Starting phenix.real_space_refine on Mon Mar 25 19:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdy_3492/03_2024/5mdy_3492_updated.pdb" } resolution = 3.35 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4638 5.49 5 Mg 450 5.21 5 S 169 5.16 5 C 75401 2.51 5 N 27756 2.21 5 O 41044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 GLU 17": "OE1" <-> "OE2" Residue "6 ARG 28": "NH1" <-> "NH2" Residue "6 GLU 30": "OE1" <-> "OE2" Residue "7 GLU 36": "OE1" <-> "OE2" Residue "7 GLU 41": "OE1" <-> "OE2" Residue "7 GLU 43": "OE1" <-> "OE2" Residue "7 GLU 47": "OE1" <-> "OE2" Residue "7 ARG 59": "NH1" <-> "NH2" Residue "7 ARG 67": "NH1" <-> "NH2" Residue "7 ARG 69": "NH1" <-> "NH2" Residue "7 ARG 70": "NH1" <-> "NH2" Residue "7 GLU 79": "OE1" <-> "OE2" Residue "7 GLU 87": "OE1" <-> "OE2" Residue "7 GLU 90": "OE1" <-> "OE2" Residue "7 GLU 96": "OE1" <-> "OE2" Residue "7 GLU 103": "OE1" <-> "OE2" Residue "7 GLU 105": "OE1" <-> "OE2" Residue "7 GLU 113": "OE1" <-> "OE2" Residue "7 GLU 141": "OE1" <-> "OE2" Residue "7 GLU 147": "OE1" <-> "OE2" Residue "7 ARG 151": "NH1" <-> "NH2" Residue "7 ARG 159": "NH1" <-> "NH2" Residue "7 GLU 187": "OE1" <-> "OE2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 GLU 222": "OE1" <-> "OE2" Residue "7 ARG 263": "NH1" <-> "NH2" Residue "7 GLU 300": "OE1" <-> "OE2" Residue "7 GLU 307": "OE1" <-> "OE2" Residue "7 ARG 312": "NH1" <-> "NH2" Residue "7 ARG 338": "NH1" <-> "NH2" Residue "7 ARG 343": "NH1" <-> "NH2" Residue "7 GLU 363": "OE1" <-> "OE2" Residue "7 ARG 368": "NH1" <-> "NH2" Residue "7 ARG 369": "NH1" <-> "NH2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 55": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "P GLU 112": "OE1" <-> "OE2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 85": "OE1" <-> "OE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X GLU 43": "OE1" <-> "OE2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "a GLU 11": "OE1" <-> "OE2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 12": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 118": "OE1" <-> "OE2" Residue "g GLU 133": "OE1" <-> "OE2" Residue "g GLU 169": "OE1" <-> "OE2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "h GLU 28": "OE1" <-> "OE2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h GLU 110": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h GLU 152": "OE1" <-> "OE2" Residue "h GLU 161": "OE1" <-> "OE2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h GLU 166": "OE1" <-> "OE2" Residue "h GLU 188": "OE1" <-> "OE2" Residue "h GLU 206": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 147": "OE1" <-> "OE2" Residue "i GLU 160": "OE1" <-> "OE2" Residue "i GLU 166": "OE1" <-> "OE2" Residue "i GLU 172": "OE1" <-> "OE2" Residue "i GLU 197": "OE1" <-> "OE2" Residue "i GLU 202": "OE1" <-> "OE2" Residue "j GLU 10": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 55": "OE1" <-> "OE2" Residue "j GLU 65": "OE1" <-> "OE2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j GLU 101": "OE1" <-> "OE2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "j GLU 151": "OE1" <-> "OE2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k ARG 2": "NH1" <-> "NH2" Residue "k GLU 5": "OE1" <-> "OE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k GLU 65": "OE1" <-> "OE2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "k GLU 73": "OE1" <-> "OE2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 3": "NH1" <-> "NH2" Residue "l ARG 5": "NH1" <-> "NH2" Residue "l GLU 21": "OE1" <-> "OE2" Residue "l GLU 40": "OE1" <-> "OE2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l GLU 58": "OE1" <-> "OE2" Residue "l GLU 63": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l GLU 123": "OE1" <-> "OE2" Residue "m GLU 42": "OE1" <-> "OE2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m GLU 52": "OE1" <-> "OE2" Residue "m GLU 73": "OE1" <-> "OE2" Residue "m GLU 124": "OE1" <-> "OE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n GLU 36": "OE1" <-> "OE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 113": "NH1" <-> "NH2" Residue "n ARG 119": "NH1" <-> "NH2" Residue "n ARG 122": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o GLU 24": "OE1" <-> "OE2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o GLU 81": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p GLU 83": "OE1" <-> "OE2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q GLU 76": "OE1" <-> "OE2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "q ARG 86": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "s GLU 26": "OE1" <-> "OE2" Residue "s GLU 39": "OE1" <-> "OE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "s GLU 86": "OE1" <-> "OE2" Residue "t GLU 6": "OE1" <-> "OE2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u GLU 34": "OE1" <-> "OE2" Residue "u GLU 45": "OE1" <-> "OE2" Residue "u GLU 47": "OE1" <-> "OE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v GLU 26": "OE1" <-> "OE2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v GLU 52": "OE1" <-> "OE2" Residue "v GLU 63": "OE1" <-> "OE2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w GLU 16": "OE1" <-> "OE2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x GLU 20": "OE1" <-> "OE2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x GLU 65": "OE1" <-> "OE2" Residue "x ARG 81": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 8": "OE1" <-> "OE2" Residue "z GLU 24": "OE1" <-> "OE2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z GLU 39": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z GLU 63": "OE1" <-> "OE2" Residue "z ARG 66": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149460 Number of models: 1 Model: "" Number of chains: 68 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 287, 'rna2p_pyr': 163, 'rna3p': 16, 'rna3p_pur': 1380, 'rna3p_pyr': 1051} Link IDs: {'rna2p': 455, 'rna3p': 2447} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 88, 'rna3p': 10, 'rna3p_pur': 752, 'rna3p_pyr': 565} Link IDs: {'rna2p': 205, 'rna3p': 1328} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "5" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Unusual residues: {'8AN': 1} Classifications: {'RNA': 75, 'undetermined': 1} Modifications used: {'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'p': 1, 'rna2p': 13, 'rna3p': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "7" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2597 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 16, 'TRANS': 307} Chain breaks: 3 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1089 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 495 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 293 Unusual residues: {' MG': 293} Classifications: {'undetermined': 293} Link IDs: {None: 292} Chain: "2" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Unusual residues: {' MG': 143} Classifications: {'undetermined': 143} Link IDs: {None: 142} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "5" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 14 Unusual residues: {' MG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0L9B SG CYS a 16 128.639 196.763 41.766 1.00163.40 S ATOM A0L9N SG CYS a 18 129.714 198.243 42.775 1.00165.33 S ATOM A0LDL SG CYS a 37 129.803 196.216 43.293 1.00158.62 S ATOM A0LE6 SG CYS a 40 131.459 197.296 42.774 1.00157.81 S ATOM A0MYG SG CYS f 11 180.861 134.249 118.195 1.00 76.94 S ATOM A0N20 SG CYS f 27 182.093 132.774 118.862 1.00 76.55 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13145 " occ=0.50 Time building chain proxies: 59.57, per 1000 atoms: 0.40 Number of scatterers: 149460 At special positions: 0 Unit cell: (244.4, 287.04, 273.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 169 16.00 P 4638 15.00 Mg 450 11.99 O 41044 8.00 N 27756 7.00 C 75401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 69.46 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb=" ZN f 102 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 102 " - pdb=" ND1 HIS f 33 " Number of angles added : 6 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11628 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 194 helices and 75 sheets defined 40.5% alpha, 18.6% beta 1540 base pairs and 2375 stacking pairs defined. Time for finding SS restraints: 79.82 Creating SS restraints... Processing helix chain '6' and resid 15 through 23 Proline residue: 6 23 - end of helix Processing helix chain '7' and resid 17 through 45 removed outlier: 3.762A pdb=" N GLY 7 28 " --> pdb=" O LYS 7 24 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE 7 32 " --> pdb=" O GLY 7 28 " (cutoff:3.500A) Proline residue: 7 33 - end of helix removed outlier: 4.012A pdb=" N THR 7 37 " --> pdb=" O PRO 7 33 " (cutoff:3.500A) Processing helix chain '7' and resid 48 through 53 Processing helix chain '7' and resid 54 through 89 removed outlier: 3.540A pdb=" N ASP 7 73 " --> pdb=" O ARG 7 69 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR 7 74 " --> pdb=" O ARG 7 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE 7 75 " --> pdb=" O THR 7 71 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG 7 76 " --> pdb=" O VAL 7 72 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER 7 77 " --> pdb=" O ASP 7 73 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU 7 78 " --> pdb=" O THR 7 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 7 82 " --> pdb=" O LEU 7 78 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU 7 86 " --> pdb=" O LEU 7 82 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU 7 87 " --> pdb=" O GLN 7 83 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU 7 88 " --> pdb=" O GLY 7 84 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 121 Proline residue: 7 102 - end of helix removed outlier: 3.673A pdb=" N GLU 7 105 " --> pdb=" O LYS 7 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU 7 106 " --> pdb=" O PRO 7 102 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA 7 107 " --> pdb=" O GLU 7 103 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN 7 121 " --> pdb=" O GLN 7 117 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 161 Processing helix chain '7' and resid 188 through 194 removed outlier: 3.883A pdb=" N LEU 7 192 " --> pdb=" O ASN 7 188 " (cutoff:3.500A) Processing helix chain '7' and resid 280 through 312 removed outlier: 3.504A pdb=" N ASN 7 284 " --> pdb=" O SER 7 280 " (cutoff:3.500A) Processing helix chain '7' and resid 345 through 352 Processing helix chain '7' and resid 354 through 369 Processing helix chain 'B' and resid 10 through 16 removed outlier: 7.218A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.018A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.787A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 5.295A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.712A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.554A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.663A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 97 through 104 removed outlier: 4.129A pdb=" N ASP C 103 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.385A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 6.617A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.554A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 5.575A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 21 removed outlier: 4.865A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 46 removed outlier: 4.633A pdb=" N ILE E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 46' Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.620A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 112 removed outlier: 4.766A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix removed outlier: 5.780A pdb=" N ARG E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.817A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.638A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.005A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.635A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.625A pdb=" N ILE F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 40 through 48 removed outlier: 3.695A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 73 removed outlier: 3.836A pdb=" N LEU G 54 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'H' and resid 3 through 22 removed outlier: 3.669A pdb=" N ASP H 7 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA H 22 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.516A pdb=" N LYS H 37 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 Proline residue: H 68 - end of helix removed outlier: 4.207A pdb=" N CYS H 71 " --> pdb=" O THR H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 removed outlier: 4.348A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 73 through 79' Processing helix chain 'H' and resid 94 through 106 removed outlier: 4.100A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 6.061A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 48 removed outlier: 3.974A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 Processing helix chain 'I' and resid 101 through 113 removed outlier: 3.708A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.747A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.673A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.711A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 4.173A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.122A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.873A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.740A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.584A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.332A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.153A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.220A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.555A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.429A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.485A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.711A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.525A pdb=" N LYS P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.632A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.635A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.972A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 4.163A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.995A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.548A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.192A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.519A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.694A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.899A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.554A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.857A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 4.259A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.629A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 63 removed outlier: 4.700A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.209A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 63 Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.660A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 4.092A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.804A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.612A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 24 through 32 removed outlier: 4.174A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix removed outlier: 5.763A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 24 through 32' Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix removed outlier: 3.671A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.208A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 3.538A pdb=" N VAL g 107 " --> pdb=" O ASN g 103 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 Processing helix chain 'h' and resid 6 through 12 removed outlier: 4.024A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 Processing helix chain 'h' and resid 72 through 78 removed outlier: 3.871A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.467A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.556A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.268A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.825A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.512A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 