=" CD1 LEU 8 315 " pdb=" CD2 LEU 8 315 " both_signs ideal model delta sigma weight residual False -2.59 -1.71 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" CG LEU b 60 " pdb=" CB LEU b 60 " pdb=" CD1 LEU b 60 " pdb=" CD2 LEU b 60 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 30125 not shown) Planarity restraints: 13281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 103 " -0.122 2.00e-02 2.50e+03 8.62e-02 1.30e+02 pdb=" CG PHE u 103 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE u 103 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE u 103 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE u 103 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE u 103 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE u 103 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 8 346 " -0.034 2.00e-02 2.50e+03 7.76e-02 1.05e+02 pdb=" CG PHE 8 346 " 0.157 2.00e-02 2.50e+03 pdb=" CD1 PHE 8 346 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE 8 346 " -0.108 2.00e-02 2.50e+03 pdb=" CE1 PHE 8 346 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE 8 346 " 0.034 2.00e-02 2.50e+03 pdb=" CZ PHE 8 346 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE v 165 " 0.113 2.00e-02 2.50e+03 7.37e-02 9.50e+01 pdb=" CG PHE v 165 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 PHE v 165 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE v 165 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE v 165 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE v 165 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE v 165 " 0.082 2.00e-02 2.50e+03 ... (remaining 13278 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 41 1.82 - 2.59: 2163 2.59 - 3.36: 169678 3.36 - 4.13: 470362 4.13 - 4.90: 671503 Nonbonded interactions: 1313747 Sorted by model distance: nonbonded pdb=" C2 A A1927 " pdb=" N6 A a1442 " model vdw 1.051 3.420 nonbonded pdb=" N6 A A1930 " pdb=" O2' A a1357 " model vdw 1.083 2.520 nonbonded pdb=" ND1 HIS d 163 " pdb=" CD1 ILE d 179 " model vdw 1.255 3.540 nonbonded pdb=" N LEU 0 87 " pdb=" NH1 ARG m 105 " model vdw 1.262 3.200 nonbonded pdb=" NH1 ARG L 97 " pdb=" OP2 C a 310 " model vdw 1.284 2.520 ... (remaining 1313742 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: 4.690 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: 0.190 Extract box with map and model: 16.980 Check model and map are aligned: 1.590 Set scattering table: 1.020 Process input model: 523.120 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.440 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: 0.040 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 553.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.008 0.393 159552 Z= 0.467 Angle : 1.051 31.737 237707 Z= 0.528 Chirality : 0.050 1.192 30128 Planarity : 0.008 0.166 13281 Dihedral : 22.794 178.877 90423 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.93 % Favored : 88.51 % Rotamer: Outliers : 0.76 % Allowed : 3.86 % Favored : 95.37 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.08), residues: 6213 helix: -3.17 (0.08), residues: 1910 sheet: -2.68 (0.15), residues: 918 loop : -3.06 (0.09), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.004 TRP w 150 HIS 0.035 0.003 HIS 8 294 PHE 0.157 0.005 PHE 8 346 TYR 0.091 0.004 TYR w 130 ARG 0.153 0.002 ARG v 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1956 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1915 time to evaluate : 6.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 13 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5598 (mp) REVERT: 7 49 SER cc_start: 0.8200 (t) cc_final: 0.7872 (p) REVERT: C 73 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7422 (mtpp) REVERT: C 86 TYR cc_start: 0.7977 (m-80) cc_final: 0.7741 (m-10) REVERT: C 128 LEU cc_start: 0.8529 (tp) cc_final: 0.8202 (tp) REVERT: D 170 GLU cc_start: 0.7600 (pm20) cc_final: 0.6916 (pm20) REVERT: E 218 LYS cc_start: 0.7119 (tttm) cc_final: 0.6867 (mmmt) REVERT: G 112 THR cc_start: 0.6842 (p) cc_final: 0.6621 (p) REVERT: K 116 VAL cc_start: 0.8683 (t) cc_final: 0.8437 (p) REVERT: K 186 GLU cc_start: 0.6676 (tp30) cc_final: 0.6473 (tp30) REVERT: L 65 THR cc_start: 0.8809 (t) cc_final: 0.8461 (p) REVERT: M 242 ILE cc_start: 0.8169 (mt) cc_final: 0.7361 (mt) REVERT: N 11 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8099 (mttt) REVERT: N 47 ILE cc_start: 0.8796 (mm) cc_final: 0.8504 (mt) REVERT: N 66 VAL cc_start: 0.8790 (t) cc_final: 0.8487 (p) REVERT: N 109 VAL cc_start: 0.8478 (t) cc_final: 0.8257 (t) REVERT: O 89 LEU cc_start: 0.8789 (tm) cc_final: 0.8557 (tp) REVERT: Q 140 VAL cc_start: 0.7717 (p) cc_final: 0.7391 (p) REVERT: Q 203 ILE cc_start: 0.7530 (pt) cc_final: 0.7277 (pt) REVERT: Q 205 GLU cc_start: 0.7053 (pm20) cc_final: 0.6774 (pm20) REVERT: S 167 LYS cc_start: 0.7867 (tptm) cc_final: 0.7625 (tppp) REVERT: S 172 ILE cc_start: 0.8273 (mp) cc_final: 0.8064 (mp) REVERT: S 174 THR cc_start: 0.7564 (m) cc_final: 0.6739 (p) REVERT: S 208 ARG cc_start: 0.8421 (mmt-90) cc_final: 0.8133 (mmt-90) REVERT: S 230 TYR cc_start: 0.5650 (p90) cc_final: 0.4292 (p90) REVERT: T 156 LYS cc_start: 0.7551 (mttm) cc_final: 0.6563 (pttm) REVERT: X 73 LYS cc_start: 0.7577 (pmtt) cc_final: 0.7286 (pmtt) REVERT: X 92 ILE cc_start: 0.9449 (mm) cc_final: 0.9189 (mt) REVERT: X 100 LYS cc_start: 0.8110 (mttp) cc_final: 0.7833 (mttp) REVERT: X 150 TYR cc_start: 0.5418 (m-10) cc_final: 0.4822 (m-80) REVERT: Y 80 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8180 (mtpp) REVERT: Y 124 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7512 (mmmt) REVERT: Z 78 GLU cc_start: 0.7062 (tp30) cc_final: 0.6831 (mm-30) REVERT: c 22 TRP cc_start: 0.7629 (p-90) cc_final: 0.7365 (p-90) REVERT: c 110 LEU cc_start: 0.7406 (pp) cc_final: 0.7201 (pt) REVERT: c 187 GLN cc_start: 0.7834 (mm110) cc_final: 0.7603 (mm-40) REVERT: e 174 PHE cc_start: 0.7165 (m-80) cc_final: 0.6730 (m-80) REVERT: e 198 VAL cc_start: 0.8232 (t) cc_final: 0.7098 (p) REVERT: e 264 ASN cc_start: 0.7614 (m-40) cc_final: 0.7052 (m-40) REVERT: e 266 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7540 (pt) REVERT: e 305 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5259 (mm-30) REVERT: g 142 HIS cc_start: 0.6284 (t-90) cc_final: 0.5207 (t-170) REVERT: h 1 MET cc_start: 0.3413 (ptp) cc_final: 0.3143 (ptp) REVERT: h 31 ILE cc_start: 0.8188 (tt) cc_final: 0.7826 (tt) REVERT: h 38 ILE cc_start: 0.8071 (pt) cc_final: 0.7859 (tt) REVERT: h 65 HIS cc_start: 0.6520 (m-70) cc_final: 0.6235 (p-80) REVERT: h 67 ARG cc_start: -0.0441 (OUTLIER) cc_final: -0.1766 (tpt-90) REVERT: h 92 ASN cc_start: 0.7966 (p0) cc_final: 0.7633 (p0) REVERT: h 131 CYS cc_start: 0.8089 (p) cc_final: 0.7850 (p) REVERT: j 158 PHE cc_start: 0.7801 (p90) cc_final: 0.7452 (p90) REVERT: l 7 LEU cc_start: 0.8668 (tt) cc_final: 0.8317 (tt) REVERT: m 136 THR cc_start: 0.7994 (p) cc_final: 0.7642 (t) REVERT: o 61 GLN cc_start: 0.7706 (tp40) cc_final: 0.7423 (tm-30) REVERT: p 23 ASP cc_start: 0.8215 (t70) cc_final: 0.7916 (t70) REVERT: p 39 TYR cc_start: 0.8035 (t80) cc_final: 0.7792 (t80) REVERT: q 73 THR cc_start: 0.7390 (m) cc_final: 0.7174 (m) REVERT: q 80 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7661 (ptm-80) REVERT: q 81 LEU cc_start: 0.7317 (mt) cc_final: 0.6960 (pp) REVERT: q 87 TYR cc_start: 0.7830 (m-80) cc_final: 0.7446 (m-80) REVERT: t 92 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6620 (ttp-110) REVERT: t 105 ARG cc_start: 0.7744 (mmt-90) cc_final: 0.6887 (tpp-160) REVERT: y 97 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7739 (mmmt) REVERT: y 177 ASP cc_start: 0.4436 (m-30) cc_final: 0.4159 (m-30) REVERT: d 53 LYS cc_start: 0.7643 (ttmt) cc_final: 0.7320 (ttmt) REVERT: n 23 ILE cc_start: 0.7439 (mt) cc_final: 0.7129 (mt) outliers start: 41 outliers final: 11 residues processed: 1940 average time/residue: 1.4691 time to fit residues: 4638.5373 Evaluate side-chains 1473 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1458 time to evaluate : 6.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain b residue 201 ASP Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 305 GLU Chi-restraints excluded: chain h residue 67 ARG Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain v residue 24 LEU Chi-restraints excluded: chain v residue 175 GLU Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 305 GLN Chi-restraints excluded: chain 8 residue 368 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 9.9990 chunk 801 optimal weight: 7.9990 chunk 444 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 540 optimal weight: 6.9990 chunk 428 optimal weight: 20.0000 chunk 828 optimal weight: 8.9990 chunk 320 optimal weight: 0.9990 chunk 503 optimal weight: 8.9990 chunk 616 optimal weight: 8.9990 chunk 959 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: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 95 HIS ** 4 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 119 HIS ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN C 149 GLN C 193 ASN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 158 ASN D 229 HIS E 71 ASN E 91 HIS E 93 GLN E 153 ASN E 222 ASN E 257 GLN F 116 GLN F 158 ASN F 188 GLN K 97 ASN K 139 ASN K 190 GLN K 202 HIS K 220 HIS K 232 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 GLN Q 178 HIS Q 202 ASN R 28 HIS ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 189 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 106 ASN V 93 HIS V 95 HIS V 130 HIS V 133 ASN V 149 HIS X 106 ASN X 157 ASN Y 104 GLN Y 132 ASN 0 76 ASN ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN c 34 GLN c 73 GLN c 187 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 51 HIS i 106 GLN i 142 GLN i 144 GLN ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 ASN j 151 HIS k 31 HIS ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 75 GLN ** l 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 56 ASN ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 107 ASN m 125 HIS o 25 GLN r 58 GLN u 124 ASN w 172 GLN ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 GLN ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 8 GLN n 15 ASN ** n 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.127 159552 Z= 0.546 Angle : 0.948 15.782 237707 Z= 0.471 Chirality : 0.049 0.380 30128 Planarity : 0.008 0.104 13281 Dihedral : 23.948 178.555 77377 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.96 % Favored : 88.69 % Rotamer: Outliers : 5.70 % Allowed : 13.39 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -3.53 (0.09), residues: 6213 helix: -1.64 (0.10), residues: 1982 sheet: -2.18 (0.15), residues: 1022 loop : -2.91 (0.10), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP Y 109 HIS 0.021 0.003 HIS R 83 PHE 0.046 0.004 PHE F 152 TYR 0.041 0.004 TYR X 128 ARG 0.042 0.001 ARG Q 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1884 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1577 time to evaluate : 6.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 13 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6442 (mp) REVERT: 3 102 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7200 (mtm110) REVERT: 4 109 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8041 (ptpp) REVERT: 5 35 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7413 (ttp80) REVERT: 6 124 LYS cc_start: 0.8088 (mttt) cc_final: 0.7841 (mttt) REVERT: 7 49 SER cc_start: 0.8823 (t) cc_final: 0.8403 (p) REVERT: C 209 TRP cc_start: 0.7586 (m100) cc_final: 0.7011 (m100) REVERT: C 258 ARG cc_start: 0.7257 (mmp80) cc_final: 0.7025 (mmp80) REVERT: D 101 SER cc_start: 0.8447 (p) cc_final: 0.7851 (p) REVERT: D 115 ILE cc_start: 0.9333 (mm) cc_final: 0.9031 (mt) REVERT: D 172 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8470 (ttt-90) REVERT: E 212 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.4084 (tm) REVERT: E 218 LYS cc_start: 0.7588 (tttm) cc_final: 0.7377 (mmmm) REVERT: E 232 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7359 (tpt-90) REVERT: E 255 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9012 (mt) REVERT: F 145 ARG cc_start: 0.5596 (ttp80) cc_final: 0.5386 (ttp-170) REVERT: G 58 MET cc_start: 0.6470 (tmm) cc_final: 0.5813 (mpp) REVERT: G 112 THR cc_start: 0.6989 (p) cc_final: 0.6696 (p) REVERT: G 144 ILE cc_start: 0.7587 (mm) cc_final: 0.7176 (tp) REVERT: H 76 ASN cc_start: 0.6829 (m-40) cc_final: 0.6596 (m110) REVERT: K 186 GLU cc_start: 0.6708 (tp30) cc_final: 0.6401 (tp30) REVERT: K 213 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9246 (tp) REVERT: N 52 ARG cc_start: 0.7244 (mmm160) cc_final: 0.6858 (mtp85) REVERT: N 66 VAL cc_start: 0.9317 (t) cc_final: 0.8947 (p) REVERT: O 85 ILE cc_start: 0.9215 (tt) cc_final: 0.8989 (tt) REVERT: Q 121 ASP cc_start: 0.7568 (p0) cc_final: 0.6497 (p0) REVERT: Q 152 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7093 (ttm-80) REVERT: Q 178 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.7355 (m90) REVERT: R 40 ILE cc_start: 0.9227 (mm) cc_final: 0.8847 (mt) REVERT: S 132 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7085 (ptm-80) REVERT: S 143 TYR cc_start: 0.7935 (m-80) cc_final: 0.7675 (m-10) REVERT: S 159 ASN cc_start: 0.8087 (p0) cc_final: 0.7671 (p0) REVERT: S 174 THR cc_start: 0.7740 (m) cc_final: 0.7164 (p) REVERT: S 220 LYS cc_start: 0.8520 (tptt) cc_final: 0.8168 (tttp) REVERT: T 156 LYS cc_start: 0.7614 (mttm) cc_final: 0.6788 (tptt) REVERT: U 107 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6463 (mtt-85) REVERT: U 149 GLU cc_start: 0.7811 (tp30) cc_final: 0.7606 (tp30) REVERT: U 153 ASN cc_start: 0.8088 (m-40) cc_final: 0.7747 (m110) REVERT: V 53 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7413 (ptt180) REVERT: X 150 TYR cc_start: 0.5850 (m-10) cc_final: 0.5036 (m-80) REVERT: X 155 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7513 (ttp-110) REVERT: X 159 ARG cc_start: 0.7211 (tpt-90) cc_final: 0.6779 (tpt-90) REVERT: X 163 GLU cc_start: 0.5931 (mm-30) cc_final: 0.5482 (mm-30) REVERT: Y 104 GLN cc_start: 0.7996 (pt0) cc_final: 0.7769 (pt0) REVERT: Y 105 TYR cc_start: 0.8649 (m-80) cc_final: 0.8282 (m-80) REVERT: Y 126 