4.962A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.596A pdb=" N ASN i 89 " --> pdb=" O ASN i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.490A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.843A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.742A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.837A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.366A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 Processing helix chain 'j' and resid 132 through 148 removed outlier: 5.492A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 11 through 17 removed outlier: 3.813A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 11 through 17' Processing helix chain 'k' and resid 18 through 33 removed outlier: 3.567A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 3.558A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 32 removed outlier: 5.411A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 4.021A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.503A pdb=" N ALA l 61 " --> pdb=" O SER l 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.655A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.618A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 40 removed outlier: 4.476A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 56 Proline residue: n 51 - end of helix removed outlier: 3.648A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.955A pdb=" N GLN n 75 " --> pdb=" O GLY n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.949A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 4.042A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.053A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.747A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 76 removed outlier: 3.602A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 91 through 104 removed outlier: 4.343A pdb=" N SER p 95 " --> pdb=" O PRO p 91 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.827A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.763A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.655A pdb=" N SER r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.141A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.547A pdb=" N ILE r 77 " --> pdb=" O ILE r 73 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.723A pdb=" N GLU s 10 " --> pdb=" O MET s 6 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL s 11 " --> pdb=" O LYS s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 52 Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 44 removed outlier: 4.009A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.739A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.533A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.844A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.645A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.362A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 41 Processing helix chain 'y' and resid 43 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.783A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 68 removed outlier: 4.677A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '7' and resid 162 through 167 removed outlier: 3.663A pdb=" N GLN 7 163 " --> pdb=" O LYS 7 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL 7 167 " --> pdb=" O GLN 7 181 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN 7 181 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA 7 129 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN 7 128 " --> pdb=" O GLU 7 226 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE 7 224 " --> pdb=" O ILE 7 130 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE 7 218 " --> pdb=" O GLY 7 136 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU 7 341 " --> pdb=" O ASP 7 336 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '7' and resid 261 through 265 removed outlier: 3.679A pdb=" N VAL 7 262 " --> pdb=" O CYS 7 275 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL 7 273 " --> pdb=" O VAL 7 264 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '7' and resid 168 through 171 Processing sheet with id= 4, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 5, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.741A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.371A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.359A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 3 through 9 removed outlier: 4.250A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 13.211A pdb=" N GLY C 198 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 11.708A pdb=" N LYS C 114 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C 204 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.592A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.567A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.249A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 1 through 5 removed outlier: 4.387A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 117 through 120 Processing sheet with id= 14, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.788A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.513A pdb=" N THR F 51 " --> pdb=" O LYS F 44 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 18, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.923A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS F 86 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG F 163 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 90 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 18 through 21 removed outlier: 6.012A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 76 through 80 removed outlier: 6.350A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 23 through 27 removed outlier: 4.063A pdb=" N LEU H 23 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA H 25 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL H 27 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 55 through 58 removed outlier: 4.381A pdb=" N VAL I 69 " --> pdb=" O VAL I 57 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 52 through 57 removed outlier: 3.509A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.648A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.729A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.923A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.528A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.988A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.291A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.626A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.872A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 49 through 53 removed outlier: 4.720A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 34, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.954A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 36, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 37, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.219A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 2 through 8 removed outlier: 6.635A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 73 through 79 removed outlier: 5.171A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.417A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL T 34 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY T 75 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 40 through 44 removed outlier: 4.599A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 43, first strand: chain 'V' and resid 2 through 5 removed outlier: 3.748A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.630A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.982A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 67 through 71 Processing sheet with id= 47, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.541A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 49, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.118A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU Z 58 " --> pdb=" O LYS Z 6 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.577A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS a 16 " --> pdb=" O ASN a 20 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 20 through 26 removed outlier: 7.381A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.267A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= 54, first strand: chain 'g' and resid 67 through 71 Processing sheet with id= 55, first strand: chain 'h' and resid 53 through 59 Processing sheet with id= 56, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.835A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.685A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.631A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.727A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 32 through 41 removed outlier: 6.991A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.672A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU k 40 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP k 42 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL k 7 " --> pdb=" O MET k 88 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 43 through 46 removed outlier: 3.557A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 73 through 79 removed outlier: 6.303A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.152A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'm' and resid 74 through 77 removed outlier: 4.203A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 67, first strand: chain 'o' and resid 37 through 42 removed outlier: 4.117A pdb=" N GLY o 38 " --> pdb=" O ASP o 75 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP o 75 " --> pdb=" O GLY o 38 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN o 99 " --> pdb=" O ARG o 9 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 69, first strand: chain 'p' and resid 42 through 45 removed outlier: 3.608A pdb=" N GLY p 19 " --> pdb=" O ASN p 81 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.114A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.183A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.034A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'v' and resid 7 through 11 removed outlier: 3.671A pdb=" N LEU v 8 " --> pdb=" O ILE v 61 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 74 Processing sheet with id= 75, first strand: chain 'x' and resid 30 through 34 removed outlier: 4.898A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 2166 hydrogen bonds defined for protein. 6384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3876 hydrogen bonds 6152 hydrogen bond angles 0 basepair planarities 1540 basepair parallelities 2375 stacking parallelities Total time for adding SS restraints: 318.76 Time building geometry restraints manager: 74.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.47: 97351 1.47 - 1.78: 63977 1.78 - 2.09: 297 2.09 - 2.40: 0 2.40 - 2.71: 1 Bond restraints: 161626 Sorted by residual: bond pdb=" O3' C 12196 " pdb=" P U 12197 " ideal model delta sigma weight residual 1.607 2.706 -1.099 1.50e-02 4.44e+03 5.37e+03 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.441 0.361 2.00e-02 2.50e+03 3.26e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.441 0.361 2.00e-02 2.50e+03 3.25e+02 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.802 1.447 0.355 2.00e-02 2.50e+03 3.16e+02 bond pdb=" N1 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.635 1.372 0.263 2.00e-02 2.50e+03 1.73e+02 ... (remaining 161621 not shown) Histogram of bond angle deviations from ideal: 73.97 - 88.43: 4 88.43 - 102.90: 11163 102.90 - 117.36: 137120 117.36 - 131.83: 91632 131.83 - 146.29: 1243 Bond angle restraints: 241162 Sorted by residual: angle pdb=" O3' C 12196 " pdb=" P U 12197 " pdb=" O5' U 12197 " ideal model delta sigma weight residual 104.00 77.66 26.34 1.50e+00 4.44e-01 3.08e+02 angle pdb=" C 0TD q 89 " pdb=" N LEU q 90 " pdb=" CA LEU q 90 " ideal model delta sigma weight residual 121.70 94.18 27.52 1.80e+00 3.09e-01 2.34e+02 angle pdb=" O2' OMG 12251 " pdb=" C2' OMG 12251 " pdb=" C1' OMG 12251 " ideal model delta sigma weight residual 108.40 129.21 -20.81 1.50e+00 4.44e-01 1.93e+02 angle pdb=" C3' 2MA 12503 " pdb=" C2' 2MA 12503 " pdb=" C1' 2MA 12503 " ideal model delta sigma weight residual 101.50 88.01 13.49 1.00e+00 1.00e+00 1.82e+02 angle pdb=" C3' C 12196 " pdb=" O3' C 12196 " pdb=" P U 12197 " ideal model delta sigma weight residual 120.20 100.10 20.10 1.50e+00 4.44e-01 1.80e+02 ... (remaining 241157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 90312 35.86 - 71.71: 11673 71.71 - 107.57: 1263 107.57 - 143.43: 30 143.43 - 179.28: 39 Dihedral angle restraints: 103317 sinusoidal: 85301 harmonic: 18016 Sorted by residual: dihedral pdb=" C5' A 1 404 " pdb=" C4' A 1 404 " pdb=" C3' A 1 404 " pdb=" O3' A 1 404 " ideal model delta sinusoidal sigma weight residual 147.00 71.83 75.17 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" C5' G 1 271 " pdb=" C4' G 1 271 " pdb=" C3' G 1 271 " pdb=" O3' G 1 271 " ideal model delta sinusoidal sigma weight residual 147.00 83.82 63.18 1 8.00e+00 1.56e-02 8.23e+01 dihedral pdb=" O4' U 2 467 " pdb=" C1' U 2 467 " pdb=" N1 U 2 467 " pdb=" C2 U 2 467 " ideal model delta sinusoidal sigma weight residual 200.00 42.20 157.80 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 103314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 30494 0.331 - 0.662: 107 0.662 - 0.993: 10 0.993 - 1.324: 9 1.324 - 1.655: 7 Chirality restraints: 30627 Sorted by residual: chirality pdb=" C2* PSU 5 55 " pdb=" C3* PSU 5 55 " pdb=" O2* PSU 5 55 " pdb=" C1* PSU 5 55 " both_signs ideal model delta sigma weight residual False -2.75 -1.10 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C3' 2MA 12503 " pdb=" C4' 2MA 12503 " pdb=" O3' 2MA 12503 " pdb=" C2' 2MA 12503 " both_signs ideal model delta sigma weight residual False -2.74 -1.14 -1.60 2.00e-01 2.50e+01 6.41e+01 chirality pdb=" C2* PSU 2 516 " pdb=" C3* PSU 2 516 " pdb=" O2* PSU 2 516 " pdb=" C1* PSU 2 516 " both_signs ideal model delta sigma weight residual False -2.75 -1.16 -1.59 2.00e-01 2.50e+01 6.34e+01 ... (remaining 30624 not shown) Planarity restraints: 13343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2U 5 20 " -1.101 2.00e-02 2.50e+03 6.35e-01 9.08e+03 pdb=" C4' H2U 5 20 " 0.131 2.00e-02 2.50e+03 pdb=" O4' H2U 5 20 " 0.644 2.00e-02 2.50e+03 pdb=" C3' H2U 5 20 " 0.014 2.00e-02 2.50e+03 pdb=" O3' H2U 5 20 " 0.858 2.00e-02 2.50e+03 pdb=" C2' H2U 5 20 " -0.417 2.00e-02 2.50e+03 pdb=" O2' H2U 5 20 " -0.859 2.00e-02 2.50e+03 pdb=" C1' H2U 5 20 " 0.557 2.00e-02 2.50e+03 pdb=" N1 H2U 5 20 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " -0.019 2.00e-02 2.50e+03 6.34e-01 9.06e+03 pdb=" C4' 2MG 21207 " -0.478 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " -0.719 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " 0.622 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " 0.651 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " -1.018 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " -0.213 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " 0.972 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " -0.003 2.00e-02 2.50e+03 6.28e-01 8.88e+03 pdb=" C4' 7MG 2 527 " 0.448 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.535 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.596 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.708 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.110 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 1.138 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.219 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -0.924 2.00e-02 2.50e+03 ... (remaining 13340 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 115 2.11 - 2.81: 33005 2.81 - 3.50: 205411 3.50 - 4.20: 495853 4.20 - 4.90: 648572 Nonbonded interactions: 1382956 Sorted by model distance: nonbonded pdb=" O4 U 11082 " pdb=" N1 A 11086 " model vdw 1.409 2.496 nonbonded pdb=" O4 U 11019 " pdb=" N1 A 11142 " model vdw 1.447 2.496 nonbonded pdb=" O4 U 2 827 " pdb=" N1 A 2 872 " model vdw 1.474 2.496 nonbonded pdb=" N1 A 12013 " pdb=" O4 U 12613 " model vdw 1.479 2.496 nonbonded pdb=" OP1 G 1 784 " pdb="MG MG 13019 " model vdw 1.597 2.170 ... (remaining 1382951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 17.900 Check model and map are aligned: 1.610 Set scattering table: 1.030 Process input model: 668.210 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.480 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 700.