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8685 (tp) REVERT: Z 121 GLU cc_start: 0.7471 (tp30) cc_final: 0.7183 (tp30) REVERT: b 202 ILE cc_start: 0.3851 (OUTLIER) cc_final: 0.3262 (mm) REVERT: c 23 PHE cc_start: 0.5028 (OUTLIER) cc_final: 0.4430 (m-80) REVERT: c 66 GLN cc_start: 0.6416 (mp10) cc_final: 0.5995 (mp10) REVERT: c 100 GLN cc_start: 0.6888 (tp-100) cc_final: 0.6531 (tp-100) REVERT: c 111 ASN cc_start: 0.7448 (t0) cc_final: 0.7126 (p0) REVERT: e 195 LYS cc_start: 0.8504 (mttt) cc_final: 0.8113 (mmtp) REVERT: e 231 TYR cc_start: 0.7179 (t80) cc_final: 0.6762 (t80) REVERT: e 245 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.7157 (t) REVERT: e 264 ASN cc_start: 0.7422 (m-40) cc_final: 0.6763 (m-40) REVERT: e 280 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7228 (ttm170) REVERT: e 282 THR cc_start: 0.9209 (m) cc_final: 0.8903 (p) REVERT: g 149 ARG cc_start: 0.6930 (mmm160) cc_final: 0.6520 (mmm-85) REVERT: h 19 ASN cc_start: 0.7082 (p0) cc_final: 0.6665 (p0) REVERT: h 34 ASN cc_start: 0.7716 (m-40) cc_final: 0.7279 (m110) REVERT: j 145 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7692 (tt) REVERT: k 81 ARG cc_start: 0.7436 (ttm110) cc_final: 0.7233 (ttp-110) REVERT: k 111 ARG cc_start: 0.7415 (mpt180) cc_final: 0.7211 (mmt180) REVERT: l 38 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7492 (p90) REVERT: l 75 GLN cc_start: 0.6754 (tm130) cc_final: 0.6045 (tm-30) REVERT: m 136 THR cc_start: 0.7949 (p) cc_final: 0.7746 (p) REVERT: p 1 MET cc_start: 0.5950 (ttm) cc_final: 0.5634 (ttp) REVERT: q 64 LYS cc_start: 0.7305 (mmtm) cc_final: 0.7045 (tppt) REVERT: q 96 LYS cc_start: 0.8204 (pttt) cc_final: 0.7635 (pttp) REVERT: q 100 HIS cc_start: 0.7645 (t-90) cc_final: 0.7365 (t-90) REVERT: r 55 THR cc_start: 0.7598 (p) cc_final: 0.7366 (m) REVERT: t 81 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6926 (mttt) REVERT: t 117 LYS cc_start: 0.8250 (mttt) cc_final: 0.8001 (ptpt) REVERT: t 141 LYS cc_start: 0.7959 (mmpt) cc_final: 0.7748 (mmmt) REVERT: t 151 ASN cc_start: 0.8252 (m-40) cc_final: 0.7968 (m110) REVERT: y 91 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7069 (ttt90) REVERT: y 96 ASP cc_start: 0.7681 (m-30) cc_final: 0.7365 (m-30) REVERT: y 130 ARG cc_start: 0.7865 (mpt90) cc_final: 0.7312 (mpt180) REVERT: d 23 ASN cc_start: 0.4710 (OUTLIER) cc_final: 0.3874 (m-40) REVERT: d 51 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7877 (tttm) REVERT: d 53 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7646 (ttmt) REVERT: d 169 PHE cc_start: 0.6020 (t80) cc_final: 0.5777 (t80) outliers start: 307 outliers final: 165 residues processed: 1733 average time/residue: 1.4315 time to fit residues: 4141.4247 Evaluate side-chains 1623 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1439 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 39 SER Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 18 CYS Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 120 LEU Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 7 residue 60 MET Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 233 THR Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 54 MET Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 148 ILE Chi-restraints excluded: chain Q residue 149 VAL Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain X residue 80 LYS Chi-restraints excluded: chain X residue 114 THR Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 140 LYS Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 111 ARG Chi-restraints excluded: chain Z residue 115 MET Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 112 ILE Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 162 VAL Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 245 THR Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 96 ILE Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain h residue 133 ILE Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain j residue 139 LYS Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain k residue 50 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 134 GLU Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 101 SER Chi-restraints excluded: chain y residue 160 VAL Chi-restraints excluded: chain w residue 167 ILE Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain d residue 81 GLN Chi-restraints excluded: chain d residue 82 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 61 THR Chi-restraints excluded: chain 8 residue 283 ILE Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 314 ILE Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 6.9990 chunk 297 optimal weight: 0.7980 chunk 798 optimal weight: 7.9990 chunk 653 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 961 optimal weight: 10.0000 chunk 1038 optimal weight: 7.9990 chunk 856 optimal weight: 10.0000 chunk 953 optimal weight: 9.9990 chunk 327 optimal weight: 1.9990 chunk 771 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 118 GLN ** 4 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 84 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN E 93 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN G 102 ASN K 170 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 GLN O 84 GLN O 87 HIS ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** S 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN T 106 ASN U 132 ASN U 179 ASN X 106 ASN X 157 ASN ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 187 GLN e 158 GLN e 186 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN g 142 HIS ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 127 HIS ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 107 ASN m 125 HIS ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 GLN d 34 ASN d 81 GLN ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 ASN ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 69 HIS 8 58 GLN ** 8 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 159552 Z= 0.283 Angle : 0.697 19.034 237707 Z= 0.352 Chirality : 0.039 0.274 30128 Planarity : 0.006 0.097 13281 Dihedral : 23.810 177.675 77358 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.04 % Favored : 89.65 % Rotamer: Outliers : 6.28 % Allowed : 17.13 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.10), residues: 6213 helix: -0.86 (0.11), residues: 1982 sheet: -1.74 (0.16), residues: 939 loop : -2.64 (0.10), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP c 22 HIS 0.033 0.002 HIS Q 178 PHE 0.039 0.002 PHE F 152 TYR 0.036 0.002 TYR 2 56 ARG 0.014 0.001 ARG c 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1824 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1486 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 7 ARG cc_start: 0.8027 (ptm160) cc_final: 0.7817 (ptp90) REVERT: 2 13 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6400 (mp) REVERT: 4 109 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7889 (pttp) REVERT: 5 3 ILE cc_start: 0.8102 (mp) cc_final: 0.7843 (mt) REVERT: 7 49 SER cc_start: 0.8895 (t) cc_final: 0.8353 (p) REVERT: C 104 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7340 (ptm160) REVERT: C 159 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7607 (tttm) REVERT: C 190 GLN cc_start: 0.6947 (pt0) cc_final: 0.6105 (pt0) REVERT: C 209 TRP cc_start: 0.7368 (m100) cc_final: 0.7113 (m100) REVERT: D 115 ILE cc_start: 0.9175 (mm) cc_final: 0.8956 (mt) REVERT: E 212 LEU cc_start: 0.4349 (OUTLIER) cc_final: 0.4016 (tm) REVERT: E 218 LYS cc_start: 0.7720 (tttm) cc_final: 0.7394 (mmmm) REVERT: E 232 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8070 (tpt170) REVERT: G 58 MET cc_start: 0.6310 (tmm) cc_final: 0.5790 (mpp) REVERT: G 112 THR cc_start: 0.6999 (p) cc_final: 0.6733 (p) REVERT: H 60 LEU cc_start: 0.3083 (OUTLIER) cc_final: 0.2763 (pp) REVERT: K 103 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8551 (mmtt) REVERT: L 65 THR cc_start: 0.8774 (t) cc_final: 0.8559 (p) REVERT: N 16 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7164 (ptm-80) REVERT: N 46 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: N 66 VAL cc_start: 0.9262 (t) cc_final: 0.8796 (p) REVERT: N 82 ARG cc_start: 0.5144 (tmt170) cc_final: 0.4829 (tmm160) REVERT: N 91 GLU cc_start: 0.6485 (tp30) cc_final: 0.6126 (tp30) REVERT: N 116 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6903 (ttm110) REVERT: O 85 ILE cc_start: 0.9150 (tt) cc_final: 0.8942 (tt) REVERT: O 89 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8661 (tp) REVERT: Q 152 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7141 (mtp85) REVERT: Q 205 GLU cc_start: 0.7235 (pm20) cc_final: 0.6955 (pm20) REVERT: S 132 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7057 (ptm-80) REVERT: S 143 TYR cc_start: 0.7924 (m-80) cc_final: 0.7689 (m-10) REVERT: S 220 LYS cc_start: 0.8460 (tptt) cc_final: 0.8094 (tttp) REVERT: U 149 GLU cc_start: 0.7722 (tp30) cc_final: 0.7364 (tp30) REVERT: U 153 ASN cc_start: 0.8071 (m-40) cc_final: 0.7556 (m110) REVERT: V 139 LYS cc_start: 0.7374 (mppt) cc_final: 0.7089 (mppt) REVERT: X 150 TYR cc_start: 0.5771 (m-10) cc_final: 0.4967 (m-80) REVERT: X 155 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7235 (ttp-110) REVERT: X 156 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7149 (mm-30) REVERT: X 157 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.6307 (m110) REVERT: Y 118 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8149 (mmtt) REVERT: Z 78 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6930 (mm-30) REVERT: Z 116 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8619 (mp) REVERT: b 30 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.4800 (pmt100) REVERT: b 202 ILE cc_start: 0.3525 (OUTLIER) cc_final: 0.3023 (mm) REVERT: c 37 GLN cc_start: 0.8009 (tp40) cc_final: 0.7473 (tm-30) REVERT: c 38 LYS cc_start: 0.7265 (mtmm) cc_final: 0.6704 (pttp) REVERT: c 67 LYS cc_start: 0.6229 (mttt) cc_final: 0.5358 (tptm) REVERT: c 96 LYS cc_start: 0.5324 (mtpt) cc_final: 0.5043 (mttp) REVERT: c 111 ASN cc_start: 0.7713 (t0) cc_final: 0.7493 (p0) REVERT: e 195 LYS cc_start: 0.8684 (mttt) cc_final: 0.8402 (mmtp) REVERT: e 211 ASN cc_start: 0.8158 (t0) cc_final: 0.7799 (t0) REVERT: e 231 TYR cc_start: 0.6875 (t80) cc_final: 0.6495 (t80) REVERT: e 245 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7111 (t) REVERT: e 264 ASN cc_start: 0.7374 (m-40) cc_final: 0.6735 (m-40) REVERT: e 280 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7459 (ttm170) REVERT: e 282 THR cc_start: 0.9273 (m) cc_final: 0.8900 (p) REVERT: g 149 ARG cc_start: 0.6563 (mmm160) cc_final: 0.6265 (mmm-85) REVERT: h 19 ASN cc_start: 0.6933 (p0) cc_final: 0.6558 (p0) REVERT: h 34 ASN cc_start: 0.7649 (m-40) cc_final: 0.7141 (m110) REVERT: h 39 LEU cc_start: 0.8407 (mt) cc_final: 0.8125 (mm) REVERT: i 67 PHE cc_start: 0.3370 (m-80) cc_final: 0.3159 (m-80) REVERT: i 144 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7216 (mt0) REVERT: i 148 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6553 (tm) REVERT: j 145 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7559 (tt) REVERT: l 33 THR cc_start: 0.8693 (m) cc_final: 0.8469 (t) REVERT: l 75 GLN cc_start: 0.6775 (tm130) cc_final: 0.6250 (tm-30) REVERT: m 136 THR cc_start: 0.8048 (p) cc_final: 0.7788 (t) REVERT: q 64 LYS cc_start: 0.7154 (mmtm) cc_final: 0.6945 (tppt) REVERT: q 96 LYS cc_start: 0.8152 (pttt) cc_final: 0.7783 (pttp) REVERT: t 81 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6645 (mttt) REVERT: t 92 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6821 (ttp-110) REVERT: t 141 LYS cc_start: 0.7980 (mmpt) cc_final: 0.7752 (mmmt) REVERT: y 91 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7139 (ttt90) REVERT: y 96 ASP cc_start: 0.7583 (m-30) cc_final: 0.7210 (m-30) REVERT: d 23 ASN cc_start: 0.4243 (OUTLIER) cc_final: 0.3569 (m-40) REVERT: d 51 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7784 (tttp) REVERT: v 70 MET cc_start: 0.2807 (pmm) cc_final: 0.1883 (pmm) outliers start: 338 outliers final: 191 residues processed: 1661 average time/residue: 1.3860 time to fit residues: 3845.9622 Evaluate side-chains 1623 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1411 time to evaluate : 6.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 18 CYS Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 136 CYS Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 233 THR Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 138 LYS Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 183 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 94 ARG Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 122 GLU Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 157 ASN Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 108 MET Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 126 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 112 ILE Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 161 ARG Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 245 THR Chi-restraints excluded: chain e residue 253 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 113 GLN Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 134 GLU Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 161 SER Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain w residue 167 ILE Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain d residue 67 LYS Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 50 ILE Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 176 VAL Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 10.0000 chunk 722 optimal weight: 20.0000 chunk 499 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 458 optimal weight: 7.9990 chunk 645 optimal weight: 20.0000 chunk 965 optimal weight: 10.0000 chunk 1021 optimal weight: 30.0000 chunk 504 optimal weight: 7.9990 chunk 914 optimal weight: 20.0000 chunk 275 optimal weight: 2.9990 overall best weight: 5.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 102 GLN 7 52 GLN C 54 HIS C 84 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN E 93 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN N 13 HIS ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 189 GLN ** S 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 106 ASN ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 HIS c 18 HIS c 34 GLN ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 186 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 HIS g 41 GLN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 ASN h 51 HIS h 65 HIS ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 126 GLN ** d 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 ASN d 133 GLN ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 176 ASN v 163 ASN ** x 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 269 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 159552 Z= 0.457 Angle : 0.840 19.717 237707 Z= 0.419 Chirality : 0.045 0.312 30128 Planarity : 0.007 0.094 13281 Dihedral : 23.884 177.326 77356 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.31 % Favored : 87.38 % Rotamer: Outliers : 8.23 % Allowed : 17.80 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.10), residues: 6213 helix: -0.77 (0.11), residues: 2000 sheet: -1.82 (0.16), residues: 1006 loop : -2.69 (0.10), residues: 3207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP Y 109 HIS 0.041 0.002 HIS g 142 PHE 0.027 0.003 PHE H 73 TYR 0.038 0.003 TYR h 132 ARG 0.011 0.001 ARG n 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1941 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 443 poor density : 1498 time to evaluate : 6.312 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: 2 13 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6567 (mp) REVERT: 3 121 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7700 (mtm110) REVERT: 4 117 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8030 (tptp) REVERT: 5 3 ILE cc_start: 0.8253 (mp) cc_final: 0.8002 (mt) REVERT: 7 49 SER cc_start: 0.9048 (t) cc_final: 0.8364 (p) REVERT: C 58 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6626 (p90) REVERT: C 120 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8216 (mp) REVERT: C 159 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7612 (tttm) REVERT: C 160 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7866 (tp) REVERT: C 209 TRP cc_start: 0.7451 (m100) cc_final: 0.7158 (m100) REVERT: D 218 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6555 (mtpt) REVERT: D 250 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8024 (mtt) REVERT: D 253 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7846 (ttp-170) REVERT: E 146 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.5051 (ptt-90) REVERT: E 212 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.4825 (tm) REVERT: F 217 LYS cc_start: 0.3401 (pptt) cc_final: 0.2035 (pptt) REVERT: G 58 MET cc_start: 0.6229 (tmm) cc_final: 0.5799 (mpp) REVERT: G 112 THR cc_start: 0.6737 (p) cc_final: 0.6439 (p) REVERT: K 195 ILE cc_start: 0.8928 (mm) cc_final: 0.8343 (tt) REVERT: L 99 PHE cc_start: 0.7936 (m-10) cc_final: 0.7680 (m-10) REVERT: N 16 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7268 (ptm-80) REVERT: N 46 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8728 (mt0) REVERT: N 66 VAL cc_start: 0.9423 (t) cc_final: 0.9061 (p) REVERT: N 91 GLU cc_start: 0.6935 (tp30) cc_final: 0.6618 (tp30) REVERT: N 116 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6795 (ttm110) REVERT: N 130 GLN cc_start: 0.8242 (pm20) cc_final: 0.7998 (pm20) REVERT: O 85 ILE cc_start: 0.9202 (tt) cc_final: 0.8975 (tt) REVERT: O 89 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8732 (tp) REVERT: Q 152 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7399 (mtt-85) REVERT: Q 178 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.6834 (m90) REVERT: Q 205 GLU cc_start: 0.7459 (pm20) cc_final: 0.7182 (pm20) REVERT: R 25 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7310 (ttt-90) REVERT: R 40 ILE cc_start: 0.9177 (mm) cc_final: 0.8900 (mt) REVERT: R 59 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7983 (ttm170) REVERT: S 143 TYR cc_start: 0.8097 (m-10) cc_final: 0.7833 (m-10) REVERT: S 174 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7490 (p) REVERT: S 220 LYS cc_start: 0.8506 (tptt) cc_final: 0.8253 (tttp) REVERT: T 41 MET cc_start: 0.7641 (ppp) cc_final: 0.7291 (ppp) REVERT: T 156 LYS cc_start: 0.7686 (mttm) cc_final: 0.6846 (tptt) REVERT: U 153 ASN cc_start: 0.8011 (m-40) cc_final: 0.7644 (m110) REVERT: U 154 PHE cc_start: 0.7520 (t80) cc_final: 0.7303 (t80) REVERT: V 85 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7879 (ptpt) REVERT: X 76 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7457 (ptp90) REVERT: X 150 TYR cc_start: 0.5787 (m-10) cc_final: 0.4914 (m-80) REVERT: X 153 ARG cc_start: 0.7697 (tpm170) cc_final: 0.7437 (tpt170) REVERT: X 155 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7678 (ttp-110) REVERT: X 156 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7554 (mm-30) REVERT: X 163 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5735 (mm-30) REVERT: Y 102 ASN cc_start: 0.8909 (p0) cc_final: 0.8587 (p0) REVERT: Z 78 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7141 (mm-30) REVERT: Z 120 ARG cc_start: 0.8172 (tpt90) cc_final: 0.7591 (mmm160) REVERT: b 22 HIS cc_start: 0.4598 (OUTLIER) cc_final: 0.4092 (m-70) REVERT: b 145 LEU cc_start: 0.7129 (tp) cc_final: 0.6593 (mm) REVERT: b 191 ILE cc_start: 0.6985 (mt) cc_final: 0.6728 (mp) REVERT: b 202 ILE cc_start: 0.3677 (OUTLIER) cc_final: 0.3129 (mm) REVERT: c 35 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7232 (mm-30) REVERT: c 37 GLN cc_start: 0.8013 (tp40) cc_final: 0.7606 (tm-30) REVERT: c 49 LYS cc_start: 0.7798 (ttpp) cc_final: 0.7557 (tmmt) REVERT: c 67 LYS cc_start: 0.6531 (mttt) cc_final: 0.5671 (tttp) REVERT: c 111 ASN cc_start: 0.7800 (t0) cc_final: 0.7507 (p0) REVERT: c 173 ILE cc_start: 0.7380 (mp) cc_final: 0.7180 (mm) REVERT: e 170 LYS cc_start: 0.8399 (pttm) cc_final: 0.7925 (ptpp) REVERT: e 195 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8016 (tppt) REVERT: e 282 THR cc_start: 0.9315 (m) cc_final: 0.8971 (p) REVERT: g 33 HIS cc_start: 0.7090 (p90) cc_final: 0.6347 (p-80) REVERT: g 111 ARG cc_start: 0.6992 (mtp85) cc_final: 0.6620 (ptm160) REVERT: h 18 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7149 (tmm) REVERT: h 19 ASN cc_start: 0.7335 (p0) cc_final: 0.6495 (p0) REVERT: h 30 ASN cc_start: 0.7136 (t0) cc_final: 0.6749 (t0) REVERT: h 34 ASN cc_start: 0.7470 (m110) cc_final: 0.6831 (m110) REVERT: h 39 LEU cc_start: 0.8443 (mt) cc_final: 0.8228 (mm) REVERT: i 144 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7257 (mt0) REVERT: i 190 LYS cc_start: 0.8374 (tttp) cc_final: 0.7603 (ttpt) REVERT: j 141 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8356 (mm) REVERT: j 145 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7729 (tt) REVERT: k 32 VAL cc_start: 0.7994 (t) cc_final: 0.7737 (p) REVERT: k 70 PHE cc_start: 0.7252 (t80) cc_final: 0.6840 (t80) REVERT: k 81 ARG cc_start: 0.7421 (ttm110) cc_final: 0.7181 (ttp-110) REVERT: l 66 TYR cc_start: 0.8540 (t80) cc_final: 0.8217 (t80) REVERT: p 73 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7506 (ttm170) REVERT: q 96 LYS cc_start: 0.8333 (pttt) cc_final: 0.7846 (pttp) REVERT: t 81 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6618 (mttt) REVERT: t 92 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6904 (ttp-110) REVERT: t 141 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7916 (mmmt) REVERT: t 164 LYS cc_start: 0.7742 (mmpt) cc_final: 0.7388 (mmtt) REVERT: t 165 LYS cc_start: 0.6525 (ptpp) cc_final: 0.6229 (ptpp) REVERT: y 91 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7583 (ttt-90) REVERT: y 96 ASP cc_start: 0.7663 (m-30) cc_final: 0.7295 (m-30) REVERT: d 23 ASN cc_start: 0.4624 (OUTLIER) cc_final: 0.4171 (m-40) REVERT: d 51 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8022 (tttm) REVERT: d 64 GLN cc_start: 0.7898 (tt0) cc_final: 0.7565 (mt0) REVERT: v 70 MET cc_start: 0.2883 (pmm) cc_final: 0.2160 (pmm) REVERT: n 60 HIS cc_start: 0.5841 (OUTLIER) cc_final: 0.5141 (m-70) REVERT: 8 72 MET cc_start: 0.3437 (OUTLIER) cc_final: 0.2805 (mpp) outliers start: 443 outliers final: 295 residues processed: 1725 average time/residue: 1.3977 time to fit residues: 4039.2514 Evaluate side-chains 1769 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1443 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 18 CYS Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 93 LEU Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 107 LYS Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 117 LYS Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 11 CYS Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 7 residue 60 MET Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 233 THR Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 138 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 183 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 154 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 99 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 114 THR Chi-restraints excluded: chain X residue 118 LEU Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 140 LYS Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 108 MET Chi-restraints excluded: chain Z residue 111 ARG Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 126 THR Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 78 MET Chi-restraints excluded: chain c residue 112 ILE Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 194 ASP Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 253 VAL Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 284 VAL Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain f residue 140 MET Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 LEU Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 96 ILE Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 119 LEU Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 50 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 29 GLU Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 73 ARG Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 115 ASP Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain r residue 62 ILE Chi-restraints excluded: chain r residue 74 LEU Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 134 GLU Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 101 SER Chi-restraints excluded: chain y residue 107 HIS Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 152 SER Chi-restraints excluded: chain y residue 160 VAL Chi-restraints excluded: chain y residue 161 SER Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain w residue 167 ILE Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain d residue 67 LYS Chi-restraints excluded: chain d residue 82 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 127 SER Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 172 LYS Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 176 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain x residue 63 LYS Chi-restraints excluded: chain 8 residue 72 MET Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 10.0000 chunk 579 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 760 optimal weight: 7.9990 chunk 421 optimal weight: 2.9990 chunk 871 optimal weight: 10.0000 chunk 706 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 521 optimal weight: 3.9990 chunk 917 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 209 GLN H 76 ASN K 170 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS ** Q 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 106 ASN V 68 HIS ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS h 51 HIS h 78 HIS i 161 HIS ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 56 ASN m 83 ASN ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 GLN ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 165 GLN w 172 GLN d 85 GLN ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 ASN d 133 GLN ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN ** x 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 159552 Z= 0.269 Angle : 0.687 20.582 237707 Z= 0.347 Chirality : 0.038 0.260 30128 Planarity : 0.006 0.090 13281 Dihedral : 23.789 176.333 77356 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.01 % Favored : 89.70 % Rotamer: Outliers : 7.21 % Allowed : 20.29 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.10), residues: 6213 helix: -0.34 (0.11), residues: 1998 sheet: -1.63 (0.16), residues: 956 loop : -2.59 (0.10), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP c 22 HIS 0.045 0.002 HIS Q 178 PHE 0.028 0.002 PHE m 106 TYR 0.029 0.002 TYR D 141 ARG 0.010 0.001 ARG 3 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1864 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1476 time to evaluate : 6.413 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: 3 121 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7667 (mtm110) REVERT: 4 109 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7917 (pttp) REVERT: 4 117 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8149 (tptp) REVERT: 4 120 LEU cc_start: 0.8295 (mp) cc_final: 0.8082 (mp) REVERT: 7 49 SER cc_start: 0.8998 (t) cc_final: 0.8285 (p) REVERT: 7 74 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7534 (mtp-110) REVERT: C 28 LEU cc_start: 0.8175 (tp) cc_final: 0.7774 (mt) REVERT: C 96 GLU cc_start: 0.6826 (mp0) cc_final: 0.6273 (mp0) REVERT: C 104 ARG cc_start: 0.7628 (ttp-170) cc_final: 0.7208 (ptm160) REVERT: C 159 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7710 (tttm) REVERT: C 190 GLN cc_start: 0.6967 (pt0) cc_final: 0.6513 (pt0) REVERT: D 218 LYS cc_start: 0.7253 (mtpt) cc_final: 0.6802 (mtpt) REVERT: D 250 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8100 (mtt) REVERT: E 212 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.4865 (tm) REVERT: E 217 GLU cc_start: 0.7488 (tp30) cc_final: 0.7166 (tp30) REVERT: F 217 LYS cc_start: 0.3086 (pptt) cc_final: 0.2623 (pptt) REVERT: G 58 MET cc_start: 0.6008 (tmm) cc_final: 0.5778 (mpp) REVERT: G 124 GLU cc_start: 0.6318 (mm-30) cc_final: 0.5803 (mm-30) REVERT: H 60 LEU cc_start: 0.2625 (OUTLIER) cc_final: 0.2338 (pp) REVERT: K 195 ILE cc_start: 