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.099 161626 Z= 0.576 Angle : 1.384 38.292 241162 Z= 0.921 Chirality : 0.109 1.655 30627 Planarity : 0.020 0.635 13343 Dihedral : 24.041 179.282 91689 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.98 % Favored : 93.48 % Rotamer: Outliers : 9.85 % Allowed : 12.99 % Favored : 77.16 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.09), residues: 6207 helix: 0.31 (0.08), residues: 2168 sheet: -2.23 (0.13), residues: 1142 loop : -2.37 (0.09), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP Q 61 HIS 0.015 0.003 HIS O 34 PHE 0.052 0.004 PHE Q 106 TYR 0.038 0.004 TYR S 38 ARG 0.024 0.002 ARG a 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1781 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 509 poor density : 1272 time to evaluate : 6.564 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: 6 27 GLN cc_start: 0.6290 (tt0) cc_final: 0.5779 (pt0) REVERT: 6 33 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7914 (mmmt) REVERT: 6 34 LYS cc_start: 0.8324 (tttt) cc_final: 0.8121 (tttm) REVERT: 7 31 ASP cc_start: 0.2508 (OUTLIER) cc_final: 0.2251 (m-30) REVERT: 7 46 LEU cc_start: 0.2430 (OUTLIER) cc_final: 0.1443 (mm) REVERT: 7 59 ARG cc_start: 0.3176 (OUTLIER) cc_final: 0.2807 (mtt180) REVERT: 7 60 LYS cc_start: 0.4551 (tmtt) cc_final: 0.4261 (mmtt) REVERT: 7 105 GLU cc_start: 0.3638 (OUTLIER) cc_final: 0.3292 (pt0) REVERT: 7 141 GLU cc_start: 0.7809 (tp30) cc_final: 0.7358 (tp30) REVERT: 7 151 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7406 (mmm160) REVERT: 7 177 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.6267 (mp) REVERT: 7 196 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: 7 222 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: 7 263 ARG cc_start: 0.6713 (ptt180) cc_final: 0.6359 (ptt-90) REVERT: 7 285 LYS cc_start: 0.5184 (ttpt) cc_final: 0.4916 (mttt) REVERT: 7 327 TYR cc_start: 0.8552 (m-80) cc_final: 0.8232 (m-80) REVERT: B 13 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8606 (tpt170) REVERT: B 18 LYS cc_start: 0.8900 (mttt) cc_final: 0.8677 (mmtp) REVERT: B 23 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8067 (mt-10) REVERT: B 35 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: B 125 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7350 (mtpt) REVERT: B 156 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8974 (mtp180) REVERT: B 183 LYS cc_start: 0.8692 (tttt) cc_final: 0.8263 (mtpp) REVERT: B 203 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8018 (ttp-110) REVERT: B 229 ASP cc_start: 0.8451 (m-30) cc_final: 0.8107 (m-30) REVERT: B 271 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8036 (ptt-90) REVERT: C 11 MET cc_start: 0.9038 (mtp) cc_final: 0.8819 (mtp) REVERT: C 13 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8483 (ptm160) REVERT: C 46 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7816 (mtm180) REVERT: C 56 LYS cc_start: 0.8113 (mttp) cc_final: 0.7481 (mmmt) REVERT: D 22 ASP cc_start: 0.7754 (m-30) cc_final: 0.7550 (m-30) REVERT: D 40 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7756 (ttt180) REVERT: D 91 ASP cc_start: 0.7954 (t70) cc_final: 0.7718 (t70) REVERT: D 93 SER cc_start: 0.8439 (m) cc_final: 0.8138 (p) REVERT: D 108 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (mt) REVERT: D 122 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: E 7 TYR cc_start: 0.8017 (t80) cc_final: 0.7761 (t80) REVERT: E 10 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7949 (t70) REVERT: E 17 MET cc_start: 0.7096 (mmt) cc_final: 0.6755 (tmm) REVERT: E 133 ARG cc_start: 0.7592 (mpt-90) cc_final: 0.7035 (mpt180) REVERT: E 142 ASP cc_start: 0.4740 (t70) cc_final: 0.4386 (m-30) REVERT: E 143 TYR cc_start: 0.7248 (t80) cc_final: 0.7039 (t80) REVERT: F 39 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6895 (t70) REVERT: F 99 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6958 (ttpp) REVERT: F 117 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7754 (mm) REVERT: F 133 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7365 (tp) REVERT: F 141 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.6942 (pp) REVERT: F 153 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7757 (ttm170) REVERT: G 19 VAL cc_start: 0.5909 (m) cc_final: 0.5599 (p) REVERT: G 20 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.5463 (t0) REVERT: G 40 THR cc_start: 0.5551 (OUTLIER) cc_final: 0.5229 (t) REVERT: G 41 LYS cc_start: 0.4534 (OUTLIER) cc_final: 0.4296 (pttp) REVERT: G 87 GLU cc_start: -0.0168 (OUTLIER) cc_final: -0.0525 (mt-10) REVERT: G 114 GLU cc_start: 0.3931 (OUTLIER) cc_final: 0.3315 (tm-30) REVERT: H 38 MET cc_start: 0.1031 (OUTLIER) cc_final: 0.0814 (mtm) REVERT: J 75 TYR cc_start: 0.9089 (m-80) cc_final: 0.8629 (m-80) REVERT: J 95 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7441 (mtp-110) REVERT: J 98 GLU cc_start: 0.8439 (mp0) cc_final: 0.8187 (mt-10) REVERT: J 120 ARG cc_start: 0.8590 (mtt90) cc_final: 0.8090 (mtt-85) REVERT: K 8 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7978 (pp) REVERT: L 10 GLU cc_start: 0.8049 (tp30) cc_final: 0.7813 (tp30) REVERT: L 59 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (mtp180) REVERT: L 78 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7588 (mmt-90) REVERT: L 84 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7197 (mmmt) REVERT: L 99 ASN cc_start: 0.8599 (t0) cc_final: 0.7172 (t0) REVERT: M 2 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7916 (mp) REVERT: M 10 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8395 (mtm-85) REVERT: M 17 ASN cc_start: 0.8863 (t0) cc_final: 0.8620 (t0) REVERT: M 50 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7360 (ttp-170) REVERT: N 22 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7415 (mtm180) REVERT: N 30 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7268 (mmm-85) REVERT: N 65 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8582 (mp) REVERT: N 69 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7662 (mmt90) REVERT: O 67 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6875 (p0) REVERT: O 80 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6826 (mm-30) REVERT: O 98 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8465 (mm110) REVERT: O 116 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5086 (mt0) REVERT: P 93 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8396 (mtm180) REVERT: P 112 GLU cc_start: 0.8438 (pt0) cc_final: 0.7984 (tp30) REVERT: P 113 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7566 (ttt90) REVERT: Q 11 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8105 (tpp-160) REVERT: Q 15 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7455 (mmtt) REVERT: Q 71 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: Q 84 LYS cc_start: 0.6168 (mmtt) cc_final: 0.5874 (tttm) REVERT: R 78 ARG cc_start: 0.8702 (tpp-160) cc_final: 0.8431 (tpp-160) REVERT: S 71 VAL cc_start: 0.9277 (t) cc_final: 0.9040 (p) REVERT: T 9 LYS cc_start: 0.8141 (mttt) cc_final: 0.7718 (mttt) REVERT: T 25 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: T 33 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7337 (mttp) REVERT: T 36 LYS cc_start: 0.8525 (tttm) cc_final: 0.8221 (tptp) REVERT: T 73 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7639 (ttm-80) REVERT: T 87 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8688 (mp) REVERT: U 62 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: V 1 MET cc_start: 0.3386 (OUTLIER) cc_final: 0.2916 (ttt) REVERT: V 7 GLU cc_start: 0.7293 (mp0) cc_final: 0.7010 (mp0) REVERT: V 25 LYS cc_start: 0.8465 (mttt) cc_final: 0.8084 (mtpt) REVERT: V 34 LYS cc_start: 0.5695 (OUTLIER) cc_final: 0.5367 (ptpp) REVERT: V 51 GLN cc_start: 0.7831 (pp30) cc_final: 0.7456 (pp30) REVERT: V 69 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: W 56 ASP cc_start: 0.8557 (p0) cc_final: 0.8328 (p0) REVERT: W 77 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8075 (mtt90) REVERT: W 78 LYS cc_start: 0.8438 (mptt) cc_final: 0.7722 (mmtt) REVERT: W 82 ILE cc_start: 0.8711 (mm) cc_final: 0.8482 (mm) REVERT: Y 20 ASN cc_start: 0.7595 (m-40) cc_final: 0.7309 (m-40) REVERT: Y 24 GLU cc_start: 0.7715 (tt0) cc_final: 0.7461 (mt-10) REVERT: Z 10 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.9004 (t) REVERT: Z 11 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8626 (mtm-85) REVERT: Z 25 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7987 (tt) REVERT: Z 54 MET cc_start: 0.8560 (mtm) cc_final: 0.8198 (mtt) REVERT: a 20 ASN cc_start: 0.5147 (t0) cc_final: 0.4886 (t0) REVERT: a 22 MET cc_start: 0.6178 (ttm) cc_final: 0.5876 (ptm) REVERT: a 39 LYS cc_start: 0.7020 (tttt) cc_final: 0.6756 (tmtt) REVERT: a 56 ARG cc_start: 0.4765 (mtp85) cc_final: 0.3589 (mmp80) REVERT: b 36 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: b 52 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7570 (ttp-170) REVERT: c 53 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7235 (tptp) REVERT: f 30 GLU cc_start: 0.8402 (tp30) cc_final: 0.6952 (mm-30) REVERT: g 28 LYS cc_start: 0.7132 (tttt) cc_final: 0.6497 (pttp) REVERT: g 58 ASN cc_start: 0.3965 (t0) cc_final: 0.3735 (t0) REVERT: g 105 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7485 (pttt) REVERT: g 190 ASN cc_start: 0.7403 (p0) cc_final: 0.6896 (p0) REVERT: h 54 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7186 (mtp-110) REVERT: h 114 LYS cc_start: 0.8044 (tptt) cc_final: 0.7812 (tptp) REVERT: h 161 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7126 (pm20) REVERT: i 85 ASN cc_start: 0.8168 (t0) cc_final: 0.7921 (t0) REVERT: i 88 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7571 (tm-30) REVERT: i 95 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: i 104 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7569 (mmp-170) REVERT: i 116 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: i 121 LYS cc_start: 0.7667 (mttt) cc_final: 0.6923 (mmtt) REVERT: i 124 MET cc_start: 0.7788 (mtt) cc_final: 0.7277 (ttp) REVERT: i 191 LEU cc_start: 0.7719 (mt) cc_final: 0.7323 (mt) REVERT: j 54 ARG cc_start: 0.8772 (mmt90) cc_final: 0.8552 (mtp180) REVERT: k 7 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (t) REVERT: k 9 MET cc_start: 0.7885 (mtp) cc_final: 0.7562 (mtp) REVERT: k 58 HIS cc_start: 0.8846 (t70) cc_final: 0.8186 (t70) REVERT: k 74 LEU cc_start: 0.7086 (tp) cc_final: 0.6780 (tp) REVERT: l 10 ARG cc_start: 0.6904 (ptp-170) cc_final: 0.5190 (ptp-110) REVERT: l 23 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6056 (tm) REVERT: l 67 GLU cc_start: 0.7362 (tp30) cc_final: 0.7043 (tt0) REVERT: l 72 THR cc_start: 0.7800 (p) cc_final: 0.7324 (p) REVERT: l 78 ARG cc_start: 0.3909 (tpt170) cc_final: 0.3664 (mtm180) REVERT: l 79 ARG cc_start: 0.4292 (OUTLIER) cc_final: 0.4003 (tpt-90) REVERT: l 90 GLU cc_start: 0.7014 (tp30) cc_final: 0.6792 (pm20) REVERT: l 94 VAL cc_start: 0.7836 (t) cc_final: 0.7566 (m) REVERT: l 139 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6613 (mt-10) REVERT: l 146 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6043 (mt-10) REVERT: m 27 MET cc_start: 0.8733 (ptp) cc_final: 0.8498 (ptp) REVERT: m 48 ASP cc_start: 0.7260 (t70) cc_final: 0.6923 (m-30) REVERT: m 60 GLU cc_start: 0.7607 (tt0) cc_final: 0.6795 (tm-30) REVERT: m 77 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7853 (tpt-90) REVERT: m 83 LEU cc_start: 0.8700 (tm) cc_final: 0.8406 (tp) REVERT: m 108 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8305 (mmtp) REVERT: o 18 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7506 (tt) REVERT: o 25 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5875 (mm) REVERT: o 27 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5518 (mt-10) REVERT: o 37 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6074 (tpp-160) REVERT: p 108 THR cc_start: 0.8269 (m) cc_final: 0.7796 (p) REVERT: q 12 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7243 (ptp-170) REVERT: q 22 PRO cc_start: 0.8732 (Cg_endo) cc_final: 0.8346 (Cg_exo) REVERT: q 74 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8221 (mp) REVERT: q 76 GLU cc_start: 0.8112 (mp0) cc_final: 0.7756 (tt0) REVERT: q 81 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8354 (mp) REVERT: q 94 ARG cc_start: 0.8280 (mtt180) cc_final: 0.8034 (mtt-85) REVERT: q 102 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7157 (mp) REVERT: r 29 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7567 (mtt180) REVERT: s 83 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8308 (mmmt) REVERT: s 90 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7831 (mtt90) REVERT: t 45 GLU cc_start: 0.6970 (tt0) cc_final: 0.6750 (mt-10) REVERT: u 14 ARG cc_start: 0.8879 (mtp-110) cc_final: 0.8592 (mtp180) REVERT: u 26 ASN cc_start: 0.9059 (m-40) cc_final: 0.8739 (m110) REVERT: u 47 GLU cc_start: 0.6030 (pt0) cc_final: 0.5803 (mp0) REVERT: u 76 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7248 (ttmt) REVERT: v 39 LYS cc_start: 0.8084 (mttt) cc_final: 0.7511 (ptpt) REVERT: v 75 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7847 (pp) REVERT: w 12 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6427 (mmp-170) REVERT: w 25 ASP cc_start: 0.7668 (t0) cc_final: 0.7361 (t0) REVERT: w 30 LYS cc_start: 0.8065 (tttt) cc_final: 0.7524 (ttpp) REVERT: w 47 THR cc_start: 0.8643 (m) cc_final: 0.8340 (m) REVERT: w 66 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8277 (p) REVERT: x 3 ARG cc_start: 0.8476 (ttt90) cc_final: 0.8092 (ttt90) REVERT: x 44 MET cc_start: 0.8245 (mtp) cc_final: 0.7687 (mmm) REVERT: x 66 MET cc_start: 0.8109 (mtt) cc_final: 0.7640 (mtt) REVERT: y 24 ARG cc_start: 0.7668 (mmp80) cc_final: 0.6975 (mtt180) REVERT: z 33 ARG cc_start: 0.7767 (tmt170) cc_final: 0.7323 (mtt180) REVERT: z 36 GLU cc_start: 0.8426 (tt0) cc_final: 0.8019 (tp30) REVERT: z 55 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6216 (ppt170) REVERT: z 67 ARG cc_start: 0.4247 (OUTLIER) cc_final: 0.3977 (mmp-170) outliers start: 509 outliers final: 174 residues processed: 1657 average time/residue: 1.4580 time to fit residues: 4010.8943 Evaluate side-chains 1228 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 974 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 20 LEU Chi-restraints excluded: chain 6 residue 24 LEU Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 7 residue 20 ARG Chi-restraints excluded: chain 7 residue 29 ILE Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 46 LEU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 105 GLU Chi-restraints excluded: chain 7 residue 121 ASN Chi-restraints excluded: chain 7 residue 128 ASN Chi-restraints excluded: chain 7 residue 145 TRP Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 151 ARG Chi-restraints excluded: chain 7 residue 152 MET Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 182 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 185 LYS Chi-restraints excluded: chain 7 residue 196 GLU Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 290 LYS Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain 7 residue 358 ILE Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 98 GLN Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 71 GLN Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 11 ARG Chi-restraints excluded: chain Z residue 14 ILE Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 18 CYS Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 8 PRO Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 52 ARG Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 3 LYS Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 11 CYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 128 LYS Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 212 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 142 HIS Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 37 ARG Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 29 ARG Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 