0.8666 (mm) cc_final: 0.8141 (tt) REVERT: L 7 HIS cc_start: 0.7306 (m-70) cc_final: 0.6981 (m-70) REVERT: M 192 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6542 (mmm-85) REVERT: N 16 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7133 (ptm-80) REVERT: N 91 GLU cc_start: 0.6598 (tp30) cc_final: 0.6323 (tp30) REVERT: N 130 GLN cc_start: 0.8131 (pm20) cc_final: 0.7666 (pp30) REVERT: O 55 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7102 (mtm110) REVERT: P 59 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: P 122 LYS cc_start: 0.7690 (mmtm) cc_final: 0.7490 (mmtm) REVERT: Q 178 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7462 (m-70) REVERT: Q 205 GLU cc_start: 0.7269 (pm20) cc_final: 0.7058 (pm20) REVERT: S 132 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7337 (ptm-80) REVERT: S 143 TYR cc_start: 0.8075 (m-10) cc_final: 0.7813 (m-10) REVERT: S 174 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7495 (p) REVERT: S 200 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.7103 (p90) REVERT: T 97 ASN cc_start: 0.6240 (t0) cc_final: 0.5947 (t0) REVERT: U 107 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6388 (mtt-85) REVERT: U 149 GLU cc_start: 0.7770 (tp30) cc_final: 0.7466 (tp30) REVERT: U 153 ASN cc_start: 0.8055 (m-40) cc_final: 0.7684 (m110) REVERT: X 88 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8424 (mtpp) REVERT: X 150 TYR cc_start: 0.5752 (m-10) cc_final: 0.5063 (m-80) REVERT: X 155 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7540 (ttp-110) REVERT: X 156 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7644 (mm-30) REVERT: X 157 ASN cc_start: 0.8403 (m-40) cc_final: 0.8067 (m-40) REVERT: X 163 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5556 (mm-30) REVERT: Z 116 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8625 (mp) REVERT: b 145 LEU cc_start: 0.7077 (tp) cc_final: 0.6583 (mm) REVERT: b 190 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5826 (mm) REVERT: c 23 PHE cc_start: 0.7969 (t80) cc_final: 0.7586 (t80) REVERT: c 37 GLN cc_start: 0.7927 (tp40) cc_final: 0.7608 (tm-30) REVERT: c 49 LYS cc_start: 0.7772 (ttpp) cc_final: 0.7535 (tmmt) REVERT: c 67 LYS cc_start: 0.6427 (mttt) cc_final: 0.5639 (tptt) REVERT: c 93 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6771 (mp0) REVERT: c 111 ASN cc_start: 0.7809 (t0) cc_final: 0.7551 (p0) REVERT: c 145 MET cc_start: 0.8152 (mtp) cc_final: 0.7840 (mtp) REVERT: c 147 LYS cc_start: 0.8063 (tppt) cc_final: 0.7627 (tppp) REVERT: c 173 ILE cc_start: 0.7371 (mp) cc_final: 0.7157 (mm) REVERT: c 177 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6502 (mt-10) REVERT: e 170 LYS cc_start: 0.8196 (pttm) cc_final: 0.7729 (ptpp) REVERT: e 195 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8048 (tppt) REVERT: e 282 THR cc_start: 0.9306 (m) cc_final: 0.8938 (p) REVERT: g 29 ARG cc_start: 0.7000 (mmt180) cc_final: 0.6491 (mmt180) REVERT: g 35 LYS cc_start: 0.7330 (mppt) cc_final: 0.7018 (mptt) REVERT: g 111 ARG cc_start: 0.6911 (mtp85) cc_final: 0.6504 (ptm160) REVERT: h 19 ASN cc_start: 0.7343 (p0) cc_final: 0.6490 (p0) REVERT: h 34 ASN cc_start: 0.7501 (m110) cc_final: 0.7020 (m110) REVERT: h 87 LEU cc_start: 0.7464 (tp) cc_final: 0.7048 (pp) REVERT: i 144 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7291 (mt0) REVERT: k 32 VAL cc_start: 0.7843 (t) cc_final: 0.7609 (p) REVERT: k 70 PHE cc_start: 0.7002 (t80) cc_final: 0.6441 (t80) REVERT: k 81 ARG cc_start: 0.7348 (ttm110) cc_final: 0.7126 (ttp-110) REVERT: m 116 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: o 53 LEU cc_start: 0.8115 (tp) cc_final: 0.7912 (tp) REVERT: p 23 ASP cc_start: 0.8034 (t0) cc_final: 0.7747 (t70) REVERT: q 96 LYS cc_start: 0.8318 (pttt) cc_final: 0.7952 (pttm) REVERT: q 122 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7303 (mtmt) REVERT: t 81 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6604 (mttt) REVERT: t 92 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6783 (ttp-110) REVERT: t 131 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7691 (tt) REVERT: t 164 LYS cc_start: 0.7746 (mmpt) cc_final: 0.7325 (mmtt) REVERT: y 91 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7589 (ttt-90) REVERT: y 96 ASP cc_start: 0.7493 (m-30) cc_final: 0.7120 (m-30) REVERT: y 130 ARG cc_start: 0.8004 (mpt-90) cc_final: 0.7659 (mpt180) REVERT: d 23 ASN cc_start: 0.4157 (OUTLIER) cc_final: 0.3840 (m-40) REVERT: d 64 GLN cc_start: 0.7843 (tt0) cc_final: 0.7497 (mt0) REVERT: v 70 MET cc_start: 0.3205 (pmm) cc_final: 0.2403 (pmm) REVERT: n 84 ARG cc_start: 0.6868 (tpp80) cc_final: 0.6652 (mtm-85) REVERT: 8 72 MET cc_start: 0.3625 (OUTLIER) cc_final: 0.3171 (mpp) outliers start: 388 outliers final: 266 residues processed: 1677 average time/residue: 1.3679 time to fit residues: 3848.4882 Evaluate side-chains 1713 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1425 time to evaluate : 6.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 39 SER Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 18 CYS Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 46 LEU Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 117 LYS Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 11 CYS Chi-restraints excluded: chain 5 residue 24 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 127 LYS Chi-restraints excluded: chain 7 residue 60 MET Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 88 GLN Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 192 ARG Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 218 SER Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 93 HIS Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 148 ILE Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 183 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 230 SER Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 122 GLU Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 108 MET Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 189 CYS Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 78 MET Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 194 ASP Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 161 ARG Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 209 ARG Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 LEU Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain h residue 133 ILE Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 122 LEU Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 167 ILE Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 116 GLU Chi-restraints excluded: chain m residue 123 ILE Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 29 GLU Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 113 GLN Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 103 ARG Chi-restraints excluded: chain t residue 118 SER Chi-restraints excluded: chain t residue 131 LEU Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 101 SER Chi-restraints excluded: chain y residue 107 HIS Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 141 HIS Chi-restraints excluded: chain y residue 157 ILE Chi-restraints excluded: chain y residue 161 SER Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain w residue 136 ASP Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain w residue 167 ILE Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 67 LYS Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 172 LYS Chi-restraints excluded: chain d residue 179 ILE Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain 8 residue 72 MET Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 8.9990 chunk 920 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 599 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 1022 optimal weight: 8.9990 chunk 848 optimal weight: 10.0000 chunk 473 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 338 optimal weight: 10.0000 chunk 536 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 209 GLN E 181 ASN G 46 GLN H 76 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 106 ASN ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 HIS ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 154 GLN ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 166 ASN ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 25 GLN ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 GLN s 47 HIS ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 141 HIS d 34 ASN ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 133 GLN ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN n 48 GLN ** x 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 159552 Z= 0.469 Angle : 0.846 20.560 237707 Z= 0.420 Chirality : 0.045 0.316 30128 Planarity : 0.007 0.090 13281 Dihedral : 23.868 177.836 77356 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.62 % Favored : 87.09 % Rotamer: Outliers : 8.29 % Allowed : 20.53 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.15 % 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: -2.63 (0.10), residues: 6213 helix: -0.50 (0.11), residues: 1997 sheet: -1.77 (0.16), residues: 1000 loop : -2.62 (0.10), residues: 3216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP c 22 HIS 0.011 0.002 HIS R 83 PHE 0.034 0.003 PHE m 106 TYR 0.038 0.003 TYR 2 54 ARG 0.027 0.001 ARG g 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1925 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 446 poor density : 1479 time to evaluate : 6.371 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: 3 121 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7668 (mtm110) REVERT: 7 49 SER cc_start: 0.9025 (t) cc_final: 0.8331 (p) REVERT: 7 61 LYS cc_start: 0.8058 (tptt) cc_final: 0.7431 (mtpp) REVERT: 7 74 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7468 (mtp-110) REVERT: C 58 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6518 (p90) REVERT: C 96 GLU cc_start: 0.7013 (mp0) cc_final: 0.6732 (mp0) REVERT: C 159 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7667 (tttm) REVERT: D 132 ASP cc_start: 0.7969 (t0) cc_final: 0.7728 (t0) REVERT: D 218 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6368 (mtpt) REVERT: D 250 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8067 (mtt) REVERT: D 253 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7825 (ttp-170) REVERT: E 146 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.5154 (ptt-90) REVERT: E 212 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5479 (tm) REVERT: E 217 GLU cc_start: 0.7610 (tp30) cc_final: 0.7402 (tp30) REVERT: G 124 GLU cc_start: 0.6528 (mm-30) cc_final: 0.5968 (mm-30) REVERT: H 60 LEU cc_start: 0.2722 (OUTLIER) cc_final: 0.2380 (pp) REVERT: K 186 GLU cc_start: 0.7217 (tt0) cc_final: 0.6987 (tp30) REVERT: M 106 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: M 192 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6547 (mmm-85) REVERT: M 222 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8017 (ttmm) REVERT: N 16 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7260 (ptm-80) REVERT: N 65 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7480 (m100) REVERT: N 82 ARG cc_start: 0.5769 (tmt170) cc_final: 0.5390 (tmt170) REVERT: N 91 GLU cc_start: 0.6935 (tp30) cc_final: 0.6678 (tp30) REVERT: N 130 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: N 131 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7659 (p90) REVERT: O 92 GLU cc_start: 0.6818 (mp0) cc_final: 0.6516 (mp0) REVERT: P 59 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8082 (ttm170) REVERT: P 91 LYS cc_start: 0.6801 (tmtt) cc_final: 0.5980 (tptp) REVERT: P 122 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7477 (mmtm) REVERT: Q 152 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7611 (mtt-85) REVERT: Q 178 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.6962 (m90) REVERT: Q 205 GLU cc_start: 0.7504 (pm20) cc_final: 0.7209 (pm20) REVERT: R 25 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7324 (ttt-90) REVERT: R 40 ILE cc_start: 0.9189 (mm) cc_final: 0.8882 (mt) REVERT: R 59 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7997 (ttm170) REVERT: S 132 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7858 (ptm-80) REVERT: S 143 TYR cc_start: 0.8168 (m-10) cc_final: 0.7941 (m-10) REVERT: S 174 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7541 (p) REVERT: S 200 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.6943 (p90) REVERT: U 153 ASN cc_start: 0.7988 (m-40) cc_final: 0.7707 (m110) REVERT: V 141 GLN cc_start: 0.5291 (pm20) cc_final: 0.5080 (pm20) REVERT: X 102 HIS cc_start: 0.8112 (m90) cc_final: 0.7912 (m90) REVERT: X 150 TYR cc_start: 0.5568 (m-10) cc_final: 0.4819 (m-80) REVERT: X 155 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7626 (ttp-110) REVERT: X 156 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7548 (mm-30) REVERT: X 157 ASN cc_start: 0.8344 (m-40) cc_final: 0.7966 (m-40) REVERT: X 163 GLU cc_start: 0.6155 (mm-30) cc_final: 0.5765 (mm-30) REVERT: 0 87 LEU cc_start: -0.2432 (OUTLIER) cc_final: -0.2738 (tt) REVERT: b 145 LEU cc_start: 0.7229 (tp) cc_final: 0.6714 (mm) REVERT: b 190 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6192 (mm) REVERT: b 202 ILE cc_start: 0.3748 (OUTLIER) cc_final: 0.3355 (mm) REVERT: c 49 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7571 (tmmt) REVERT: c 93 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6870 (mp0) REVERT: c 111 ASN cc_start: 0.7922 (t0) cc_final: 0.7686 (t0) REVERT: c 173 ILE cc_start: 0.7413 (mp) cc_final: 0.7205 (mm) REVERT: c 177 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6862 (mt-10) REVERT: e 195 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8217 (tppt) REVERT: e 220 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.5948 (p90) REVERT: e 282 THR cc_start: 0.9312 (m) cc_final: 0.8909 (p) REVERT: g 111 ARG cc_start: 0.6989 (mtp85) cc_final: 0.6481 (ptm160) REVERT: h 19 ASN cc_start: 0.7469 (p0) cc_final: 0.6980 (p0) REVERT: h 30 ASN cc_start: 0.7332 (t0) cc_final: 0.6885 (t0) REVERT: h 34 ASN cc_start: 0.7471 (m110) cc_final: 0.6780 (m110) REVERT: i 144 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7204 (mt0) REVERT: i 156 LYS cc_start: 0.5806 (ttpp) cc_final: 0.5251 (ttmt) REVERT: j 141 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8340 (mm) REVERT: j 145 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7576 (tt) REVERT: k 32 VAL cc_start: 0.7807 (t) cc_final: 0.7579 (p) REVERT: k 70 PHE cc_start: 0.7171 (t80) cc_final: 0.6889 (t80) REVERT: k 125 MET cc_start: 0.7261 (tmm) cc_final: 0.6932 (tmm) REVERT: l 47 SER cc_start: 0.7645 (t) cc_final: 0.7221 (m) REVERT: l 66 TYR cc_start: 0.8542 (t80) cc_final: 0.8313 (t80) REVERT: m 116 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: p 59 LYS cc_start: 0.7650 (mptt) cc_final: 0.7385 (mptt) REVERT: p 69 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.6012 (t0) REVERT: q 96 LYS cc_start: 0.8381 (pttt) cc_final: 0.7841 (pttp) REVERT: t 92 ARG cc_start: 0.7276 (mtt180) cc_final: 0.6878 (ttp-110) REVERT: t 101 LYS cc_start: 0.6090 (tttt) cc_final: 0.5419 (tttp) REVERT: t 128 ILE cc_start: 0.7681 (mp) cc_final: 0.7436 (mt) REVERT: t 131 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7415 (tt) REVERT: t 164 LYS cc_start: 0.7769 (mmpt) cc_final: 0.7392 (mmtt) REVERT: u 120 ARG cc_start: 0.5687 (ttp-170) cc_final: 0.5263 (ttt180) REVERT: y 91 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7783 (ttt-90) REVERT: y 96 ASP cc_start: 0.7638 (m-30) cc_final: 0.7360 (m-30) REVERT: d 41 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.5657 (mmm-85) REVERT: d 64 GLN cc_start: 0.7942 (tt0) cc_final: 0.7581 (mt0) REVERT: n 60 HIS cc_start: 0.6121 (OUTLIER) cc_final: 0.5352 (m-70) REVERT: n 84 ARG cc_start: 0.6970 (tpp80) cc_final: 0.6633 (mtm-85) REVERT: 8 366 MET cc_start: 0.1526 (ttp) cc_final: 0.1295 (tpp) outliers start: 446 outliers final: 316 residues processed: 1722 average time/residue: 1.3918 time to fit residues: 4004.7362 Evaluate side-chains 1809 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1461 time to evaluate : 6.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 18 CYS Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 46 LEU Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 11 CYS Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 112 ILE Chi-restraints excluded: chain 7 residue 60 MET Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 192 ARG Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 218 SER Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 183 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 230 SER Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 94 ARG Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 154 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 99 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 140 LYS Chi-restraints excluded: chain Z residue 108 MET Chi-restraints excluded: chain Z residue 111 ARG Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 87 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 189 CYS Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 78 MET Chi-restraints excluded: chain c residue 112 ILE Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 194 ASP Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 161 ARG Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 213 ILE Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 277 ASN Chi-restraints excluded: chain e residue 284 VAL Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain f residue 140 MET Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 LEU Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 96 ILE Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 119 LEU Chi-restraints excluded: chain i residue 122 LEU Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 139 LYS Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 29 GLN Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 96 GLU Chi-restraints excluded: chain m residue 116 GLU Chi-restraints excluded: chain m residue 123 ILE Chi-restraints excluded: chain m residue 138 ASN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 29 GLU Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 93 LYS Chi-restraints excluded: chain q residue 108 VAL Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain r residue 62 ILE Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain t residue 103 ARG Chi-restraints excluded: chain t residue 118 SER Chi-restraints excluded: chain t residue 131 LEU Chi-restraints excluded: chain t residue 137 SER Chi-restraints excluded: chain t residue 145 LYS Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 101 SER Chi-restraints excluded: chain y residue 107 HIS Chi-restraints excluded: chain y residue 141 HIS Chi-restraints excluded: chain y residue 152 SER Chi-restraints excluded: chain y residue 160 VAL Chi-restraints excluded: chain y residue 161 SER Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 67 LYS Chi-restraints excluded: chain d residue 82 VAL Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 179 ILE Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 93 ILE Chi-restraints excluded: chain v residue 176 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain 8 residue 72 MET Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 582 optimal weight: 4.9990 chunk 746 optimal weight: 7.9990 chunk 578 optimal weight: 5.9990 chunk 860 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 chunk 1018 optimal weight: 5.9990 chunk 637 optimal weight: 0.9990 chunk 621 optimal weight: 2.9990 chunk 470 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 58 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN Q 158 ASN R 83 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 GLN ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 186 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 78 HIS ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 GLN ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 141 HIS d 85 GLN ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 133 GLN v 135 ASN n 18 GLN ** x 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 159552 Z= 0.334 Angle : 0.735 20.423 237707 Z= 0.369 Chirality : 0.040 0.285 30128 Planarity : 0.006 0.086 13281 Dihedral : 23.807 177.815 77356 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.15 % Favored : 88.59 % Rotamer: Outliers : 7.62 % Allowed : 22.01 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.12 % 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: -2.43 (0.10), residues: 6213 helix: -0.35 (0.11), residues: 2010 sheet: -1.62 (0.16), residues: 982 loop : -2.51 (0.10), residues: 3221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP q 111 HIS 0.038 0.002 HIS Q 178 PHE 0.030 0.002 PHE G 108 TYR 0.036 0.002 TYR 2 56 ARG 0.017 0.001 ARG q 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1909 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 1499 time to evaluate : 6.375 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: 3 121 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7642 (mtm110) REVERT: 4 109 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7971 (pttp) REVERT: 7 49 SER cc_start: 0.9008 (t) cc_final: 0.8304 (p) REVERT: 7 61 LYS cc_start: 0.7989 (tptt) cc_final: 0.7431 (mtpp) REVERT: 7 74 ARG cc_start: 0.7725 (mtm180) cc_final: 0.7495 (mtp-110) REVERT: C 28 LEU cc_start: 0.8063 (tp) cc_final: 0.7641 (mt) REVERT: C 58 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6700 (p90) REVERT: C 96 GLU cc_start: 0.7027 (mp0) cc_final: 0.6770 (mp0) REVERT: C 159 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7648 (tttm) REVERT: D 132 ASP cc_start: 0.7920 (t0) cc_final: 0.7652 (t0) REVERT: D 218 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6358 (mtpt) REVERT: D 250 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8060 (mtt) REVERT: D 253 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7656 (ttp-170) REVERT: E 146 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5103 (ptt-90) REVERT: E 212 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5342 (tm) REVERT: E 217 GLU cc_start: 0.7539 (tp30) cc_final: 0.7329 (tp30) REVERT: H 60 LEU cc_start: 0.2706 (OUTLIER) cc_final: 0.2309 (pp) REVERT: K 195 ILE cc_start: 0.8783 (mm) cc_final: 0.8249 (tt) REVERT: K 241 LEU cc_start: 0.7716 (tp) cc_final: 0.7500 (tt) REVERT: M 192 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6572 (mmm-85) REVERT: M 222 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8015 (ttmm) REVERT: M 223 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8071 (mm-30) REVERT: M 236 PRO cc_start: 0.8745 (Cg_endo) cc_final: 0.8482 (Cg_exo) REVERT: N 16 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7166 (ptm-80) REVERT: N 65 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.7439 (m100) REVERT: N 82 ARG cc_start: 0.5781 (tmt170) cc_final: 0.4295 (tmt-80) REVERT: N 91 GLU cc_start: 0.6881 (tp30) cc_final: 0.6619 (tp30) REVERT: N 130 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7667 (pp30) REVERT: P 59 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8043 (ttm170) REVERT: P 91 LYS cc_start: 0.6675 (tmtt) cc_final: 0.6016 (tptp) REVERT: P 146 TYR cc_start: 0.8557 (m-80) cc_final: 0.8246 (m-10) REVERT: Q 178 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7622 (m-70) REVERT: Q 205 GLU cc_start: 0.7354 (pm20) cc_final: 0.7117 (pm20) REVERT: R 25 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7306 (ttt-90) REVERT: R 59 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7877 (ttm170) REVERT: R 83 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7287 (t70) REVERT: R 87 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7950 (ptpt) REVERT: S 132 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7743 (ptm-80) REVERT: S 143 TYR cc_start: 0.8171 (m-10) cc_final: 0.7907 (m-10) REVERT: S 174 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7468 (p) REVERT: S 200 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7174 (p90) REVERT: S 206 TYR cc_start: 0.8774 (t80) cc_final: 0.8470 (t80) REVERT: T 156 LYS cc_start: 0.7705 (mttm) cc_final: 0.6912 (tptp) REVERT: U 153 ASN cc_start: 0.8004 (m-40) cc_final: 0.7710 (m110) REVERT: U 167 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7859 (ttm110) REVERT: V 63 LYS cc_start: 0.7824 (tptp) cc_final: 0.7561 (tptp) REVERT: X 76 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7365 (ptp90) REVERT: X 150 TYR cc_start: 0.5479 (m-10) cc_final: 0.4770 (m-80) REVERT: X 155 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7495 (ttp-110) REVERT: X 156 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7423 (mm-30) REVERT: X 163 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5754 (mm-30) REVERT: 0 59 MET cc_start: 0.4736 (OUTLIER) cc_final: 0.2599 (pmm) REVERT: 0 87 LEU cc_start: -0.2256 (OUTLIER) cc_final: -0.2546 (tt) REVERT: b 145 LEU cc_start: 0.7210 (tp) cc_final: 0.6723 (mm) REVERT: b 202 ILE cc_start: 0.3620 (OUTLIER) cc_final: 0.3234 (mm) REVERT: c 37 GLN cc_start: 0.8001 (tp40) cc_final: 0.7638 (tm-30) REVERT: c 38 LYS cc_start: 0.7386 (mtmm) cc_final: 0.6813 (mtmm) REVERT: c 49 LYS cc_start: 0.7778 (ttpp) cc_final: 0.7569 (tmmt) REVERT: c 67 LYS cc_start: 0.6771 (mttp) cc_final: 0.5192 (tptm) REVERT: c 93 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6841 (mp0) REVERT: c 145 MET cc_start: 0.8226 (mtp) cc_final: 0.7972 (mtm) REVERT: c 173 ILE cc_start: 0.7470 (mp) cc_final: 0.7263 (mm) REVERT: e 171 HIS cc_start: 0.6902 (p90) cc_final: 0.6679 (p90) REVERT: e 195 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8328 (tppt) REVERT: e 220 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.5676 (p90) REVERT: e 282 THR cc_start: 0.9316 (m) cc_final: 0.8916 (p) REVERT: e 306 LEU cc_start: 0.5699 (tp) cc_final: 0.5294 (mm) REVERT: f 114 LEU cc_start: 0.6666 (mm) cc_final: 0.6460 (mp) REVERT: g 111 ARG cc_start: 0.6993 (mtp85) cc_final: 0.6470 (ptm160) REVERT: h 19 ASN cc_start: 0.7517 (p0) cc_final: 0.7288 (p0) REVERT: h 30 ASN cc_start: 0.7306 (t0) cc_final: 0.6854 (t0) REVERT: h 34 ASN cc_start: 0.7452 (m110) cc_final: 0.6746 (m110) REVERT: i 131 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.4767 (p90) REVERT: i 144 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7296 (mt0) REVERT: i 156 LYS cc_start: 0.5929 (ttpp) cc_final: 0.5361 (ttmt) REVERT: i 194 PHE cc_start: 0.6385 (p90) cc_final: 0.5980 (p90) REVERT: j 145 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7569 (tt) REVERT: k 70 PHE cc_start: 0.7165 (t80) cc_final: 0.6727 (t80) REVERT: l 47 SER cc_start: 0.7505 (t) cc_final: 0.7158 (m) REVERT: l 66 TYR cc_start: 0.8552 (t80) cc_final: 0.8315 (t80) REVERT: m 116 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: p 8 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5999 (ttm170) REVERT: p 23 ASP cc_start: 0.8087 (t0) cc_final: 0.7876 (t70) REVERT: p 59 LYS cc_start: 0.7646 (mptt) cc_final: 0.7207 (mptt) REVERT: p 69 ASP cc_start: 0.6567 (OUTLIER) cc_final: 0.6035 (t0) REVERT: q 96 LYS cc_start: 0.8357 (pttt) cc_final: 0.7785 (pttp) REVERT: t 92 ARG cc_start: 0.7251 (mtt180) cc_final: 0.7022 (ttm-80) REVERT: t 128 ILE cc_start: 0.7591 (mp) cc_final: 0.7300 (mt) REVERT: t 131 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7314 (tt) REVERT: t 164 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7380 (mmtt) REVERT: y 91 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7749 (ttt-90) REVERT: y 96 ASP cc_start: 0.7559 (m-30) cc_final: 0.7287 (m-30) REVERT: d 41 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5638 (mmm-85) REVERT: d 51 LYS cc_start: 0.7921 (tttp) cc_final: 0.7526 (tttm) REVERT: d 64 GLN cc_start: 0.7881 (tt0) cc_final: 0.7523 (mt0) REVERT: n 60 HIS cc_start: 0.6035 (OUTLIER) cc_final: 0.5321 (m-70) REVERT: n 84 ARG cc_start: 0.6789 (tpp80) cc_final: 0.6473 (mtm-85) outliers start: 410 outliers final: 309 residues processed: 1709 average time/residue: 1.4295 time to fit residues: 4091.0229 Evaluate side-chains 1800 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 1457 time to evaluate : 6.