55 ARG Chi-restraints excluded: chain z residue 67 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 903 optimal weight: 4.9990 chunk 811 optimal weight: 0.7980 chunk 450 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 chunk 547 optimal weight: 1.9990 chunk 433 optimal weight: 10.0000 chunk 838 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 509 optimal weight: 7.9990 chunk 624 optimal weight: 50.0000 chunk 971 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 HIS 7 163 GLN 7 332 ASN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN D 90 GLN D 115 GLN E 21 ASN E 127 ASN F 22 GLN G 43 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN J 128 ASN J 131 ASN K 3 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN P 77 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 HIS Z 9 GLN a 41 HIS ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 ASN g 89 GLN g 120 GLN g 227 GLN h 3 GLN i 136 GLN ** j 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 132 ASN l 148 ASN n 110 GLN n 126 GLN o 15 HIS p 29 ASN x 52 HIS y 55 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 161626 Z= 0.365 Angle : 0.791 15.119 241162 Z= 0.417 Chirality : 0.045 0.462 30627 Planarity : 0.007 0.141 13343 Dihedral : 23.637 179.998 79849 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 7.57 % Allowed : 16.95 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.10), residues: 6207 helix: 2.11 (0.11), residues: 2196 sheet: -1.69 (0.14), residues: 1149 loop : -1.75 (0.10), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 7 52 HIS 0.009 0.002 HIS B 230 PHE 0.022 0.002 PHE k 8 TYR 0.021 0.002 TYR V 31 ARG 0.008 0.001 ARG v 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 1049 time to evaluate : 6.597 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: 6 27 GLN cc_start: 0.6462 (tt0) cc_final: 0.5742 (pt0) REVERT: 7 30 PHE cc_start: 0.0834 (OUTLIER) cc_final: 0.0501 (t80) REVERT: 7 46 LEU cc_start: 0.2336 (OUTLIER) cc_final: 0.2080 (mm) REVERT: 7 59 ARG cc_start: 0.2916 (OUTLIER) cc_final: 0.2583 (mtt180) REVERT: 7 60 LYS cc_start: 0.4277 (tmtt) cc_final: 0.3916 (mmtt) REVERT: 7 128 ASN cc_start: 0.6081 (OUTLIER) cc_final: 0.5186 (m-40) REVERT: 7 141 GLU cc_start: 0.7520 (tp30) cc_final: 0.7055 (tp30) REVERT: 7 169 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6859 (tt) REVERT: 7 196 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6635 (mm-30) REVERT: 7 239 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5921 (mm-30) REVERT: 7 285 LYS cc_start: 0.5593 (ttpt) cc_final: 0.5278 (mttt) REVERT: 7 301 ARG cc_start: 0.6433 (ttp80) cc_final: 0.5936 (mtm110) REVERT: 7 336 ASP cc_start: 0.8114 (t70) cc_final: 0.7847 (t0) REVERT: 7 339 THR cc_start: 0.6737 (p) cc_final: 0.6411 (p) REVERT: 7 342 MET cc_start: 0.6713 (ttp) cc_final: 0.6447 (ttp) REVERT: 7 344 HIS cc_start: 0.5882 (m-70) cc_final: 0.5551 (m170) REVERT: 7 364 TRP cc_start: 0.7475 (t60) cc_final: 0.7099 (t60) REVERT: B 13 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8547 (tpt170) REVERT: B 23 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8014 (mt-10) REVERT: B 35 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: B 183 LYS cc_start: 0.8497 (tttt) cc_final: 0.8079 (mtpp) REVERT: B 203 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8011 (ttp-110) REVERT: B 258 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8342 (ttm170) REVERT: C 77 ARG cc_start: 0.8145 (ptt90) cc_final: 0.7728 (ptt90) REVERT: C 128 ARG cc_start: 0.8528 (mpp80) cc_final: 0.7795 (mpt90) REVERT: C 137 SER cc_start: 0.9322 (m) cc_final: 0.9085 (p) REVERT: D 22 ASP cc_start: 0.7607 (m-30) cc_final: 0.7379 (m-30) REVERT: D 69 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8377 (ptt180) REVERT: D 91 ASP cc_start: 0.8130 (t70) cc_final: 0.7872 (t70) REVERT: D 122 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: D 168 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6987 (m-30) REVERT: D 185 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7721 (mmtt) REVERT: E 7 TYR cc_start: 0.8234 (t80) cc_final: 0.7876 (t80) REVERT: E 26 MET cc_start: 0.8523 (mmt) cc_final: 0.8314 (mmt) REVERT: E 133 ARG cc_start: 0.7540 (mpt-90) cc_final: 0.7008 (mpt180) REVERT: E 142 ASP cc_start: 0.4488 (t0) cc_final: 0.4260 (m-30) REVERT: E 150 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4293 (mtt180) REVERT: E 167 ARG cc_start: 0.6499 (ttp80) cc_final: 0.6096 (tmt170) REVERT: F 39 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.6542 (t0) REVERT: F 73 ASN cc_start: 0.7315 (t0) cc_final: 0.6706 (m-40) REVERT: F 133 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7469 (tp) REVERT: G 19 VAL cc_start: 0.5990 (m) cc_final: 0.5632 (p) REVERT: G 20 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.5703 (t0) REVERT: G 114 GLU cc_start: 0.4099 (OUTLIER) cc_final: 0.3543 (pp20) REVERT: J 36 LEU cc_start: 0.8964 (mt) cc_final: 0.8634 (mt) REVERT: J 75 TYR cc_start: 0.8894 (m-80) cc_final: 0.8414 (m-80) REVERT: J 95 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7398 (mtp85) REVERT: J 98 GLU cc_start: 0.8453 (mp0) cc_final: 0.8143 (mt-10) REVERT: J 118 MET cc_start: 0.8311 (mmm) cc_final: 0.8067 (mmm) REVERT: J 128 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7847 (t0) REVERT: K 8 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8048 (pp) REVERT: K 17 ARG cc_start: 0.8336 (mmp80) cc_final: 0.7561 (mtm-85) REVERT: K 70 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8555 (mmm160) REVERT: L 10 GLU cc_start: 0.7924 (tp30) cc_final: 0.7672 (tp30) REVERT: L 84 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7199 (mmmt) REVERT: L 99 ASN cc_start: 0.8586 (t0) cc_final: 0.7449 (t0) REVERT: M 2 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7917 (mp) REVERT: M 17 ASN cc_start: 0.8960 (t0) cc_final: 0.8726 (t0) REVERT: M 50 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7337 (ttp-170) REVERT: N 30 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7644 (mtp85) REVERT: N 69 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8037 (mmt90) REVERT: O 9 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7157 (ttm110) REVERT: O 13 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7702 (ttm170) REVERT: O 36 TYR cc_start: 0.8693 (m-80) cc_final: 0.8481 (m-80) REVERT: O 80 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6953 (mm-30) REVERT: O 88 LYS cc_start: 0.6525 (tttt) cc_final: 0.6043 (mptt) REVERT: O 116 GLN cc_start: 0.5721 (OUTLIER) cc_final: 0.4839 (mt0) REVERT: P 16 ASP cc_start: 0.5176 (OUTLIER) cc_final: 0.4713 (p0) REVERT: P 112 GLU cc_start: 0.8418 (pt0) cc_final: 0.7972 (tp30) REVERT: Q 15 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7594 (mmtt) REVERT: Q 84 LYS cc_start: 0.6748 (mmtt) cc_final: 0.6458 (tttm) REVERT: R 16 GLU cc_start: 0.7378 (mp0) cc_final: 0.7014 (mp0) REVERT: R 23 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6836 (mm-30) REVERT: R 43 ASN cc_start: 0.6814 (t0) cc_final: 0.6216 (p0) REVERT: S 48 LYS cc_start: 0.8443 (tttt) cc_final: 0.8047 (ttpt) REVERT: S 95 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8288 (ttm110) REVERT: T 9 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7847 (mttt) REVERT: T 25 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6781 (mm-30) REVERT: T 69 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.6817 (mmt180) REVERT: T 87 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8574 (mt) REVERT: U 6 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7580 (mtt90) REVERT: U 37 GLU cc_start: 0.7976 (tt0) cc_final: 0.7747 (tp30) REVERT: U 73 PHE cc_start: 0.8203 (t80) cc_final: 0.7984 (t80) REVERT: U 98 SER cc_start: 0.6451 (t) cc_final: 0.6114 (p) REVERT: V 1 MET cc_start: 0.3435 (OUTLIER) cc_final: 0.2846 (ttt) REVERT: V 7 GLU cc_start: 0.7224 (mp0) cc_final: 0.6982 (mp0) REVERT: V 25 LYS cc_start: 0.8346 (mttt) cc_final: 0.8086 (mtmm) REVERT: V 48 MET cc_start: 0.8010 (tpt) cc_final: 0.7764 (ttt) REVERT: W 78 LYS cc_start: 0.8552 (mptt) cc_final: 0.7750 (mmtt) REVERT: W 82 ILE cc_start: 0.8697 (mm) cc_final: 0.8363 (mm) REVERT: Y 20 ASN cc_start: 0.7987 (m-40) cc_final: 0.7626 (m-40) REVERT: Z 3 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6221 (tptt) REVERT: Z 45 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7252 (mmt90) REVERT: a 20 ASN cc_start: 0.5317 (t0) cc_final: 0.4998 (t0) REVERT: a 39 LYS cc_start: 0.7313 (tttt) cc_final: 0.6989 (tmtt) REVERT: c 53 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6986 (tptp) REVERT: d 24 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8318 (p) REVERT: f 30 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6533 (mm-30) REVERT: g 27 MET cc_start: 0.5350 (OUTLIER) cc_final: 0.5027 (mmm) REVERT: g 28 LYS cc_start: 0.6784 (tttt) cc_final: 0.6194 (pttp) REVERT: g 64 LYS cc_start: 0.7546 (mttp) cc_final: 0.7182 (ptmt) REVERT: g 105 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7431 (pttt) REVERT: g 113 ARG cc_start: 0.7016 (tpt170) cc_final: 0.6806 (tpt90) REVERT: g 132 LYS cc_start: 0.3262 (OUTLIER) cc_final: 0.3010 (tptt) REVERT: h 43 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7077 (mp) REVERT: h 46 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7808 (mm-30) REVERT: h 54 ARG cc_start: 0.7272 (ttp80) cc_final: 0.6994 (mtp85) REVERT: h 114 LYS cc_start: 0.8305 (tptt) cc_final: 0.7963 (tptp) REVERT: h 129 MET cc_start: 0.7682 (mtm) cc_final: 0.7179 (mtm) REVERT: h 144 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5848 (mm) REVERT: h 161 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6917 (pm20) REVERT: h 178 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9011 (mt) REVERT: h 206 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7711 (mt-10) REVERT: i 95 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: i 116 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: i 124 MET cc_start: 0.7800 (mtt) cc_final: 0.7283 (ptm) REVERT: i 191 LEU cc_start: 0.7545 (mt) cc_final: 0.7244 (mt) REVERT: j 54 ARG cc_start: 0.8889 (mmt90) cc_final: 0.8517 (mtp180) REVERT: j 156 LYS cc_start: 0.8077 (tttt) cc_final: 0.7850 (tttt) REVERT: k 58 HIS cc_start: 0.8795 (t70) cc_final: 0.8158 (t70) REVERT: k 80 PHE cc_start: 0.6084 (m-80) cc_final: 0.5786 (m-80) REVERT: l 67 GLU cc_start: 0.7608 (tp30) cc_final: 0.7328 (tt0) REVERT: l 78 ARG cc_start: 0.3494 (ttt180) cc_final: 0.3122 (mtm180) REVERT: l 79 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3874 (tpt-90) REVERT: l 139 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6831 (mt-10) REVERT: l 146 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5943 (mt-10) REVERT: m 27 MET cc_start: 0.8756 (ptp) cc_final: 0.8498 (ptp) REVERT: m 48 ASP cc_start: 0.7784 (t70) cc_final: 0.7142 (m-30) REVERT: m 60 GLU cc_start: 0.7535 (tt0) cc_final: 0.6562 (tm-30) REVERT: m 77 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8028 (mtp180) REVERT: m 96 MET cc_start: 0.7700 (ttt) cc_final: 0.7369 (mtp) REVERT: n 123 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8112 (tmt90) REVERT: n 124 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8419 (mtp-110) REVERT: o 8 ILE cc_start: 0.6526 (mt) cc_final: 0.6283 (tt) REVERT: o 18 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7566 (tt) REVERT: o 25 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5755 (mm) REVERT: o 62 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7913 (mtt90) REVERT: p 108 THR cc_start: 0.8390 (m) cc_final: 0.8151 (p) REVERT: p 126 LYS cc_start: 0.8031 (tptt) cc_final: 0.7653 (mtmt) REVERT: q 76 GLU cc_start: 0.8170 (mp0) cc_final: 0.7835 (tt0) REVERT: q 81 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8374 (mp) REVERT: q 94 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8147 (mtt-85) REVERT: r 59 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: r 75 MET cc_start: 0.7697 (mmm) cc_final: 0.7467 (mmp) REVERT: s 90 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7818 (mtm-85) REVERT: t 58 ARG cc_start: 0.8557 (ttt180) cc_final: 0.8311 (ttt90) REVERT: u 26 ASN cc_start: 0.9003 (m-40) cc_final: 0.8796 (m-40) REVERT: u 61 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7842 (p) REVERT: u 76 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7503 (ttmt) REVERT: v 14 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8132 (m) REVERT: v 19 LYS cc_start: 0.7992 (mttt) cc_final: 0.7562 (mtmt) REVERT: v 39 LYS cc_start: 0.8152 (mttt) cc_final: 0.7439 (ptmt) REVERT: w 12 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6225 (mmp-170) REVERT: w 30 LYS cc_start: 0.7749 (tttt) cc_final: 0.7362 (ttpp) REVERT: x 44 MET cc_start: 0.8145 (mtp) cc_final: 0.7695 (mmm) REVERT: x 66 MET cc_start: 0.8144 (mtt) cc_final: 0.7587 (mtt) REVERT: y 16 LYS cc_start: 0.7874 (tttt) cc_final: 0.7319 (tptt) REVERT: y 24 ARG cc_start: 0.8056 (mmp80) cc_final: 0.7309 (mtt180) REVERT: y 33 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7275 (tttp) REVERT: y 53 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: z 21 ARG cc_start: 0.4816 (tpt170) cc_final: 0.4147 (tpt170) REVERT: z 36 GLU cc_start: 0.8331 (tt0) cc_final: 0.7933 (tp30) REVERT: z 49 LYS cc_start: 0.7807 (tttt) cc_final: 0.7605 (tptt) REVERT: z 55 ARG cc_start: 0.6320 (OUTLIER) cc_final: 0.6107 (ppt170) REVERT: z 67 ARG cc_start: 0.4396 (OUTLIER) cc_final: 0.4185 (mmp-170) outliers start: 391 outliers final: 220 residues processed: 1331 average time/residue: 1.4745 time to fit residues: 3322.8190 Evaluate side-chains 1241 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 964 time to evaluate : 6.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 24 LEU Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 29 ILE Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 46 LEU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 81 ASP Chi-restraints excluded: chain 7 residue 128 ASN Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 169 LEU Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 182 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 185 LYS Chi-restraints excluded: chain 7 residue 196 GLU Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 271 ILE Chi-restraints excluded: chain 7 residue 290 LYS Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain a residue 40 CYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 11 CYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 30 GLU Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 27 MET Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 212 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 123 GLU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 126 GLN Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 65 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 61 VAL Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 55 ARG Chi-restraints excluded: chain z residue 67 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 540 optimal weight: 0.9980 chunk 301 optimal weight: 7.9990 chunk 808 optimal weight: 4.9990 chunk 661 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 973 optimal weight: 9.9990 chunk 1051 optimal weight: 10.0000 chunk 866 optimal weight: 4.9990 chunk 965 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 780 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 116 HIS ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN E 127 ASN F 128 GLN G 66 ASN G 135 HIS I 11 GLN N 13 ASN O 61 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN T 91 GLN V 49 ASN V 80 HIS W 12 ASN X 17 ASN c 26 ASN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS g 190 ASN h 69 HIS ** i 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN l 130 ASN ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 64 GLN q 72 HIS ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 161626 Z= 0.266 Angle : 0.685 14.776 241162 Z= 0.364 Chirality : 0.038 0.442 30627 Planarity : 0.007 0.131 13343 Dihedral : 23.364 179.991 79618 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 7.04 % Allowed : 19.31 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 6207 helix: 2.06 (0.11), residues: 2209 sheet: -1.29 (0.14), residues: 1106 loop : -1.47 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 7 52 HIS 0.007 0.001 HIS J 47 PHE 0.026 0.002 PHE k 8 TYR 0.021 0.002 TYR R 2 ARG 0.009 0.001 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1017 time to evaluate : 6.