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 18 CYS Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 46 LEU Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 11 CYS Chi-restraints excluded: chain 5 residue 24 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 112 ILE Chi-restraints excluded: chain 6 residue 127 LYS Chi-restraints excluded: chain 7 residue 60 MET Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 88 GLN Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 192 ARG Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 218 SER Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 93 HIS Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 183 ILE Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 230 SER Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 94 ARG Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 154 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 99 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 108 MET Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain 0 residue 59 MET Chi-restraints excluded: chain 0 residue 87 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 189 CYS Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 78 MET Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 194 ASP Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 161 ARG Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 172 MET Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 209 ARG Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 213 ILE Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 277 ASN Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 LEU Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 96 ILE Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 122 LEU Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 29 GLN Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 116 GLU Chi-restraints excluded: chain m residue 123 ILE Chi-restraints excluded: chain m residue 138 ASN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 8 ARG Chi-restraints excluded: chain p residue 29 GLU Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 93 LYS Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain t residue 103 ARG Chi-restraints excluded: chain t residue 118 SER Chi-restraints excluded: chain t residue 131 LEU Chi-restraints excluded: chain t residue 145 LYS Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 101 SER Chi-restraints excluded: chain y residue 107 HIS Chi-restraints excluded: chain y residue 116 LEU Chi-restraints excluded: chain y residue 161 SER Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 67 LYS Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 179 ILE Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 93 ILE Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain v residue 176 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain 8 residue 72 MET Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 30.0000 chunk 406 optimal weight: 4.9990 chunk 608 optimal weight: 5.9990 chunk 306 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 647 optimal weight: 6.9990 chunk 694 optimal weight: 7.9990 chunk 503 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 800 optimal weight: 0.0370 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 38 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 159552 Z= 0.338 Angle : 0.742 20.429 237707 Z= 0.372 Chirality : 0.040 0.278 30128 Planarity : 0.006 0.092 13281 Dihedral : 23.794 176.645 77356 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.26 % Favored : 87.54 % Rotamer: Outliers : 7.60 % Allowed : 22.31 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.12 % 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: 6213 helix: -0.27 (0.11), residues: 2001 sheet: -1.55 (0.17), residues: 951 loop : -2.53 (0.10), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP q 111 HIS 0.036 0.002 HIS R 83 PHE 0.027 0.002 PHE m 106 TYR 0.031 0.002 TYR 2 56 ARG 0.015 0.001 ARG e 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1891 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 409 poor density : 1482 time to evaluate : 6.311 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: 3 121 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7623 (mtm110) REVERT: 4 109 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7960 (pttp) REVERT: 7 49 SER cc_start: 0.8997 (t) cc_final: 0.8253 (p) REVERT: 7 61 LYS cc_start: 0.7974 (tptt) cc_final: 0.7410 (mtpp) REVERT: 7 74 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7561 (mtp-110) REVERT: C 28 LEU cc_start: 0.8159 (tp) cc_final: 0.7678 (mt) REVERT: C 58 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6651 (p90) REVERT: C 94 ASP cc_start: 0.6265 (p0) cc_final: 0.5577 (p0) REVERT: C 96 GLU cc_start: 0.7076 (mp0) cc_final: 0.6865 (mp0) REVERT: C 159 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7715 (tttm) REVERT: D 132 ASP cc_start: 0.7925 (t0) cc_final: 0.7621 (t0) REVERT: D 218 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6295 (mtpt) REVERT: D 250 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8079 (mtt) REVERT: D 253 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7688 (ttp-170) REVERT: E 146 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5091 (ptt-90) REVERT: E 212 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5583 (tm) REVERT: E 217 GLU cc_start: 0.7546 (tp30) cc_final: 0.7306 (tp30) REVERT: H 60 LEU cc_start: 0.2720 (OUTLIER) cc_final: 0.2321 (pp) REVERT: K 195 ILE cc_start: 0.8793 (mm) cc_final: 0.8247 (tt) REVERT: K 241 LEU cc_start: 0.7837 (tp) cc_final: 0.7617 (tt) REVERT: M 106 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: M 192 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6576 (mmm-85) REVERT: M 222 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8016 (ttmm) REVERT: M 223 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8047 (mm-30) REVERT: M 236 PRO cc_start: 0.8766 (Cg_endo) cc_final: 0.8506 (Cg_exo) REVERT: N 16 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7131 (ptm-80) REVERT: N 65 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.7477 (m100) REVERT: N 82 ARG cc_start: 0.5854 (tmt170) cc_final: 0.4104 (tmt-80) REVERT: N 91 GLU cc_start: 0.6871 (tp30) cc_final: 0.6620 (tp30) REVERT: N 130 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7696 (pp30) REVERT: O 22 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8207 (mtt-85) REVERT: O 27 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7314 (ttp80) REVERT: O 54 MET cc_start: 0.7272 (tpp) cc_final: 0.6919 (tpp) REVERT: O 122 TYR cc_start: 0.7832 (t80) cc_final: 0.7137 (t80) REVERT: P 59 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: P 76 PHE cc_start: 0.7498 (t80) cc_final: 0.7277 (t80) REVERT: P 91 LYS cc_start: 0.6877 (tmtt) cc_final: 0.6115 (tptp) REVERT: Q 178 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.7524 (m-70) REVERT: R 25 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7283 (ttt-90) REVERT: R 40 ILE cc_start: 0.9156 (mm) cc_final: 0.8824 (mt) REVERT: R 59 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7898 (ttm170) REVERT: R 83 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7727 (t70) REVERT: S 124 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6888 (t80) REVERT: S 132 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7800 (ptm-80) REVERT: S 143 TYR cc_start: 0.8164 (m-10) cc_final: 0.7951 (m-10) REVERT: S 174 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7425 (p) REVERT: S 200 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7093 (p90) REVERT: T 148 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6535 (t80) REVERT: T 156 LYS cc_start: 0.7729 (mttm) cc_final: 0.6935 (tptp) REVERT: U 153 ASN cc_start: 0.8029 (m-40) cc_final: 0.7743 (m110) REVERT: U 167 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7830 (ttm110) REVERT: X 76 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7388 (ptp90) REVERT: X 150 TYR cc_start: 0.5471 (m-10) cc_final: 0.4766 (m-80) REVERT: X 155 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7486 (ttp-110) REVERT: X 156 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7485 (mm-30) REVERT: X 163 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5681 (mm-30) REVERT: Z 120 ARG cc_start: 0.8128 (tpt90) cc_final: 0.7917 (tpt90) REVERT: 0 59 MET cc_start: 0.4856 (OUTLIER) cc_final: 0.2729 (pmm) REVERT: 0 87 LEU cc_start: -0.2241 (OUTLIER) cc_final: -0.2503 (tt) REVERT: b 123 MET cc_start: 0.4284 (ptp) cc_final: 0.4029 (ptp) REVERT: b 145 LEU cc_start: 0.7261 (tp) cc_final: 0.6693 (mm) REVERT: b 178 ARG cc_start: 0.6946 (ttt-90) cc_final: 0.5849 (ttt-90) REVERT: b 202 ILE cc_start: 0.3517 (OUTLIER) cc_final: 0.3115 (mm) REVERT: c 37 GLN cc_start: 0.7965 (tp40) cc_final: 0.7636 (tm-30) REVERT: c 38 LYS cc_start: 0.7383 (mtmm) cc_final: 0.6870 (mtmm) REVERT: c 49 LYS cc_start: 0.7781 (ttpp) cc_final: 0.7565 (tmmt) REVERT: c 67 LYS cc_start: 0.6987 (mttp) cc_final: 0.5373 (tptm) REVERT: c 93 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6885 (mp0) REVERT: c 163 GLN cc_start: 0.8349 (tp40) cc_final: 0.8080 (tp40) REVERT: e 195 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8302 (tppt) REVERT: e 220 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.5720 (p90) REVERT: e 266 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7347 (pt) REVERT: e 282 THR cc_start: 0.9314 (m) cc_final: 0.8927 (p) REVERT: e 306 LEU cc_start: 0.5526 (tp) cc_final: 0.5208 (mm) REVERT: f 174 LEU cc_start: 0.7592 (mt) cc_final: 0.6538 (pp) REVERT: g 28 ASN cc_start: 0.6354 (t0) cc_final: 0.5935 (t0) REVERT: g 111 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6485 (ptm160) REVERT: h 19 ASN cc_start: 0.7778 (p0) cc_final: 0.7478 (p0) REVERT: h 30 ASN cc_start: 0.7256 (t0) cc_final: 0.6825 (t0) REVERT: h 34 ASN cc_start: 0.7499 (m110) cc_final: 0.6747 (m110) REVERT: h 108 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7529 (pp) REVERT: i 131 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.4869 (p90) REVERT: i 144 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7263 (mt0) REVERT: i 156 LYS cc_start: 0.5876 (ttpp) cc_final: 0.5333 (ttmt) REVERT: i 190 LYS cc_start: 0.8379 (tttp) cc_final: 0.7783 (ttpt) REVERT: i 194 PHE cc_start: 0.6390 (p90) cc_final: 0.6069 (p90) REVERT: j 145 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7595 (tt) REVERT: k 70 PHE cc_start: 0.7168 (t80) cc_final: 0.6727 (t80) REVERT: k 83 VAL cc_start: 0.4975 (OUTLIER) cc_final: 0.4642 (t) REVERT: k 125 MET cc_start: 0.7215 (tmm) cc_final: 0.6913 (tmm) REVERT: l 47 SER cc_start: 0.7480 (t) cc_final: 0.7123 (m) REVERT: l 51 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8384 (mtmm) REVERT: l 66 TYR cc_start: 0.8566 (t80) cc_final: 0.8355 (t80) REVERT: m 116 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: p 23 ASP cc_start: 0.8059 (t0) cc_final: 0.7830 (t70) REVERT: p 59 LYS cc_start: 0.7799 (mptt) cc_final: 0.7321 (mptt) REVERT: p 69 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6110 (t0) REVERT: q 96 LYS cc_start: 0.8402 (pttt) cc_final: 0.7815 (pttp) REVERT: s 44 MET cc_start: 0.7837 (mtt) cc_final: 0.7490 (mtt) REVERT: t 92 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6873 (ttm-80) REVERT: t 128 ILE cc_start: 0.7574 (mp) cc_final: 0.7286 (mt) REVERT: t 131 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7288 (tt) REVERT: t 164 LYS cc_start: 0.7700 (mmpt) cc_final: 0.7335 (mmtt) REVERT: t 165 LYS cc_start: 0.6541 (ptpp) cc_final: 0.6212 (ptpp) REVERT: y 91 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7679 (ttt-90) REVERT: y 96 ASP cc_start: 0.7502 (m-30) cc_final: 0.7224 (m-30) REVERT: y 116 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7600 (tt) REVERT: d 41 ARG cc_start: 0.5885 (OUTLIER) cc_final: 0.5683 (mmm-85) REVERT: d 64 GLN cc_start: 0.7857 (tt0) cc_final: 0.7582 (mt0) REVERT: d 191 LEU cc_start: 0.6375 (mt) cc_final: 0.5901 (mt) REVERT: v 70 MET cc_start: 0.3396 (pmm) cc_final: 0.2843 (pmm) REVERT: n 60 HIS cc_start: 0.6117 (OUTLIER) cc_final: 0.5332 (m-70) REVERT: n 84 ARG cc_start: 0.6768 (ttp80) cc_final: 0.6505 (mtm-85) outliers start: 409 outliers final: 314 residues processed: 1696 average time/residue: 1.3870 time to fit residues: 3929.2685 Evaluate side-chains 1815 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1460 time to evaluate : 6.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 18 CYS Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 46 LEU Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 120 LEU Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 11 CYS Chi-restraints excluded: chain 5 residue 18 ARG Chi-restraints excluded: chain 5 residue 24 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 112 ILE Chi-restraints excluded: chain 7 residue 60 MET Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 192 ARG Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 218 SER Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 22 ARG Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 93 HIS Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 183 ILE Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 230 SER Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 94 ARG Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 148 PHE Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 154 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 99 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 114 THR Chi-restraints excluded: chain X residue 118 LEU Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 115 MET Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain 0 residue 59 MET Chi-restraints excluded: chain 0 residue 87 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 78 MET Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 194 ASP Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 161 ARG Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 172 MET Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 191 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 209 ARG Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 213 ILE Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 247 VAL Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 277 ASN Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain f residue 140 MET Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain g residue 13 LYS Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 96 ILE Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 108 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 119 LEU Chi-restraints excluded: chain i residue 122 LEU Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 29 GLN Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 116 GLU Chi-restraints excluded: chain m residue 123 ILE Chi-restraints excluded: chain m residue 138 ASN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 29 GLU Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 93 LYS Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain r residue 62 ILE Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain t residue 103 ARG Chi-restraints excluded: chain t residue 118 SER Chi-restraints excluded: chain t residue 131 LEU Chi-restraints excluded: chain t residue 137 SER Chi-restraints excluded: chain t residue 145 LYS Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 101 SER Chi-restraints excluded: chain y residue 107 HIS Chi-restraints excluded: chain y residue 116 LEU Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 152 SER Chi-restraints excluded: chain y residue 157 ILE Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 179 ILE Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 93 ILE Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain v residue 176 VAL Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain 8 residue 72 MET Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 10.0000 chunk 976 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 949 optimal weight: 10.0000 chunk 975 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 chunk 413 optimal weight: 6.9990 chunk 745 optimal weight: 7.9990 chunk 291 optimal weight: 0.0670 chunk 857 optimal weight: 10.0000 chunk 897 optimal weight: 10.0000 overall best weight: 7.