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 27 GLN cc_start: 0.6480 (tt0) cc_final: 0.5766 (pt0) REVERT: 7 30 PHE cc_start: 0.1317 (OUTLIER) cc_final: 0.0920 (t80) REVERT: 7 43 GLU cc_start: 0.4409 (OUTLIER) cc_final: 0.4179 (tm-30) REVERT: 7 59 ARG cc_start: 0.3203 (OUTLIER) cc_final: 0.2864 (mtt180) REVERT: 7 60 LYS cc_start: 0.4316 (tmtt) cc_final: 0.3915 (mmtt) REVERT: 7 141 GLU cc_start: 0.7303 (tp30) cc_final: 0.7076 (tp30) REVERT: 7 196 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: 7 239 GLU cc_start: 0.6014 (mm-30) cc_final: 0.5791 (mm-30) REVERT: 7 285 LYS cc_start: 0.5666 (ttpt) cc_final: 0.5313 (mttt) REVERT: 7 290 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6244 (ptmm) REVERT: 7 301 ARG cc_start: 0.6315 (ttp80) cc_final: 0.5903 (mtm110) REVERT: 7 331 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6497 (mtpm) REVERT: 7 336 ASP cc_start: 0.8020 (t70) cc_final: 0.7668 (t0) REVERT: 7 339 THR cc_start: 0.6876 (p) cc_final: 0.6407 (p) REVERT: 7 364 TRP cc_start: 0.7456 (t60) cc_final: 0.6993 (t60) REVERT: B 13 ARG cc_start: 0.8691 (tpt90) cc_final: 0.8272 (tpt170) REVERT: B 35 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7762 (tp30) REVERT: B 183 LYS cc_start: 0.8577 (tttt) cc_final: 0.8262 (mtpp) REVERT: B 258 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8278 (ttm170) REVERT: B 260 ASN cc_start: 0.8314 (t0) cc_final: 0.8036 (t0) REVERT: C 88 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6389 (mt-10) REVERT: D 21 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7187 (ptp-170) REVERT: D 69 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7297 (ptp-170) REVERT: D 168 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: E 7 TYR cc_start: 0.8311 (t80) cc_final: 0.8047 (t80) REVERT: E 38 MET cc_start: 0.7650 (mtt) cc_final: 0.7395 (ttp) REVERT: E 56 ASP cc_start: 0.7159 (m-30) cc_final: 0.6934 (m-30) REVERT: E 96 MET cc_start: 0.8097 (tmm) cc_final: 0.7814 (ttp) REVERT: E 133 ARG cc_start: 0.7362 (mpt-90) cc_final: 0.6769 (mpt180) REVERT: E 150 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.4170 (mtt180) REVERT: E 167 ARG cc_start: 0.6547 (ttp80) cc_final: 0.6267 (tpt-90) REVERT: F 133 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7437 (tp) REVERT: G 19 VAL cc_start: 0.5757 (m) cc_final: 0.5520 (p) REVERT: G 41 LYS cc_start: 0.4618 (OUTLIER) cc_final: 0.4321 (pttp) REVERT: G 114 GLU cc_start: 0.4094 (OUTLIER) cc_final: 0.3515 (pp20) REVERT: I 135 MET cc_start: 0.0469 (ppp) cc_final: 0.0145 (tmm) REVERT: J 13 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7955 (mtt90) REVERT: J 25 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8719 (tp) REVERT: J 32 LEU cc_start: 0.8433 (mt) cc_final: 0.8231 (mt) REVERT: J 36 LEU cc_start: 0.8911 (mt) cc_final: 0.8571 (mp) REVERT: J 75 TYR cc_start: 0.8834 (m-80) cc_final: 0.8394 (m-80) REVERT: J 95 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7351 (mtp85) REVERT: J 98 GLU cc_start: 0.8510 (mp0) cc_final: 0.8309 (mp0) REVERT: J 118 MET cc_start: 0.8382 (mmm) cc_final: 0.8119 (mmm) REVERT: K 8 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8043 (pp) REVERT: K 17 ARG cc_start: 0.8319 (mmp80) cc_final: 0.7384 (mtm-85) REVERT: K 53 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7166 (mmtt) REVERT: K 70 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8704 (mmm160) REVERT: L 91 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7262 (t0) REVERT: L 99 ASN cc_start: 0.8515 (t0) cc_final: 0.7484 (t0) REVERT: M 17 ASN cc_start: 0.8980 (t0) cc_final: 0.8764 (t0) REVERT: N 4 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8585 (mmt-90) REVERT: N 30 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7517 (mtp85) REVERT: O 9 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6022 (ptt90) REVERT: O 13 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7860 (ttm170) REVERT: O 80 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7095 (mm-30) REVERT: O 88 LYS cc_start: 0.6536 (tttt) cc_final: 0.5997 (mptt) REVERT: P 10 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7363 (mm-40) REVERT: P 112 GLU cc_start: 0.8381 (pt0) cc_final: 0.7971 (tp30) REVERT: Q 15 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7627 (mmtt) REVERT: Q 84 LYS cc_start: 0.6719 (mmtt) cc_final: 0.6470 (tttm) REVERT: R 23 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6655 (mm-30) REVERT: R 43 ASN cc_start: 0.6730 (t0) cc_final: 0.6184 (p0) REVERT: R 60 LYS cc_start: 0.8402 (mttm) cc_final: 0.8166 (mmtm) REVERT: S 48 LYS cc_start: 0.8422 (tttt) cc_final: 0.7540 (ttpt) REVERT: S 52 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7481 (mt-10) REVERT: S 66 ILE cc_start: 0.8112 (mm) cc_final: 0.7895 (tp) REVERT: S 78 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7514 (mm-30) REVERT: S 95 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8194 (ttm110) REVERT: T 5 GLU cc_start: 0.7050 (tt0) cc_final: 0.6833 (tt0) REVERT: T 9 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7865 (mttt) REVERT: U 62 GLU cc_start: 0.7370 (pm20) cc_final: 0.6945 (pm20) REVERT: U 98 SER cc_start: 0.6123 (t) cc_final: 0.5913 (p) REVERT: V 1 MET cc_start: 0.3159 (OUTLIER) cc_final: 0.2785 (ttp) REVERT: V 25 LYS cc_start: 0.8296 (mttt) cc_final: 0.8041 (mtmm) REVERT: W 78 LYS cc_start: 0.8666 (mptt) cc_final: 0.7753 (mmtt) REVERT: W 82 ILE cc_start: 0.8595 (mm) cc_final: 0.8261 (mm) REVERT: W 83 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: Y 7 ARG cc_start: 0.5647 (OUTLIER) cc_final: 0.4868 (ttm-80) REVERT: Y 20 ASN cc_start: 0.8014 (m-40) cc_final: 0.7763 (m-40) REVERT: Z 37 GLU cc_start: 0.7994 (tt0) cc_final: 0.7739 (tt0) REVERT: Z 38 ARG cc_start: 0.8316 (mmp80) cc_final: 0.8045 (mmp80) REVERT: Z 45 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7549 (mmt90) REVERT: a 22 MET cc_start: 0.7101 (ptp) cc_final: 0.6428 (pmm) REVERT: a 56 ARG cc_start: 0.3640 (mmt180) cc_final: 0.2790 (mmp80) REVERT: c 53 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.6924 (tptp) REVERT: d 24 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8363 (p) REVERT: f 13 ASN cc_start: 0.7481 (m-40) cc_final: 0.7219 (m-40) REVERT: f 30 GLU cc_start: 0.8223 (tp30) cc_final: 0.6643 (mm-30) REVERT: g 27 MET cc_start: 0.5534 (OUTLIER) cc_final: 0.5323 (mmm) REVERT: g 28 LYS cc_start: 0.6907 (tttt) cc_final: 0.6191 (ptmm) REVERT: g 64 LYS cc_start: 0.7465 (mttp) cc_final: 0.7244 (ptmm) REVERT: g 105 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7422 (ptpt) REVERT: g 154 MET cc_start: 0.7096 (ttp) cc_final: 0.6841 (ttm) REVERT: h 46 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7777 (mm-30) REVERT: h 54 ARG cc_start: 0.7307 (ttp80) cc_final: 0.6817 (mtp85) REVERT: h 142 MET cc_start: 0.8346 (mmm) cc_final: 0.7999 (mmm) REVERT: h 161 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6823 (pm20) REVERT: h 178 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8875 (mt) REVERT: h 179 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7405 (ptp90) REVERT: h 206 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7602 (mt-10) REVERT: i 95 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: j 97 GLN cc_start: 0.8814 (tt0) cc_final: 0.8588 (tt0) REVERT: j 141 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7540 (mp) REVERT: j 152 MET cc_start: 0.7671 (mtp) cc_final: 0.7337 (mtt) REVERT: k 9 MET cc_start: 0.7328 (mtp) cc_final: 0.6644 (mtm) REVERT: k 80 PHE cc_start: 0.5762 (m-80) cc_final: 0.5405 (m-80) REVERT: k 104 LYS cc_start: 0.4810 (tptp) cc_final: 0.3874 (pttp) REVERT: l 10 ARG cc_start: 0.7185 (ptp-170) cc_final: 0.6369 (ptp-110) REVERT: l 23 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5745 (mm) REVERT: l 40 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: l 67 GLU cc_start: 0.7614 (tp30) cc_final: 0.7302 (tt0) REVERT: l 68 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7942 (t0) REVERT: l 78 ARG cc_start: 0.3533 (ttt180) cc_final: 0.3121 (mtm180) REVERT: l 79 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.3857 (tpt-90) REVERT: l 90 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6579 (pm20) REVERT: l 139 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6850 (mt-10) REVERT: l 146 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5963 (mt-10) REVERT: m 27 MET cc_start: 0.8719 (ptp) cc_final: 0.8518 (ptp) REVERT: m 60 GLU cc_start: 0.7574 (tt0) cc_final: 0.6597 (tm-30) REVERT: m 83 LEU cc_start: 0.8719 (tm) cc_final: 0.8426 (tp) REVERT: m 96 MET cc_start: 0.7801 (ttt) cc_final: 0.7590 (mtp) REVERT: n 123 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8138 (tmt90) REVERT: o 5 ARG cc_start: 0.4528 (pmt170) cc_final: 0.4015 (ptt-90) REVERT: o 8 ILE cc_start: 0.6632 (mt) cc_final: 0.6261 (pt) REVERT: o 18 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7532 (tt) REVERT: o 25 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5778 (mm) REVERT: o 62 ARG cc_start: 0.8276 (mtp85) cc_final: 0.8010 (mtt90) REVERT: p 108 THR cc_start: 0.8437 (m) cc_final: 0.8185 (p) REVERT: p 126 LYS cc_start: 0.7959 (tptt) cc_final: 0.7526 (mtmt) REVERT: q 30 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8178 (mmtm) REVERT: q 70 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7495 (mt-10) REVERT: q 76 GLU cc_start: 0.8208 (mp0) cc_final: 0.7886 (tt0) REVERT: q 81 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8331 (mp) REVERT: q 109 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: r 104 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8470 (p) REVERT: s 90 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: t 39 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8081 (mp) REVERT: u 61 VAL cc_start: 0.8047 (t) cc_final: 0.7841 (p) REVERT: u 76 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7489 (ttmt) REVERT: v 14 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8104 (m) REVERT: v 19 LYS cc_start: 0.7970 (mttt) cc_final: 0.7394 (mtmt) REVERT: w 12 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6119 (mmp-170) REVERT: w 30 LYS cc_start: 0.7916 (tttt) cc_final: 0.7430 (ttpp) REVERT: x 44 MET cc_start: 0.8118 (mtp) cc_final: 0.7320 (mmm) REVERT: x 56 GLN cc_start: 0.6655 (pt0) cc_final: 0.5796 (mm110) REVERT: x 62 VAL cc_start: 0.8222 (t) cc_final: 0.7798 (p) REVERT: x 66 MET cc_start: 0.8089 (mtt) cc_final: 0.7587 (mtt) REVERT: y 16 LYS cc_start: 0.7692 (tttt) cc_final: 0.7133 (tptt) REVERT: y 24 ARG cc_start: 0.8075 (mmp80) cc_final: 0.7363 (mtt180) REVERT: y 33 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7629 (ttmm) REVERT: y 53 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: z 21 ARG cc_start: 0.4847 (tpt170) cc_final: 0.4136 (tpt170) REVERT: z 34 ARG cc_start: 0.7071 (mpt180) cc_final: 0.6782 (mpt180) REVERT: z 36 GLU cc_start: 0.8282 (tt0) cc_final: 0.7935 (tp30) REVERT: z 55 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5886 (ppt170) outliers start: 364 outliers final: 227 residues processed: 1274 average time/residue: 1.3903 time to fit residues: 3007.1812 Evaluate side-chains 1230 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 952 time to evaluate : 6.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 185 LYS Chi-restraints excluded: chain 7 residue 196 GLU Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 271 ILE Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 290 LYS Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain 7 residue 358 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 71 GLN Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 11 CYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 27 MET Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 68 ASN Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 109 ASN Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 55 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 961 optimal weight: 6.9990 chunk 731 optimal weight: 0.9980 chunk 505 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 464 optimal weight: 5.9990 chunk 653 optimal weight: 6.9990 chunk 976 optimal weight: 7.9990 chunk 1034 optimal weight: 4.9990 chunk 510 optimal weight: 8.9990 chunk 925 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 21 ASN 7 348 ASN B 117 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN E 127 ASN G 18 GLN I 11 GLN J 130 HIS ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN V 49 ASN d 26 ASN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 HIS h 8 ASN ** i 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 ASN ** j 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 146 ASN ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN l 148 ASN n 126 GLN r 105 ASN t 20 ASN u 26 ASN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 161626 Z= 0.362 Angle : 0.753 15.114 241162 Z= 0.392 Chirality : 0.041 0.444 30627 Planarity : 0.007 0.137 13343 Dihedral : 23.342 179.542 79544 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 8.07 % Allowed : 20.32 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.10), residues: 6207 helix: 1.46 (0.11), residues: 2198 sheet: -1.15 (0.15), residues: 1098 loop : -1.49 (0.10), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 7 52 HIS 0.007 0.002 HIS X 36 PHE 0.022 0.002 PHE k 8 TYR 0.029 0.002 TYR R 2 ARG 0.013 0.001 ARG h 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 994 time to evaluate : 6.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 27 GLN cc_start: 0.6554 (tt0) cc_final: 0.5792 (pt0) REVERT: 7 30 PHE cc_start: 0.1331 (OUTLIER) cc_final: 0.0769 (t80) REVERT: 7 43 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.4213 (tm-30) REVERT: 7 59 ARG cc_start: 0.2997 (OUTLIER) cc_final: 0.2794 (mpp80) REVERT: 7 60 LYS cc_start: 0.3819 (tmtt) cc_final: 0.3555 (mmtt) REVERT: 7 141 GLU cc_start: 0.7616 (tp30) cc_final: 0.7383 (mm-30) REVERT: 7 190 TYR cc_start: 0.7349 (t80) cc_final: 0.6840 (t80) REVERT: 7 239 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5804 (mm-30) REVERT: 7 285 LYS cc_start: 0.5665 (ttpt) cc_final: 0.5339 (mttt) REVERT: 7 290 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6232 (ptmm) REVERT: 7 301 ARG cc_start: 0.6231 (ttp80) cc_final: 0.5865 (mtm110) REVERT: 7 336 ASP cc_start: 0.8046 (t70) cc_final: 0.7697 (t0) REVERT: 7 343 ARG cc_start: 0.6606 (tpt-90) cc_final: 0.6340 (tpt-90) REVERT: B 13 ARG cc_start: 0.8781 (tpt90) cc_final: 0.8428 (tpt170) REVERT: B 35 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: B 183 LYS cc_start: 0.8505 (tttt) cc_final: 0.8282 (mtpp) REVERT: B 229 ASP cc_start: 0.8210 (m-30) cc_final: 0.7965 (m-30) REVERT: B 258 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8225 (ttm170) REVERT: C 88 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6485 (mt-10) REVERT: D 22 ASP cc_start: 0.7627 (m-30) cc_final: 0.7392 (m-30) REVERT: D 91 ASP cc_start: 0.7971 (t70) cc_final: 0.7505 (t70) REVERT: D 168 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6776 (m-30) REVERT: E 7 TYR cc_start: 0.8331 (t80) cc_final: 0.7833 (t80) REVERT: E 38 MET cc_start: 0.7498 (mtt) cc_final: 0.7187 (ttp) REVERT: E 133 ARG cc_start: 0.7451 (mpt-90) cc_final: 0.6844 (mpt180) REVERT: E 150 ARG cc_start: 0.4787 (OUTLIER) cc_final: 0.4145 (mtt180) REVERT: E 167 ARG cc_start: 0.6756 (ttp80) cc_final: 0.6314 (tpt-90) REVERT: F 141 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7304 (pp) REVERT: G 19 VAL cc_start: 0.5720 (m) cc_final: 0.5449 (p) REVERT: G 41 LYS cc_start: 0.4690 (OUTLIER) cc_final: 0.4411 (pttp) REVERT: G 114 GLU cc_start: 0.4164 (OUTLIER) cc_final: 0.3559 (pp20) REVERT: J 25 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8761 (tp) REVERT: J 32 LEU cc_start: 0.8494 (mt) cc_final: 0.8287 (mt) REVERT: J 36 LEU cc_start: 0.8947 (mt) cc_final: 0.8610 (mp) REVERT: J 75 TYR cc_start: 0.8894 (m-80) cc_final: 0.8435 (m-80) REVERT: J 95 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7347 (mtp85) REVERT: J 98 GLU cc_start: 0.8669 (mp0) cc_final: 0.8332 (mt-10) REVERT: J 118 MET cc_start: 0.8383 (mmm) cc_final: 0.8066 (mmm) REVERT: K 8 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8098 (pp) REVERT: K 53 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7430 (mmtt) REVERT: L 91 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7329 (t0) REVERT: L 99 ASN cc_start: 0.8532 (t0) cc_final: 0.7767 (t0) REVERT: M 17 ASN cc_start: 0.9035 (t0) cc_final: 0.8815 (t0) REVERT: N 30 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7636 (mtp85) REVERT: O 9 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6997 (ttm110) REVERT: O 13 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7756 (ttm170) REVERT: O 80 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7197 (mm-30) REVERT: O 88 LYS cc_start: 0.6459 (tttt) cc_final: 0.5838 (mptt) REVERT: P 16 ASP cc_start: 0.5255 (OUTLIER) cc_final: 0.4870 (p0) REVERT: P 112 GLU cc_start: 0.8489 (pt0) cc_final: 0.8041 (tp30) REVERT: Q 84 LYS cc_start: 0.6786 (mmtt) cc_final: 0.6472 (tttm) REVERT: R 43 ASN cc_start: 0.6748 (t0) cc_final: 0.5962 (p0) REVERT: S 48 LYS cc_start: 0.8551 (tttt) cc_final: 0.7586 (ttpt) REVERT: S 52 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7549 (mt-10) REVERT: S 66 ILE cc_start: 0.8236 (mm) cc_final: 0.7812 (tt) REVERT: S 78 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7604 (mm-30) REVERT: S 95 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.8113 (ttm110) REVERT: T 9 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7723 (mttt) REVERT: T 33 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6949 (mttt) REVERT: U 62 GLU cc_start: 0.7448 (pm20) cc_final: 0.6953 (pm20) REVERT: U 98 SER cc_start: 0.6215 (t) cc_final: 0.5966 (p) REVERT: V 7 GLU cc_start: 0.7459 (mp0) cc_final: 0.6877 (mp0) REVERT: V 25 LYS cc_start: 0.8409 (mttt) cc_final: 0.8165 (mtmm) REVERT: V 51 GLN cc_start: 0.8042 (pp30) cc_final: 0.7788 (pp30) REVERT: W 78 LYS cc_start: 0.8708 (mptt) cc_final: 0.7778 (mmtt) REVERT: W 82 ILE cc_start: 0.8668 (mm) cc_final: 0.8345 (mm) REVERT: Y 7 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5016 (ttm-80) REVERT: Y 20 ASN cc_start: 0.7935 (m-40) cc_final: 0.7707 (m-40) REVERT: Z 45 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7566 (mmt90) REVERT: a 22 MET cc_start: 0.6900 (ptp) cc_final: 0.6161 (pmm) REVERT: c 53 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.6985 (tptp) REVERT: d 24 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8360 (p) REVERT: f 30 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: g 28 LYS cc_start: 0.6759 (tttt) cc_final: 0.6152 (ptmm) REVERT: g 64 LYS cc_start: 0.7414 (mttp) cc_final: 0.7199 (ptmt) REVERT: g 132 LYS cc_start: 0.3260 (OUTLIER) cc_final: 0.3025 (tppt) REVERT: g 188 ASP cc_start: 0.7898 (t0) cc_final: 0.7119 (t0) REVERT: g 190 ASN cc_start: 0.7727 (p0) cc_final: 0.7502 (p0) REVERT: h 54 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6900 (mtp85) REVERT: h 100 GLN cc_start: 0.6656 (tt0) cc_final: 0.6287 (mt0) REVERT: h 129 MET cc_start: 0.7805 (mtm) cc_final: 0.7567 (mmt) REVERT: h 136 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7354 (ptm-80) REVERT: h 144 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5776 (mm) REVERT: h 178 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8895 (mt) REVERT: h 206 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7566 (mt-10) REVERT: i 95 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: i 124 MET cc_start: 0.7600 (mtt) cc_final: 0.7161 (ttp) REVERT: i 187 GLU cc_start: 0.7030 (tt0) cc_final: 0.6668 (tm-30) REVERT: k 58 HIS cc_start: 0.8876 (t-170) cc_final: 0.8397 (t-170) REVERT: k 80 PHE cc_start: 0.5826 (m-80) cc_final: 0.5499 (m-80) REVERT: l 23 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6108 (mm) REVERT: l 40 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: l 78 ARG cc_start: 0.3656 (ttt180) cc_final: 0.2988 (mtm180) REVERT: l 79 ARG cc_start: 0.4207 (OUTLIER) cc_final: 0.3949 (ptm-80) REVERT: l 90 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6536 (pm20) REVERT: l 139 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6887 (mt-10) REVERT: m 83 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8444 (tp) REVERT: n 123 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8245 (tmt90) REVERT: o 5 ARG cc_start: 0.4798 (pmt170) cc_final: 0.4229 (ptt-90) REVERT: o 8 ILE cc_start: 0.6518 (mt) cc_final: 0.6097 (pt) REVERT: o 17 LEU cc_start: 0.7535 (tp) cc_final: 0.7159 (tp) REVERT: o 25 ILE cc_start: 0.6196 (OUTLIER) cc_final: 0.5736 (mm) REVERT: o 62 ARG cc_start: 0.8251 (mtp85) cc_final: 0.8019 (mtt90) REVERT: p 101 ASN cc_start: 0.5912 (t0) cc_final: 0.5478 (p0) REVERT: p 108 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8247 (p) REVERT: p 126 LYS cc_start: 0.8011 (tptt) cc_final: 0.7604 (mtmt) REVERT: q 18 LYS cc_start: 0.8003 (tptp) cc_final: 0.7192 (ptpt) REVERT: q 30 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8282 (mttm) REVERT: q 76 GLU cc_start: 0.8236 (mp0) cc_final: 0.7931 (tt0) REVERT: q 81 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8316 (mp) REVERT: q 109 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: s 47 LYS cc_start: 0.7291 (tptp) cc_final: 0.7024 (tttt) REVERT: t 39 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8172 (mp) REVERT: u 18 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7605 (mm-40) REVERT: u 61 VAL cc_start: 0.8040 (t) cc_final: 0.7832 (p) REVERT: v 14 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8148 (m) REVERT: v 19 LYS cc_start: 0.7750 (mttt) cc_final: 0.7224 (mtmt) REVERT: w 12 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6203 (mmp-170) REVERT: w 30 LYS cc_start: 0.8206 (tttt) cc_final: 0.7636 (ttpp) REVERT: w 66 SER cc_start: 0.8625 (m) cc_final: 0.8266 (t) REVERT: x 44 MET cc_start: 0.8033 (mtp) cc_final: 0.7468 (mmm) REVERT: x 66 MET cc_start: 0.8222 (mtt) cc_final: 0.7765 (mtt) REVERT: y 24 ARG cc_start: 0.8145 (mmp80) cc_final: 0.7271 (mtp85) REVERT: y 33 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7531 (ttmm) REVERT: z 21 ARG cc_start: 0.4828 (tpt170) cc_final: 0.4037 (tpt170) REVERT: z 36 GLU cc_start: 0.8353 (tt0) cc_final: 0.7986 (tp30) outliers start: 417 outliers final: 288 residues processed: 1287 average time/residue: 1.3691 time to fit residues: 3017.0458 Evaluate side-chains 1297 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 968 time to evaluate : 6.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 105 GLU Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 152 MET Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 163 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 182 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 196 GLU Chi-restraints excluded: chain 7 residue 199 VAL Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 242 ILE Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 290 LYS Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain 7 residue 358 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 12 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 71 GLN Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 14 ILE Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 49 ASN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain a residue 40 CYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 11 CYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 30 GLU Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 65 VAL Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 109 ASN Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 861 optimal weight: 3.9990 chunk 587 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 770 optimal weight: 4.9990 chunk 426 optimal weight: 8.9990 chunk 882 optimal weight: 0.4980 chunk 714 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 528 optimal weight: 0.6980 chunk 928 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN I 11 GLN O 29 HIS ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN T 91 GLN V 49 ASN X 17 ASN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN h 8 ASN h 123 GLN ** j 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 161626 Z= 0.174 Angle : 0.625 14.825 241162 Z= 0.334 Chirality : 0.034 0.402 30627 Planarity : 0.006 0.126 13343 Dihedral : 23.225 179.746 79501 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.81 % Rotamer: Outliers : 6.21 % Allowed : 22.60 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 6207 helix: 1.82 (0.11), residues: 2224 sheet: -0.86 (0.15), residues: 1114 loop : -1.26 (0.11), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP k 42 HIS 0.006 0.001 HIS J 47 PHE 0.025 0.001 PHE k 8 TYR 0.019 0.001 TYR R 2 ARG 0.010 0.000 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 995 time to evaluate : 6.456 Fit side-chains revert: symmetry clash REVERT: 6 27 GLN cc_start: 0.6525 (tt0) cc_final: 0.5737 (pt0) REVERT: 7 30 PHE cc_start: 0.1246 (OUTLIER) cc_final: 0.0657 (t80) REVERT: 7 43 GLU cc_start: 0.4435 (OUTLIER) cc_final: 0.4179 (tm-30) REVERT: 7 59 ARG cc_start: 0.2981 (OUTLIER) cc_final: 0.2692 (mpp80) REVERT: 7 60 LYS cc_start: 0.4041 (tmtt) cc_final: 0.3736 (mmtt) REVERT: 7 141 GLU cc_start: 0.7405 (tp30) cc_final: 0.7115 (mm-30) REVERT: 7 190 TYR cc_start: 0.7339 (t80) cc_final: 0.6905 (t80) REVERT: 7 239 GLU cc_start: 0.5941 (mm-30) cc_final: 0.5697 (mm-30) REVERT: 7 285 LYS cc_start: 0.5662 (ttpt) cc_final: 0.5426 (mttt) REVERT: 7 301 ARG cc_start: 0.6139 (ttp80) cc_final: 0.5784 (mtm110) REVERT: 7 331 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6564 (mtpm) REVERT: 7 336 ASP cc_start: 0.7967 (t70) cc_final: 0.7610 (t0) REVERT: 7 338 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.4814 (ptt-90) REVERT: 7 343 ARG cc_start: 0.6543 (tpt-90) cc_final: 0.6319 (tpt-90) REVERT: 7 364 TRP cc_start: 0.7383 (t60) cc_final: 0.6854 (t60) REVERT: B 13 ARG cc_start: 0.8469 (tpt90) cc_final: 0.8242 (tpt170) REVERT: B 35 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: B 146 MET cc_start: 0.8338 (mmm) cc_final: 0.7952 (mmm) REVERT: B 183 LYS cc_start: 0.8473 (tttt) cc_final: 0.8268 (mtpp) REVERT: B 260 ASN cc_start: 0.8319 (t0) cc_final: 0.8074 (t0) REVERT: C 88 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6515 (mt-10) REVERT: D 168 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: E 7 TYR cc_start: 0.8378 (t80) cc_final: 0.7892 (t80) REVERT: E 133 ARG cc_start: 0.7050 (mpt-90) cc_final: 0.6579 (mpt180) REVERT: E 150 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.4108 (mtt180) REVERT: E 167 ARG cc_start: 0.6638 (ttp80) cc_final: 0.6026 (tmt170) REVERT: F 141 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7214 (pp) REVERT: G 41 LYS cc_start: 0.4802 (OUTLIER) cc_final: 0.4488 (pttp) REVERT: G 114 GLU cc_start: 0.4136 (OUTLIER) cc_final: 0.3534 (pp20) REVERT: I 11 GLN cc_start: 0.4061 (OUTLIER) cc_final: 0.1600 (tp40) REVERT: J 13 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7868 (mtt90) REVERT: J 23 LYS cc_start: 0.8203 (tptp) cc_final: 0.7980 (tptm) REVERT: J 32 LEU cc_start: 0.8374 (mt) cc_final: 0.8152 (mt) REVERT: J 36 LEU cc_start: 0.8848 (mt) cc_final: 0.8521 (mp) REVERT: J 75 TYR cc_start: 0.8791 (m-80) cc_final: 0.8314 (m-80) REVERT: J 95 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7414 (mtp85) REVERT: J 98 GLU cc_start: 0.8615 (mp0) cc_final: 0.8325 (mt-10) REVERT: J 118 MET cc_start: 0.8349 (mmm) cc_final: 0.8026 (mmm) REVERT: K 8 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8058 (pp) REVERT: K 53 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7317 (mmtt) REVERT: L 78 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7533 (ttm-80) REVERT: L 91 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7280 (t0) REVERT: L 99 ASN cc_start: 0.8489 (t0) cc_final: 0.7918 (t0) REVERT: L 107 PHE cc_start: 0.8549 (m-80) cc_final: 0.8278 (m-80) REVERT: M 17 ASN cc_start: 0.8899 (t0) cc_final: 0.8625 (t0) REVERT: N 4 ARG cc_start: 0.8715 (mmm160) cc_final: 0.8472 (mmt-90) REVERT: N 30 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7657 (mtp85) REVERT: O 9 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6910 (ttm110) REVERT: O 13 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7929 (ttm170) REVERT: O 80 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7143 (mm-30) REVERT: O 88 LYS cc_start: 0.6412 (tttt) cc_final: 0.5818 (mptt) REVERT: P 16 ASP cc_start: 0.5189 (OUTLIER) cc_final: 0.4784 (p0) REVERT: P 112 GLU cc_start: 0.8443 (pt0) cc_final: 0.8011 (tp30) REVERT: Q 17 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8364 (mm) REVERT: Q 84 LYS cc_start: 0.6796 (mmtt) cc_final: 0.6504 (tttm) REVERT: R 13 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8467 (ttp80) REVERT: R 16 GLU cc_start: 0.7093 (mp0) cc_final: 0.6742 (mp0) REVERT: R 37 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8253 (mt-10) REVERT: R 43 ASN cc_start: 0.6504 (t0) cc_final: 0.5953 (p0) REVERT: S 48 LYS cc_start: 0.8511 (tttt) cc_final: 0.7506 (ttpt) REVERT: S 52 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7460 (mt-10) REVERT: S 66 ILE cc_start: 0.8148 (mm) cc_final: 0.7866 (tt) REVERT: S 78 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7477 (mm-30) REVERT: S 95 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8026 (ttm110) REVERT: T 9 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7765 (mttt) REVERT: T 33 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6977 (mttt) REVERT: U 10 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: U 62 GLU cc_start: 0.7319 (pm20) cc_final: 0.6914 (pm20) REVERT: V 1 MET cc_start: 0.2647 (pmm) cc_final: 0.2225 (ttp) REVERT: V 7 GLU cc_start: 0.7368 (mp0) cc_final: 0.6770 (mp0) REVERT: V 43 ASP cc_start: 0.7373 (t0) cc_final: 0.7089 (m-30) REVERT: W 78 LYS cc_start: 0.8660 (mptt) cc_final: 0.7748 (mmtt) REVERT: W 82 ILE cc_start: 0.8474 (mm) cc_final: 0.8142 (mm) REVERT: W 83 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: X 17 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7880 (m110) REVERT: Y 7 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.5012 (ttm-80) REVERT: Y 20 ASN cc_start: 0.7933 (m-40) cc_final: 0.7727 (m-40) REVERT: Z 45 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7602 (mmt90) REVERT: a 22 MET cc_start: 0.7264 (ptp) cc_final: 0.6707 (pmm) REVERT: c 53 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7016 (tptp) REVERT: d 1 MET cc_start: 0.8268 (mtm) cc_final: 0.7957 (mmm) REVERT: d 22 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8008 (mpt) REVERT: d 24 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (p) REVERT: f 30 GLU cc_start: 0.8351 (tp30) cc_final: 0.6702 (mm-30) REVERT: g 28 LYS cc_start: 0.6737 (tttt) cc_final: 0.6218 (pttp) REVERT: g 64 LYS cc_start: 0.7402 (mttp) cc_final: 0.7202 (ptmt) REVERT: g 132 LYS cc_start: 0.3078 (OUTLIER) cc_final: 0.2813 (mmtt) REVERT: g 154 MET cc_start: 0.7012 (ttp) cc_final: 0.6722 (ttm) REVERT: h 54 ARG cc_start: 0.7182 (ttp80) cc_final: 0.6815 (mtp85) REVERT: h 136 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7178 (ptm-80) REVERT: h 142 MET cc_start: 0.8452 (mmm) cc_final: 0.7996 (mmm) REVERT: h 144 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5897 (mt) REVERT: h 161 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6992 (pm20) REVERT: h 178 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8877 (mt) REVERT: h 206 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7458 (mt-10) REVERT: i 95 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: i 116 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: i 121 LYS cc_start: 0.7884 (mttt) cc_final: 0.7167 (mtpt) REVERT: i 124 MET cc_start: 0.7581 (mtt) cc_final: 0.7121 (ttp) REVERT: i 187 GLU cc_start: 0.6952 (tt0) cc_final: 0.6615 (tm-30) REVERT: k 9 MET cc_start: 0.6762 (mtp) cc_final: 0.6370 (mtm) REVERT: k 58 HIS cc_start: 0.8844 (t-170) cc_final: 0.8337 (t70) REVERT: k 80 PHE cc_start: 0.5857 (m-80) cc_final: 0.5544 (m-80) REVERT: k 104 LYS cc_start: 0.4844 (tptp) cc_final: 0.3981 (pttp) REVERT: l 23 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5864 (mm) REVERT: l 28 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7806 (m-40) REVERT: l 40 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: l 78 ARG cc_start: 0.3667 (ttt180) cc_final: 0.3350 (mmt-90) REVERT: l 79 ARG cc_start: 0.4146 (OUTLIER) cc_final: 0.3903 (ptm-80) REVERT: l 90 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6643 (pm20) REVERT: l 139 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6809 (mt-10) REVERT: m 60 GLU cc_start: 0.7530 (tt0) cc_final: 0.6611 (tm-30) REVERT: m 83 LEU cc_start: 0.8635 (tm) cc_final: 0.8362 (tp) REVERT: n 59 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5732 (tm-30) REVERT: n 123 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8075 (tmt90) REVERT: o 8 ILE cc_start: 0.6635 (mt) cc_final: 0.6256 (pt) REVERT: o 17 LEU cc_start: 0.7490 (tp) cc_final: 0.7123 (tp) REVERT: o 25 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5745 (mm) REVERT: o 62 ARG cc_start: 0.8250 (mtp85) cc_final: 0.8016 (mtt90) REVERT: p 53 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6765 (mmm160) REVERT: p 101 ASN cc_start: 0.5598 (t0) cc_final: 0.5256 (p0) REVERT: p 126 LYS cc_start: 0.7937 (tptt) cc_final: 0.7529 (mtmt) REVERT: q 30 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8293 (mmtm) REVERT: q 70 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7335 (mt-10) REVERT: q 76 GLU cc_start: 0.8229 (mp0) cc_final: 0.7911 (tt0) REVERT: q 81 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8358 (mp) REVERT: q 109 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: r 3 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7911 (mmm160) REVERT: r 62 LYS cc_start: 0.6473 (ttmt) cc_final: 0.6222 (tppt) REVERT: r 104 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8415 (p) REVERT: t 39 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8038 (mp) REVERT: u 76 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7411 (ttmm) REVERT: v 38 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7583 (tp) REVERT: v 59 VAL cc_start: 0.8075 (p) cc_final: 0.7789 (m) REVERT: w 12 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6169 (mmp-170) REVERT: w 30 LYS cc_start: 0.8076 (tttt) cc_final: 0.7498 (ttpp) REVERT: w 66 SER cc_start: 0.8652 (m) cc_final: 0.8294 (t) REVERT: x 44 MET cc_start: 0.7964 (mtp) cc_final: 0.7094 (mmm) REVERT: y 24 ARG cc_start: 0.8089 (mmp80) cc_final: 0.7373 (mtt180) REVERT: y 33 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7523 (mptt) REVERT: z 21 ARG cc_start: 0.4753 (tpt170) cc_final: 0.3911 (tpt170) REVERT: z 36 GLU cc_start: 0.8291 (tt0) cc_final: 0.7902 (tp30) outliers start: 321 outliers final: 195 residues processed: 1224 average time/residue: 1.3852 time to fit residues: 2896.9999 Evaluate side-chains 1198 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 954 time to evaluate : 6.