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS R 83 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 GLN ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 186 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 113 GLN j 126 ASN j 149 HIS ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 80 GLN ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 GLN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 196 ASN ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 159552 Z= 0.527 Angle : 0.903 20.420 237707 Z= 0.447 Chirality : 0.048 0.327 30128 Planarity : 0.007 0.096 13281 Dihedral : 23.952 178.667 77356 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.05 % Favored : 86.75 % Rotamer: Outliers : 7.56 % Allowed : 22.81 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6213 helix: -0.58 (0.11), residues: 2018 sheet: -1.79 (0.16), residues: 991 loop : -2.68 (0.10), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP q 111 HIS 0.013 0.002 HIS M 102 PHE 0.031 0.003 PHE Z 105 TYR 0.034 0.003 TYR h 132 ARG 0.013 0.001 ARG q 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1888 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 407 poor density : 1481 time to evaluate : 5.955 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: 3 121 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7774 (mtm110) REVERT: 7 49 SER cc_start: 0.9100 (t) cc_final: 0.8443 (p) REVERT: 7 61 LYS cc_start: 0.8128 (tptt) cc_final: 0.7511 (mtpp) REVERT: C 28 LEU cc_start: 0.8311 (tp) cc_final: 0.7719 (mp) REVERT: C 58 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.6669 (p90) REVERT: C 159 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7705 (tttm) REVERT: C 232 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: D 132 ASP cc_start: 0.7893 (t0) cc_final: 0.7569 (t0) REVERT: D 143 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7746 (ttt90) REVERT: D 218 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6309 (mtpp) REVERT: D 250 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8079 (mtt) REVERT: D 253 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: E 79 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7827 (mmtt) REVERT: E 146 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.5183 (ptt-90) REVERT: E 212 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5739 (tm) REVERT: E 217 GLU cc_start: 0.7575 (tp30) cc_final: 0.7295 (tp30) REVERT: G 69 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.5051 (mt) REVERT: G 72 LEU cc_start: 0.5731 (mt) cc_final: 0.5450 (mp) REVERT: H 60 LEU cc_start: 0.2613 (OUTLIER) cc_final: 0.2216 (pp) REVERT: L 70 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8744 (mmmt) REVERT: M 106 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: M 192 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6637 (mmm-85) REVERT: M 222 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8054 (ttmm) REVERT: M 236 PRO cc_start: 0.8727 (Cg_endo) cc_final: 0.8488 (Cg_exo) REVERT: N 16 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7238 (ptm-80) REVERT: N 65 TRP cc_start: 0.7927 (OUTLIER) cc_final: 0.7527 (m100) REVERT: N 82 ARG cc_start: 0.6070 (tmt170) cc_final: 0.4144 (tmt-80) REVERT: N 91 GLU cc_start: 0.7053 (tp30) cc_final: 0.6817 (tp30) REVERT: N 130 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: N 131 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7672 (p90) REVERT: O 22 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8290 (mtt-85) REVERT: O 54 MET cc_start: 0.7362 (tpp) cc_final: 0.7054 (tpp) REVERT: P 59 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8058 (ttm170) REVERT: P 91 LYS cc_start: 0.6907 (tmtt) cc_final: 0.6115 (tptp) REVERT: P 166 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5775 (t80) REVERT: Q 178 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.6774 (m90) REVERT: R 25 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7284 (ttt-90) REVERT: R 40 ILE cc_start: 0.9188 (mm) cc_final: 0.8900 (mt) REVERT: R 59 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8025 (ttm170) REVERT: R 83 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.7863 (t70) REVERT: S 132 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8046 (ptm-80) REVERT: S 174 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7597 (p) REVERT: S 200 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6995 (p90) REVERT: T 148 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6336 (t80) REVERT: U 167 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7885 (ttm110) REVERT: X 76 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7456 (ptp90) REVERT: X 150 TYR cc_start: 0.5514 (m-10) cc_final: 0.4646 (m-80) REVERT: X 157 ASN cc_start: 0.8208 (m-40) cc_final: 0.7747 (m-40) REVERT: X 163 GLU cc_start: 0.6061 (mm-30) cc_final: 0.5760 (mm-30) REVERT: Z 91 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7129 (mtm110) REVERT: 0 59 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.2778 (pmm) REVERT: 0 87 LEU cc_start: -0.2274 (OUTLIER) cc_final: -0.2528 (tt) REVERT: b 145 LEU cc_start: 0.7321 (tp) cc_final: 0.6746 (mm) REVERT: b 178 ARG cc_start: 0.6943 (ttt-90) cc_final: 0.5901 (ttt-90) REVERT: b 202 ILE cc_start: 0.3656 (OUTLIER) cc_final: 0.3237 (mm) REVERT: c 37 GLN cc_start: 0.8098 (tp40) cc_final: 0.7728 (tm-30) REVERT: c 38 LYS cc_start: 0.7297 (mtmm) cc_final: 0.6530 (mtmt) REVERT: c 49 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7577 (tmmt) REVERT: c 93 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6748 (mp0) REVERT: c 163 GLN cc_start: 0.8332 (tp40) cc_final: 0.8120 (tp40) REVERT: e 195 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8417 (mmtt) REVERT: e 220 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.5442 (p90) REVERT: e 266 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7296 (pt) REVERT: e 282 THR cc_start: 0.9315 (m) cc_final: 0.8952 (p) REVERT: e 306 LEU cc_start: 0.5833 (tp) cc_final: 0.5444 (mm) REVERT: f 168 TYR cc_start: 0.6816 (m-80) cc_final: 0.6365 (m-80) REVERT: g 28 ASN cc_start: 0.6360 (t0) cc_final: 0.6108 (t0) REVERT: g 111 ARG cc_start: 0.7092 (mtp85) cc_final: 0.6535 (ptm160) REVERT: g 149 ARG cc_start: 0.7436 (mmm160) cc_final: 0.7208 (mmm160) REVERT: h 19 ASN cc_start: 0.7772 (p0) cc_final: 0.7113 (m110) REVERT: h 30 ASN cc_start: 0.7177 (t0) cc_final: 0.6724 (t0) REVERT: h 34 ASN cc_start: 0.7264 (m110) cc_final: 0.6470 (m-40) REVERT: h 108 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7586 (pp) REVERT: i 131 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.5051 (p90) REVERT: i 144 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7245 (mt0) REVERT: i 186 LYS cc_start: 0.7334 (mmpt) cc_final: 0.6857 (mmtp) REVERT: i 194 PHE cc_start: 0.6549 (p90) cc_final: 0.6329 (p90) REVERT: j 145 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7543 (tt) REVERT: k 83 VAL cc_start: 0.4971 (OUTLIER) cc_final: 0.4672 (t) REVERT: k 125 MET cc_start: 0.7276 (tmm) cc_final: 0.6966 (tmm) REVERT: l 47 SER cc_start: 0.7945 (t) cc_final: 0.7638 (t) REVERT: l 54 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7520 (ttm-80) REVERT: p 23 ASP cc_start: 0.8126 (t0) cc_final: 0.7876 (t70) REVERT: p 59 LYS cc_start: 0.7923 (mptt) cc_final: 0.7361 (mptt) REVERT: p 69 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6008 (t0) REVERT: q 96 LYS cc_start: 0.8392 (pttt) cc_final: 0.7855 (pttp) REVERT: r 29 ASP cc_start: 0.7008 (t0) cc_final: 0.6648 (t0) REVERT: s 44 MET cc_start: 0.7784 (mtt) cc_final: 0.7434 (mtt) REVERT: t 92 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6670 (mmp-170) REVERT: t 101 LYS cc_start: 0.6063 (tttt) cc_final: 0.5412 (tttp) REVERT: t 128 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7210 (mt) REVERT: t 164 LYS cc_start: 0.7730 (mmpt) cc_final: 0.7309 (mmtt) REVERT: t 165 LYS cc_start: 0.6396 (ptpp) cc_final: 0.6138 (ptpp) REVERT: u 120 ARG cc_start: 0.5720 (ttp-170) cc_final: 0.5288 (ttt180) REVERT: y 82 ARG cc_start: 0.7258 (mtm180) cc_final: 0.7048 (mtm-85) REVERT: y 91 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7715 (ttt-90) REVERT: y 116 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7595 (tt) REVERT: d 41 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5894 (mmm-85) REVERT: d 64 GLN cc_start: 0.8003 (tt0) cc_final: 0.7631 (mt0) REVERT: d 81 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6348 (tm130) REVERT: d 191 LEU cc_start: 0.6429 (mt) cc_final: 0.5909 (mt) REVERT: v 70 MET cc_start: 0.3698 (pmm) cc_final: 0.3295 (pmm) REVERT: n 60 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.5413 (m-70) REVERT: n 84 ARG cc_start: 0.6789 (ttp80) cc_final: 0.6536 (mtm-85) outliers start: 407 outliers final: 310 residues processed: 1699 average time/residue: 1.4975 time to fit residues: 4273.6032 Evaluate side-chains 1810 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 1454 time to evaluate : 6.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 46 LEU Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 4 residue 109 LYS Chi-restraints excluded: chain 4 residue 120 LEU Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 11 CYS Chi-restraints excluded: chain 5 residue 18 ARG Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 112 ILE Chi-restraints excluded: chain 7 residue 60 MET Chi-restraints excluded: chain 7 residue 62 THR Chi-restraints excluded: chain 7 residue 72 ILE Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 88 GLN Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 192 ARG Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 218 SER Chi-restraints excluded: chain M residue 245 SER Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 16 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 65 TRP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 22 ARG Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 93 HIS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 166 PHE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 183 ILE Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 230 SER Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 59 ARG Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 94 ARG Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 148 PHE Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 154 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 ASP Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 99 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 114 THR Chi-restraints excluded: chain X residue 118 LEU Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 91 ARG Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 59 MET Chi-restraints excluded: chain 0 residue 87 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 78 MET Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 161 ARG Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 172 MET Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 191 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 209 ARG Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 213 ILE Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 247 VAL Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 277 ASN Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 LEU Chi-restraints excluded: chain g residue 13 LYS Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 96 ILE Chi-restraints excluded: chain h residue 103 MET Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 108 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain h residue 131 CYS Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 119 LEU Chi-restraints excluded: chain i residue 122 LEU Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 149 HIS Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 54 ARG Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 102 LYS Chi-restraints excluded: chain m residue 123 ILE Chi-restraints excluded: chain m residue 138 ASN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 29 GLU Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 93 LYS Chi-restraints excluded: chain q residue 108 VAL Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain r residue 62 ILE Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain t residue 103 ARG Chi-restraints excluded: chain t residue 118 