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 24 LEU Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 41 GLU Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 199 VAL Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 271 ILE Chi-restraints excluded: chain 7 residue 290 LYS Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain 7 residue 354 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 28 ASN Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 73 GLU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 78 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 347 optimal weight: 10.0000 chunk 931 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 607 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 1035 optimal weight: 4.9990 chunk 859 optimal weight: 8.9990 chunk 479 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 342 optimal weight: 8.9990 chunk 543 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 83 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN X 17 ASN b 5 GLN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 190 ASN ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN u 63 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 161626 Z= 0.496 Angle : 0.837 15.099 241162 Z= 0.427 Chirality : 0.045 0.417 30627 Planarity : 0.007 0.142 13343 Dihedral : 23.319 179.686 79473 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.53 % Favored : 94.41 % Rotamer: Outliers : 8.46 % Allowed : 21.70 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.10), residues: 6207 helix: 1.06 (0.11), residues: 2204 sheet: -1.10 (0.15), residues: 1106 loop : -1.52 (0.11), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP k 42 HIS 0.010 0.002 HIS B 230 PHE 0.032 0.003 PHE k 8 TYR 0.024 0.003 TYR e 64 ARG 0.010 0.001 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 437 poor density : 977 time to evaluate : 6.653 Fit side-chains revert: symmetry clash REVERT: 6 27 GLN cc_start: 0.6796 (tt0) cc_final: 0.5826 (pt0) REVERT: 6 31 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6702 (mmtt) REVERT: 7 30 PHE cc_start: 0.1341 (OUTLIER) cc_final: 0.0799 (t80) REVERT: 7 43 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.4227 (tm-30) REVERT: 7 59 ARG cc_start: 0.2837 (OUTLIER) cc_final: 0.2495 (mpp80) REVERT: 7 60 LYS cc_start: 0.3884 (tmtt) cc_final: 0.3573 (mmtt) REVERT: 7 190 TYR cc_start: 0.7377 (t80) cc_final: 0.6936 (t80) REVERT: 7 239 GLU cc_start: 0.5939 (mm-30) cc_final: 0.5678 (mm-30) REVERT: 7 301 ARG cc_start: 0.6223 (ttp80) cc_final: 0.5972 (mtm110) REVERT: 7 336 ASP cc_start: 0.7994 (t0) cc_final: 0.7612 (t0) REVERT: B 183 LYS cc_start: 0.8499 (tttt) cc_final: 0.8288 (mtpp) REVERT: D 21 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7463 (ptp-170) REVERT: D 91 ASP cc_start: 0.7966 (t70) cc_final: 0.7383 (t70) REVERT: D 168 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: E 133 ARG cc_start: 0.7525 (mpt-90) cc_final: 0.6916 (mpt180) REVERT: E 150 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.4041 (mtt180) REVERT: E 167 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.5618 (tmt170) REVERT: F 141 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7347 (pp) REVERT: G 41 LYS cc_start: 0.4793 (OUTLIER) cc_final: 0.4457 (pttp) REVERT: G 114 GLU cc_start: 0.4235 (OUTLIER) cc_final: 0.3695 (pp20) REVERT: J 25 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8745 (tp) REVERT: J 32 LEU cc_start: 0.8534 (mt) cc_final: 0.8285 (mt) REVERT: J 36 LEU cc_start: 0.8974 (mt) cc_final: 0.8756 (mp) REVERT: J 75 TYR cc_start: 0.8971 (m-80) cc_final: 0.8505 (m-80) REVERT: J 95 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7304 (mtp85) REVERT: J 98 GLU cc_start: 0.8693 (mp0) cc_final: 0.8412 (mt-10) REVERT: K 53 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7560 (mmtt) REVERT: K 113 MET cc_start: 0.7993 (mmm) cc_final: 0.7713 (mmm) REVERT: L 78 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: L 91 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7392 (t0) REVERT: M 17 ASN cc_start: 0.9054 (t0) cc_final: 0.8803 (t0) REVERT: M 102 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8719 (mt) REVERT: N 30 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7583 (mtp85) REVERT: O 9 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7065 (ttm110) REVERT: O 13 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7718 (ttm170) REVERT: O 80 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7213 (mm-30) REVERT: O 88 LYS cc_start: 0.6355 (tttt) cc_final: 0.5740 (mptt) REVERT: O 94 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7604 (ptt-90) REVERT: P 16 ASP cc_start: 0.5172 (OUTLIER) cc_final: 0.4806 (p0) REVERT: P 112 GLU cc_start: 0.8485 (pt0) cc_final: 0.8005 (tp30) REVERT: Q 84 LYS cc_start: 0.6817 (mmtt) cc_final: 0.6509 (tttm) REVERT: R 37 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8429 (mt-10) REVERT: R 43 ASN cc_start: 0.6649 (t0) cc_final: 0.5850 (p0) REVERT: S 48 LYS cc_start: 0.8654 (tttt) cc_final: 0.8070 (ttpt) REVERT: S 66 ILE cc_start: 0.8240 (mm) cc_final: 0.7782 (tt) REVERT: S 78 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7591 (mm-30) REVERT: S 95 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8068 (ttm110) REVERT: T 9 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7693 (mttt) REVERT: T 33 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7033 (mtmt) REVERT: T 36 LYS cc_start: 0.8611 (tttm) cc_final: 0.8327 (tptp) REVERT: U 22 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7254 (mtp-110) REVERT: U 62 GLU cc_start: 0.7439 (pm20) cc_final: 0.6934 (pm20) REVERT: V 25 LYS cc_start: 0.8575 (mttt) cc_final: 0.8309 (mtmm) REVERT: W 78 LYS cc_start: 0.8739 (mptt) cc_final: 0.7801 (mmtt) REVERT: W 83 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: X 6 GLN cc_start: 0.8840 (mt0) cc_final: 0.8596 (mt0) REVERT: Y 7 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5028 (mpt-90) REVERT: Y 20 ASN cc_start: 0.7939 (m-40) cc_final: 0.7713 (m-40) REVERT: a 22 MET cc_start: 0.7064 (ptp) cc_final: 0.6474 (pmm) REVERT: b 32 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6253 (mtmm) REVERT: c 48 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7965 (tt) REVERT: c 53 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7045 (tptp) REVERT: d 24 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8564 (p) REVERT: f 30 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: g 28 LYS cc_start: 0.6728 (tttt) cc_final: 0.6147 (pttp) REVERT: g 64 LYS cc_start: 0.7473 (mttp) cc_final: 0.7235 (ptmt) REVERT: g 132 LYS cc_start: 0.3256 (OUTLIER) cc_final: 0.2986 (mptt) REVERT: g 188 ASP cc_start: 0.7649 (t0) cc_final: 0.7364 (t0) REVERT: h 54 ARG cc_start: 0.7363 (ttp80) cc_final: 0.6972 (mtp85) REVERT: h 136 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7146 (ptm-80) REVERT: h 161 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7190 (pm20) REVERT: h 178 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8879 (mt) REVERT: h 206 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7596 (mt-10) REVERT: i 47 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7350 (mmt-90) REVERT: i 91 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.6877 (mp) REVERT: i 95 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: i 116 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: i 124 MET cc_start: 0.7582 (mtt) cc_final: 0.7105 (ttp) REVERT: i 187 GLU cc_start: 0.7018 (tt0) cc_final: 0.6792 (tm-30) REVERT: j 152 MET cc_start: 0.7543 (mtp) cc_final: 0.7277 (mtt) REVERT: k 58 HIS cc_start: 0.8863 (t-170) cc_final: 0.8333 (t70) REVERT: k 80 PHE cc_start: 0.5933 (m-80) cc_final: 0.5554 (m-80) REVERT: k 104 LYS cc_start: 0.4924 (tptp) cc_final: 0.4106 (ttpp) REVERT: l 23 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6048 (mm) REVERT: l 78 ARG cc_start: 0.3587 (ttt180) cc_final: 0.3178 (mmt-90) REVERT: l 90 GLU cc_start: 0.7434 (mm-30) cc_final: 0.6632 (pm20) REVERT: l 139 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6747 (mt-10) REVERT: m 83 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8479 (tp) REVERT: n 59 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6025 (tm-30) REVERT: n 123 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8155 (tmt90) REVERT: o 8 ILE cc_start: 0.6528 (mt) cc_final: 0.6108 (pt) REVERT: o 25 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5803 (mm) REVERT: o 62 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7985 (mtt90) REVERT: p 101 ASN cc_start: 0.5984 (t0) cc_final: 0.5600 (p0) REVERT: p 126 LYS cc_start: 0.8061 (tptt) cc_final: 0.7640 (mtmt) REVERT: q 30 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8264 (mttm) REVERT: q 76 GLU cc_start: 0.8223 (mp0) cc_final: 0.7844 (tt0) REVERT: q 81 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8313 (mp) REVERT: r 3 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7866 (mmm160) REVERT: r 62 LYS cc_start: 0.6529 (ttmt) cc_final: 0.6243 (tppt) REVERT: r 98 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7573 (ttm-80) REVERT: t 39 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8151 (mp) REVERT: u 18 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7638 (mm-40) REVERT: v 19 LYS cc_start: 0.7811 (mttt) cc_final: 0.7499 (mtmt) REVERT: w 12 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6156 (mmp-170) REVERT: w 30 LYS cc_start: 0.8197 (tttt) cc_final: 0.7672 (ttpp) REVERT: w 66 SER cc_start: 0.8690 (m) cc_final: 0.8354 (t) REVERT: x 44 MET cc_start: 0.7729 (mtp) cc_final: 0.7516 (mmm) REVERT: x 52 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7250 (t-90) REVERT: x 66 MET cc_start: 0.8279 (mtt) cc_final: 0.7921 (mtt) REVERT: y 24 ARG cc_start: 0.8202 (mmp80) cc_final: 0.7434 (mtt180) REVERT: y 33 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7582 (mptt) REVERT: y 54 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7254 (ppp) REVERT: z 21 ARG cc_start: 0.4860 (tpt170) cc_final: 0.4009 (tpt170) REVERT: z 36 GLU cc_start: 0.8391 (tt0) cc_final: 0.8017 (tp30) outliers start: 437 outliers final: 316 residues processed: 1284 average time/residue: 1.3497 time to fit residues: 2963.1510 Evaluate side-chains 1320 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 957 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 24 LEU Chi-restraints excluded: chain 6 residue 31 LYS Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 41 GLU Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 163 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 199 VAL Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 223 VAL Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain 7 residue 354 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 71 GLN Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 14 ILE Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 49 ASN Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain a residue 39 LYS Chi-restraints excluded: chain a residue 40 CYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 11 CYS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 30 GLU Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 130 THR Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 190 ASN Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 73 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 101 ILE Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 65 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain p residue 95 SER Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 77 HIS Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 98 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 78 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 52 HIS Chi-restraints excluded: chain x residue 77 THR Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 998 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 589 optimal weight: 10.0000 chunk 756 optimal weight: 7.9990 chunk 585 optimal weight: 2.9990 chunk 871 optimal weight: 2.9990 chunk 578 optimal weight: 3.9990 chunk 1031 optimal weight: 7.9990 chunk 645 optimal weight: 0.6980 chunk 628 optimal weight: 9.9990 chunk 476 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 29 HIS N 107 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** Z 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 130 ASN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN u 26 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 57 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 161626 Z= 0.233 Angle : 0.661 14.937 241162 Z= 0.349 Chirality : 0.036 0.413 30627 Planarity : 0.006 0.127 13343 Dihedral : 23.233 179.118 79453 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 6.70 % Allowed : 23.71 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 6207 helix: 1.39 (0.11), residues: 2221 sheet: -1.01 (0.15), residues: 1132 loop : -1.36 (0.11), residues: 2854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP k 42 HIS 0.008 0.001 HIS J 47 PHE 0.026 0.001 PHE k 8 TYR 0.018 0.002 TYR e 64 ARG 0.011 0.001 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 970 time to evaluate : 6.