SER Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 137 SER Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 101 SER Chi-restraints excluded: chain y residue 107 HIS Chi-restraints excluded: chain y residue 116 LEU Chi-restraints excluded: chain y residue 152 SER Chi-restraints excluded: chain y residue 157 ILE Chi-restraints excluded: chain y residue 160 VAL Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 81 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 148 ILE Chi-restraints excluded: chain d residue 179 ILE Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 93 ILE Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain v residue 176 VAL Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain 8 residue 72 MET Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 20.0000 chunk 623 optimal weight: 3.9990 chunk 1003 optimal weight: 10.0000 chunk 612 optimal weight: 1.9990 chunk 476 optimal weight: 5.9990 chunk 697 optimal weight: 0.5980 chunk 1053 optimal weight: 0.1980 chunk 969 optimal weight: 10.0000 chunk 838 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 647 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 58 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN L 13 ASN M 88 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 ASN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 153 ASN ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 GLN ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 186 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS h 78 HIS i 142 GLN ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 71 ASN ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 23 ASN ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN d 81 GLN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 196 ASN ** n 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 72 ASN ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 159552 Z= 0.189 Angle : 0.673 17.781 237707 Z= 0.341 Chirality : 0.036 0.252 30128 Planarity : 0.005 0.087 13281 Dihedral : 23.806 178.429 77356 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.00 % Favored : 89.83 % Rotamer: Outliers : 5.09 % Allowed : 25.69 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 6213 helix: -0.12 (0.11), residues: 1998 sheet: -1.53 (0.17), residues: 965 loop : -2.50 (0.10), residues: 3250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP q 111 HIS 0.037 0.002 HIS Q 178 PHE 0.036 0.002 PHE p 77 TYR 0.034 0.002 TYR 2 56 ARG 0.016 0.001 ARG u 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12426 Ramachandran restraints generated. 6213 Oldfield, 0 Emsley, 6213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1749 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1475 time to evaluate : 6.399 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: 7 49 SER cc_start: 0.8903 (t) cc_final: 0.8120 (p) REVERT: 7 61 LYS cc_start: 0.7861 (tptt) cc_final: 0.7343 (mtpp) REVERT: C 28 LEU cc_start: 0.8089 (tp) cc_final: 0.7533 (mt) REVERT: C 94 ASP cc_start: 0.6210 (p0) cc_final: 0.5450 (p0) REVERT: C 96 GLU cc_start: 0.7185 (mp0) cc_final: 0.6785 (pm20) REVERT: C 159 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7642 (tttm) REVERT: D 132 ASP cc_start: 0.7915 (t0) cc_final: 0.7640 (t0) REVERT: D 218 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6686 (mtpt) REVERT: D 250 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7906 (mmt) REVERT: D 253 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7359 (ttp-170) REVERT: E 146 ARG cc_start: 0.5236 (OUTLIER) cc_final: 0.4984 (ptt-90) REVERT: E 217 GLU cc_start: 0.7421 (tp30) cc_final: 0.7163 (tp30) REVERT: H 60 LEU cc_start: 0.2479 (OUTLIER) cc_final: 0.2050 (pp) REVERT: K 101 TYR cc_start: 0.8758 (t80) cc_final: 0.8479 (t80) REVERT: K 195 ILE cc_start: 0.8733 (mm) cc_final: 0.8154 (tt) REVERT: K 241 LEU cc_start: 0.7792 (tp) cc_final: 0.7546 (tt) REVERT: L 18 GLU cc_start: 0.6368 (pt0) cc_final: 0.5754 (pt0) REVERT: L 107 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7470 (ttp-170) REVERT: M 236 PRO cc_start: 0.8749 (Cg_endo) cc_final: 0.8469 (Cg_exo) REVERT: N 82 ARG cc_start: 0.5937 (tmt170) cc_final: 0.3743 (tmt-80) REVERT: N 91 GLU cc_start: 0.6826 (tp30) cc_final: 0.6576 (tp30) REVERT: O 27 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7189 (ttp80) REVERT: O 122 TYR cc_start: 0.7771 (t80) cc_final: 0.7458 (t80) REVERT: P 59 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7996 (ttm170) REVERT: P 91 LYS cc_start: 0.6824 (tmtt) cc_final: 0.6031 (tptp) REVERT: P 166 PHE cc_start: 0.6309 (OUTLIER) cc_final: 0.5675 (t80) REVERT: R 25 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7269 (ttt-90) REVERT: R 83 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7584 (t70) REVERT: S 124 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6629 (t80) REVERT: S 132 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7735 (ptm-80) REVERT: S 174 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7363 (p) REVERT: S 200 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7346 (p90) REVERT: S 206 TYR cc_start: 0.8692 (t80) cc_final: 0.8387 (t80) REVERT: T 148 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6113 (t80) REVERT: T 156 LYS cc_start: 0.7719 (mttm) cc_final: 0.6881 (tptt) REVERT: U 153 ASN cc_start: 0.8414 (m-40) cc_final: 0.8172 (m110) REVERT: U 167 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7803 (ttm110) REVERT: X 150 TYR cc_start: 0.5484 (m-10) cc_final: 0.4810 (m-80) REVERT: X 155 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7992 (ttp-110) REVERT: X 156 GLU cc_start: 0.7828 (mm-30) cc_final: 0.6893 (mm-30) REVERT: X 163 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5742 (mm-30) REVERT: Y 97 ARG cc_start: 0.8284 (tmm-80) cc_final: 0.7909 (tmm-80) REVERT: 0 59 MET cc_start: 0.4671 (OUTLIER) cc_final: 0.2656 (pmm) REVERT: 0 87 LEU cc_start: -0.2156 (OUTLIER) cc_final: -0.2376 (tt) REVERT: b 104 MET cc_start: 0.5991 (mmm) cc_final: 0.5679 (mtm) REVERT: b 145 LEU cc_start: 0.7100 (tp) cc_final: 0.6615 (mm) REVERT: b 202 ILE cc_start: 0.3235 (OUTLIER) cc_final: 0.2816 (mm) REVERT: c 93 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6702 (mp0) REVERT: c 100 GLN cc_start: 0.6689 (tp40) cc_final: 0.6484 (tp40) REVERT: c 137 SER cc_start: 0.7369 (t) cc_final: 0.6612 (p) REVERT: c 163 GLN cc_start: 0.8286 (tp40) cc_final: 0.8019 (tp40) REVERT: e 195 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8495 (mmtt) REVERT: e 220 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.5461 (p90) REVERT: e 266 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7328 (pt) REVERT: e 282 THR cc_start: 0.9296 (m) cc_final: 0.8905 (p) REVERT: e 306 LEU cc_start: 0.5665 (tp) cc_final: 0.5250 (mm) REVERT: f 174 LEU cc_start: 0.7600 (mt) cc_final: 0.6426 (pp) REVERT: g 35 LYS cc_start: 0.7319 (mppt) cc_final: 0.6873 (mttt) REVERT: g 111 ARG cc_start: 0.6936 (mtp85) cc_final: 0.6422 (ptm160) REVERT: h 19 ASN cc_start: 0.7673 (p0) cc_final: 0.7050 (m110) REVERT: h 34 ASN cc_start: 0.7575 (m110) cc_final: 0.7039 (m110) REVERT: i 131 PHE cc_start: 0.5806 (OUTLIER) cc_final: 0.4759 (p90) REVERT: i 156 LYS cc_start: 0.5996 (ttpp) cc_final: 0.5391 (ttmt) REVERT: i 186 LYS cc_start: 0.7083 (mmpt) cc_final: 0.6852 (mmtt) REVERT: j 145 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7587 (tt) REVERT: k 83 VAL cc_start: 0.5244 (OUTLIER) cc_final: 0.4961 (t) REVERT: k 125 MET cc_start: 0.7185 (tmm) cc_final: 0.6828 (tmm) REVERT: l 7 LEU cc_start: 0.8790 (mt) cc_final: 0.8561 (mp) REVERT: o 59 LYS cc_start: 0.7629 (mttt) cc_final: 0.7262 (mtmt) REVERT: p 12 LYS cc_start: 0.7833 (pttt) cc_final: 0.7342 (ptpt) REVERT: p 59 LYS cc_start: 0.7939 (mptt) cc_final: 0.7366 (mmtm) REVERT: p 69 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6198 (t0) REVERT: q 96 LYS cc_start: 0.8312 (pttt) cc_final: 0.7777 (pttp) REVERT: r 29 ASP cc_start: 0.6886 (t0) cc_final: 0.6449 (t0) REVERT: s 44 MET cc_start: 0.7793 (mtt) cc_final: 0.7446 (mtt) REVERT: t 81 LYS cc_start: 0.5644 (mttt) cc_final: 0.5358 (mtpt) REVERT: t 92 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6714 (mmp-170) REVERT: t 96 ARG cc_start: 0.6248 (ttm110) cc_final: 0.5857 (ttm110) REVERT: t 101 LYS cc_start: 0.6244 (tttt) cc_final: 0.5743 (tttp) REVERT: t 128 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6937 (mt) REVERT: t 164 LYS cc_start: 0.7662 (mmpt) cc_final: 0.7289 (mmtt) REVERT: y 91 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7347 (tmt-80) REVERT: y 96 ASP cc_start: 0.7215 (m-30) cc_final: 0.7011 (m-30) REVERT: y 116 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7363 (tt) REVERT: y 130 ARG cc_start: 0.7909 (mpt-90) cc_final: 0.7632 (mpt180) REVERT: d 51 LYS cc_start: 0.7982 (tttp) cc_final: 0.7635 (tttm) REVERT: d 64 GLN cc_start: 0.7772 (tt0) cc_final: 0.7458 (mt0) REVERT: d 149 GLN cc_start: 0.6123 (mp10) cc_final: 0.5760 (mp10) REVERT: d 191 LEU cc_start: 0.6299 (mt) cc_final: 0.5869 (mt) REVERT: v 70 MET cc_start: 0.3313 (pmm) cc_final: 0.2984 (pmm) REVERT: n 23 ILE cc_start: 0.7825 (mp) cc_final: 0.7561 (mt) REVERT: n 60 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.5254 (m-70) outliers start: 274 outliers final: 206 residues processed: 1615 average time/residue: 1.4422 time to fit residues: 3936.2672 Evaluate side-chains 1657 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1424 time to evaluate : 6.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 3 residue 119 SER Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 120 LEU Chi-restraints excluded: chain 4 residue 139 ASP Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 11 CYS Chi-restraints excluded: chain 5 residue 18 ARG Chi-restraints excluded: chain 6 residue 112 ILE Chi-restraints excluded: chain 7 residue 72 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain P residue 59 ARG Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 166 PHE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 230 SER Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 94 ARG Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 132 ARG Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 105 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 148 PHE Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain V residue 57 LYS Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 124 LYS Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 154 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 114 THR Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 59 MET Chi-restraints excluded: chain 0 residue 87 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 161 ARG Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 172 MET Chi-restraints excluded: chain e residue 182 ASP Chi-restraints excluded: chain e residue 191 VAL Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 247 VAL Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 175 LEU Chi-restraints excluded: chain g residue 13 LYS Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 96 ILE Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain h residue 131 CYS Chi-restraints excluded: chain h residue 133 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 122 LEU Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 149 HIS Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 121 ASP Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 123 ILE Chi-restraints excluded: chain m residue 138 ASN Chi-restraints excluded: chain p residue 29 GLU Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 71 ASP Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain t residue 103 ARG Chi-restraints excluded: chain t residue 118 SER Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain y residue 91 ARG Chi-restraints excluded: chain y residue 107 HIS Chi-restraints excluded: chain y residue 116 LEU Chi-restraints excluded: chain y residue 157 ILE Chi-restraints excluded: chain y residue 161 SER Chi-restraints excluded: chain w residue 100 VAL Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain d residue 81 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 179 ILE Chi-restraints excluded: chain v residue 26 VAL Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 93 ILE Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain v residue 176 VAL Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 75 ARG Chi-restraints excluded: chain 8 residue 72 MET Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 368 ARG Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 8.9990 chunk 666 optimal weight: 8.9990 chunk 893 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 773 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 839 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 862 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS R 83 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 GLN ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS c 154 GLN ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 186 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS i 113 GLN i 142 GLN j 149 HIS ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 GLN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 196 ASN ** n 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 72 ASN ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116013 restraints weight = 270069.510| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.40 r_work: 0.3216 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 159552 Z= 0.420 Angle : 0.807 23.675 237707 Z= 0.402 Chirality : 0.043 0.298 30128 Planarity : 0.007 0.097 13281 Dihedral : 23.819 177.538 77356 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.67 % Favored : 87.16 % Rotamer: Outliers : 5.57 % Allowed : 25.93 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 6213 helix: -0.30 (0.11), residues: 2013 sheet: -1.65 (0.16), residues: 996 loop : -2.59 (0.10), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP c 22 HIS 0.011 0.002 HIS j 149 PHE 0.029 0.003 PHE X 101 TYR 0.045 0.003 TYR R 75 ARG 0.014 0.001 ARG Q 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52999.31 seconds wall clock time: 918 minutes 7.08 seconds (55087.08 seconds total)