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 27 GLN cc_start: 0.6800 (tt0) cc_final: 0.5766 (pt0) REVERT: 7 30 PHE cc_start: 0.1467 (OUTLIER) cc_final: 0.0907 (t80) REVERT: 7 59 ARG cc_start: 0.2745 (OUTLIER) cc_final: 0.2465 (mpp80) REVERT: 7 60 LYS cc_start: 0.4180 (tmtt) cc_final: 0.3858 (mmtt) REVERT: 7 149 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7070 (tt) REVERT: 7 190 TYR cc_start: 0.7343 (t80) cc_final: 0.6887 (t80) REVERT: 7 239 GLU cc_start: 0.5866 (mm-30) cc_final: 0.5633 (mm-30) REVERT: 7 331 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6523 (mtpm) REVERT: 7 336 ASP cc_start: 0.7996 (t0) cc_final: 0.7648 (t0) REVERT: 7 338 ARG cc_start: 0.5585 (OUTLIER) cc_final: 0.4984 (ptt-90) REVERT: 7 343 ARG cc_start: 0.6604 (tpt-90) cc_final: 0.6401 (tpt-90) REVERT: B 13 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8228 (tpt170) REVERT: B 146 MET cc_start: 0.8354 (mmm) cc_final: 0.7973 (mmm) REVERT: B 183 LYS cc_start: 0.8464 (tttt) cc_final: 0.8223 (mtpp) REVERT: D 168 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: E 133 ARG cc_start: 0.7157 (mpt-90) cc_final: 0.6679 (mpt180) REVERT: E 150 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.3975 (mtt180) REVERT: E 167 ARG cc_start: 0.5854 (ttp80) cc_final: 0.5612 (tmt170) REVERT: F 141 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7371 (pp) REVERT: G 41 LYS cc_start: 0.4774 (OUTLIER) cc_final: 0.4457 (pttp) REVERT: G 114 GLU cc_start: 0.4059 (OUTLIER) cc_final: 0.3419 (pp20) REVERT: J 23 LYS cc_start: 0.8247 (tptp) cc_final: 0.8022 (tptm) REVERT: J 32 LEU cc_start: 0.8406 (mt) cc_final: 0.8175 (mt) REVERT: J 36 LEU cc_start: 0.8886 (mt) cc_final: 0.8661 (mp) REVERT: J 75 TYR cc_start: 0.8871 (m-80) cc_final: 0.8422 (m-80) REVERT: J 95 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7399 (mtp85) REVERT: J 98 GLU cc_start: 0.8637 (mp0) cc_final: 0.8377 (mt-10) REVERT: J 118 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: K 8 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7788 (pp) REVERT: K 53 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7531 (mmtt) REVERT: L 91 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7343 (t0) REVERT: L 96 LYS cc_start: 0.7237 (mttt) cc_final: 0.6987 (mttt) REVERT: M 17 ASN cc_start: 0.8949 (t0) cc_final: 0.8660 (t0) REVERT: N 30 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7515 (mtp85) REVERT: O 9 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6090 (ptt90) REVERT: O 13 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7801 (ttm170) REVERT: O 80 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7192 (mm-30) REVERT: O 88 LYS cc_start: 0.6347 (tttt) cc_final: 0.5733 (mptt) REVERT: P 16 ASP cc_start: 0.5133 (OUTLIER) cc_final: 0.4709 (p0) REVERT: P 112 GLU cc_start: 0.8438 (pt0) cc_final: 0.7975 (tp30) REVERT: Q 84 LYS cc_start: 0.6798 (mmtt) cc_final: 0.6515 (tttm) REVERT: R 37 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8290 (mt-10) REVERT: R 43 ASN cc_start: 0.6465 (t0) cc_final: 0.5834 (p0) REVERT: S 48 LYS cc_start: 0.8508 (tttt) cc_final: 0.7974 (ttpt) REVERT: S 66 ILE cc_start: 0.8300 (mm) cc_final: 0.7826 (tt) REVERT: S 78 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7516 (mm-30) REVERT: S 95 ARG cc_start: 0.8457 (ttp-110) cc_final: 0.8010 (ttm110) REVERT: T 9 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7750 (mttt) REVERT: T 33 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6912 (mttt) REVERT: U 10 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: U 62 GLU cc_start: 0.7279 (pm20) cc_final: 0.6885 (pm20) REVERT: V 7 GLU cc_start: 0.7236 (mp0) cc_final: 0.7016 (mp0) REVERT: W 78 LYS cc_start: 0.8696 (mptt) cc_final: 0.7742 (mmtt) REVERT: W 82 ILE cc_start: 0.8564 (mm) cc_final: 0.8222 (mm) REVERT: W 83 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: X 6 GLN cc_start: 0.8820 (mt0) cc_final: 0.8582 (mt0) REVERT: X 8 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8265 (t) REVERT: Y 7 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.4985 (ttm-80) REVERT: Y 20 ASN cc_start: 0.7872 (m-40) cc_final: 0.7662 (m-40) REVERT: Z 45 ARG cc_start: 0.7832 (mmt90) cc_final: 0.7489 (mmt90) REVERT: a 22 MET cc_start: 0.7200 (ptp) cc_final: 0.6673 (pmm) REVERT: b 32 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6116 (mtmm) REVERT: c 53 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.6988 (tptp) REVERT: d 24 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8310 (p) REVERT: g 27 MET cc_start: 0.5963 (ttt) cc_final: 0.5618 (mtp) REVERT: g 28 LYS cc_start: 0.6681 (tttt) cc_final: 0.6068 (ptmm) REVERT: g 64 LYS cc_start: 0.7437 (mttp) cc_final: 0.7190 (ptmt) REVERT: g 132 LYS cc_start: 0.3054 (OUTLIER) cc_final: 0.2802 (mptt) REVERT: g 188 ASP cc_start: 0.7331 (t0) cc_final: 0.6494 (t0) REVERT: h 54 ARG cc_start: 0.7301 (ttp80) cc_final: 0.6956 (mtp85) REVERT: h 136 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7045 (ptm-80) REVERT: h 161 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7112 (pm20) REVERT: h 178 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8904 (mt) REVERT: h 206 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7426 (mt-10) REVERT: i 47 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7380 (mmt-90) REVERT: i 95 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: i 116 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: i 121 LYS cc_start: 0.7910 (mttt) cc_final: 0.7224 (mtpt) REVERT: i 124 MET cc_start: 0.7583 (mtt) cc_final: 0.7106 (ttp) REVERT: i 187 GLU cc_start: 0.6930 (tt0) cc_final: 0.6387 (tm-30) REVERT: k 9 MET cc_start: 0.7572 (mtp) cc_final: 0.6934 (mtm) REVERT: k 58 HIS cc_start: 0.8842 (t-170) cc_final: 0.8298 (t70) REVERT: k 80 PHE cc_start: 0.5989 (m-80) cc_final: 0.5619 (m-80) REVERT: k 104 LYS cc_start: 0.4846 (tptp) cc_final: 0.3977 (pttp) REVERT: l 23 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6161 (mm) REVERT: l 78 ARG cc_start: 0.3855 (ttt180) cc_final: 0.3442 (mmt180) REVERT: l 90 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6628 (pm20) REVERT: l 139 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6715 (mt-10) REVERT: m 60 GLU cc_start: 0.7344 (tt0) cc_final: 0.6586 (tm-30) REVERT: m 77 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8077 (mtp180) REVERT: m 83 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8365 (tp) REVERT: n 123 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8059 (tmt90) REVERT: o 8 ILE cc_start: 0.6578 (mt) cc_final: 0.6150 (pt) REVERT: o 17 LEU cc_start: 0.7538 (tp) cc_final: 0.7066 (tp) REVERT: o 25 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5818 (mm) REVERT: o 62 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7946 (mtt90) REVERT: p 101 ASN cc_start: 0.5701 (t0) cc_final: 0.5371 (p0) REVERT: p 126 LYS cc_start: 0.7977 (tptt) cc_final: 0.7563 (mtmt) REVERT: q 30 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8183 (mttm) REVERT: q 70 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7405 (mt-10) REVERT: q 76 GLU cc_start: 0.8203 (mp0) cc_final: 0.7828 (tt0) REVERT: q 81 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8340 (mp) REVERT: r 3 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7921 (mmm160) REVERT: r 62 LYS cc_start: 0.6434 (ttmt) cc_final: 0.6188 (tppt) REVERT: r 75 MET cc_start: 0.7507 (tpp) cc_final: 0.7110 (mtp) REVERT: r 104 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8621 (p) REVERT: t 39 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8082 (mp) REVERT: u 18 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: u 76 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7518 (ttmt) REVERT: v 49 GLU cc_start: 0.5894 (tt0) cc_final: 0.5360 (pm20) REVERT: w 12 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6176 (mmp-170) REVERT: w 24 LYS cc_start: 0.7592 (mppt) cc_final: 0.7298 (mppt) REVERT: w 30 LYS cc_start: 0.8023 (tttt) cc_final: 0.7480 (ttpp) REVERT: w 66 SER cc_start: 0.8621 (m) cc_final: 0.8263 (t) REVERT: x 44 MET cc_start: 0.7636 (mtp) cc_final: 0.7368 (mmm) REVERT: y 24 ARG cc_start: 0.8141 (mmp80) cc_final: 0.7429 (mtt180) REVERT: y 33 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7569 (mptt) REVERT: y 54 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7154 (ppp) REVERT: z 21 ARG cc_start: 0.4902 (tpt170) cc_final: 0.4031 (tpt170) REVERT: z 36 GLU cc_start: 0.8332 (tt0) cc_final: 0.7943 (tp30) outliers start: 346 outliers final: 256 residues processed: 1213 average time/residue: 1.3482 time to fit residues: 2796.7273 Evaluate side-chains 1251 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 951 time to evaluate : 6.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 24 LEU Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 41 GLU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 199 VAL Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 223 VAL Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 242 ILE Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 271 ILE Chi-restraints excluded: chain 7 residue 290 LYS Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain 7 residue 354 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 39 LYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 78 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 638 optimal weight: 0.7980 chunk 411 optimal weight: 10.0000 chunk 615 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 chunk 202 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 655 optimal weight: 0.0370 chunk 702 optimal weight: 6.9990 chunk 509 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 810 optimal weight: 20.0000 overall best weight: 3.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN S 15 GLN V 49 ASN Z 9 GLN b 5 GLN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 89 GLN h 3 GLN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN u 26 ASN u 63 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 161626 Z= 0.335 Angle : 0.720 14.856 241162 Z= 0.374 Chirality : 0.039 0.404 30627 Planarity : 0.007 0.135 13343 Dihedral : 23.240 179.777 79450 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 7.22 % Allowed : 23.51 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 6207 helix: 1.24 (0.11), residues: 2217 sheet: -1.04 (0.15), residues: 1114 loop : -1.43 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP k 42 HIS 0.007 0.001 HIS B 230 PHE 0.026 0.002 PHE k 8 TYR 0.020 0.002 TYR 7 333 ARG 0.011 0.001 ARG j 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 970 time to evaluate : 6.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 27 GLN cc_start: 0.6681 (tt0) cc_final: 0.5770 (pt0) REVERT: 6 31 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6630 (mmtt) REVERT: 7 30 PHE cc_start: 0.1437 (OUTLIER) cc_final: 0.0934 (t80) REVERT: 7 43 GLU cc_start: 0.4409 (OUTLIER) cc_final: 0.4161 (tm-30) REVERT: 7 59 ARG cc_start: 0.2804 (OUTLIER) cc_final: 0.2561 (mpp80) REVERT: 7 149 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7121 (tt) REVERT: 7 190 TYR cc_start: 0.7345 (t80) cc_final: 0.6919 (t80) REVERT: 7 239 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5654 (mm-30) REVERT: 7 336 ASP cc_start: 0.8013 (t0) cc_final: 0.7638 (t0) REVERT: 7 343 ARG cc_start: 0.6640 (tpt-90) cc_final: 0.6401 (tpt-90) REVERT: B 146 MET cc_start: 0.8437 (mmm) cc_final: 0.8046 (mmm) REVERT: B 183 LYS cc_start: 0.8481 (tttt) cc_final: 0.8271 (mtpp) REVERT: D 168 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: E 7 TYR cc_start: 0.8366 (t80) cc_final: 0.7857 (t80) REVERT: E 133 ARG cc_start: 0.7233 (mpt-90) cc_final: 0.6732 (mpt180) REVERT: E 150 ARG cc_start: 0.4606 (OUTLIER) cc_final: 0.3867 (mtt180) REVERT: E 167 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.5603 (tmt170) REVERT: F 141 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7395 (pp) REVERT: G 41 LYS cc_start: 0.4776 (OUTLIER) cc_final: 0.4447 (pttp) REVERT: G 114 GLU cc_start: 0.4078 (OUTLIER) cc_final: 0.3578 (pp20) REVERT: J 13 ARG cc_start: 0.8301 (mtt90) cc_final: 0.7927 (mtt90) REVERT: J 23 LYS cc_start: 0.8284 (tptp) cc_final: 0.8058 (tptm) REVERT: J 25 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8675 (tp) REVERT: J 32 LEU cc_start: 0.8449 (mt) cc_final: 0.8193 (mt) REVERT: J 36 LEU cc_start: 0.8920 (mt) cc_final: 0.8681 (mp) REVERT: J 75 TYR cc_start: 0.8918 (m-80) cc_final: 0.8474 (m-80) REVERT: J 95 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7383 (mtp85) REVERT: J 98 GLU cc_start: 0.8699 (mp0) cc_final: 0.8438 (mt-10) REVERT: J 118 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8310 (mmm) REVERT: K 8 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7875 (pp) REVERT: K 17 ARG cc_start: 0.8306 (mmp80) cc_final: 0.7292 (mtm-85) REVERT: K 53 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7554 (mmtt) REVERT: L 91 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7350 (t0) REVERT: M 17 ASN cc_start: 0.8990 (t0) cc_final: 0.8706 (t0) REVERT: N 30 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7503 (mtp85) REVERT: O 9 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6974 (ttm110) REVERT: O 13 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7810 (ttm170) REVERT: O 80 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7213 (mm-30) REVERT: O 88 LYS cc_start: 0.6353 (tttt) cc_final: 0.5726 (mmtt) REVERT: P 16 ASP cc_start: 0.5031 (OUTLIER) cc_final: 0.4670 (p0) REVERT: P 112 GLU cc_start: 0.8434 (pt0) cc_final: 0.7970 (tp30) REVERT: Q 84 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6532 (tttm) REVERT: R 37 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8427 (mt-10) REVERT: R 43 ASN cc_start: 0.6408 (t0) cc_final: 0.5727 (p0) REVERT: S 48 LYS cc_start: 0.8623 (tttt) cc_final: 0.8029 (ttpt) REVERT: S 66 ILE cc_start: 0.8273 (mm) cc_final: 0.7767 (tt) REVERT: S 78 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7552 (mm-30) REVERT: S 95 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8019 (ttm110) REVERT: T 9 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7720 (mttt) REVERT: T 33 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6976 (mttt) REVERT: T 36 LYS cc_start: 0.8541 (tttm) cc_final: 0.8185 (tptp) REVERT: U 10 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: U 62 GLU cc_start: 0.7297 (pm20) cc_final: 0.6940 (pm20) REVERT: V 7 GLU cc_start: 0.7329 (mp0) cc_final: 0.6826 (mp0) REVERT: V 25 LYS cc_start: 0.8434 (mttt) cc_final: 0.8206 (mtmm) REVERT: W 78 LYS cc_start: 0.8718 (mptt) cc_final: 0.7774 (mmtt) REVERT: W 83 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: X 6 GLN cc_start: 0.8828 (mt0) cc_final: 0.8592 (mt0) REVERT: X 8 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8291 (t) REVERT: Y 7 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5043 (mpt-90) REVERT: Y 20 ASN cc_start: 0.7859 (m-40) cc_final: 0.7631 (m-40) REVERT: a 22 MET cc_start: 0.7130 (ptp) cc_final: 0.6630 (pmm) REVERT: b 32 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6262 (mtmm) REVERT: c 53 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7002 (tptp) REVERT: d 24 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8463 (p) REVERT: g 27 MET cc_start: 0.6153 (ttt) cc_final: 0.5697 (mtp) REVERT: g 28 LYS cc_start: 0.6770 (tttt) cc_final: 0.6175 (pttp) REVERT: g 64 LYS cc_start: 0.7376 (mttp) cc_final: 0.7162 (ptmt) REVERT: g 132 LYS cc_start: 0.2940 (OUTLIER) cc_final: 0.2657 (mmtp) REVERT: g 137 ARG cc_start: 0.5023 (mmt-90) cc_final: 0.4720 (ptt180) REVERT: g 188 ASP cc_start: 0.7526 (t0) cc_final: 0.6579 (t0) REVERT: h 54 ARG cc_start: 0.7296 (ttp80) cc_final: 0.6969 (mtp85) REVERT: h 136 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.7131 (ptm-80) REVERT: h 140 ASN cc_start: 0.7391 (m-40) cc_final: 0.7128 (m-40) REVERT: h 144 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5614 (mt) REVERT: h 178 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8900 (mt) REVERT: h 206 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7336 (mt-10) REVERT: i 47 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7400 (mmt-90) REVERT: i 116 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: i 124 MET cc_start: 0.7598 (mtt) cc_final: 0.7115 (ttp) REVERT: j 45 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7550 (mmm160) REVERT: k 9 MET cc_start: 0.7603 (mtp) cc_final: 0.6965 (mtm) REVERT: k 80 PHE cc_start: 0.6009 (m-80) cc_final: 0.5638 (m-80) REVERT: k 104 LYS cc_start: 0.4766 (tptp) cc_final: 0.4052 (pttp) REVERT: l 23 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6143 (mm) REVERT: l 68 ASN cc_start: 0.8540 (t0) cc_final: 0.8072 (t0) REVERT: l 78 ARG cc_start: 0.4122 (ttt180) cc_final: 0.3469 (mmt180) REVERT: l 90 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6614 (pm20) REVERT: l 139 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6700 (mt-10) REVERT: m 60 GLU cc_start: 0.7387 (tt0) cc_final: 0.6570 (tm-30) REVERT: m 77 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8078 (mtp180) REVERT: m 83 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8409 (tp) REVERT: n 21 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7222 (pt) REVERT: n 123 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8054 (tmt90) REVERT: o 8 ILE cc_start: 0.6642 (mt) cc_final: 0.6193 (pt) REVERT: o 17 LEU cc_start: 0.7557 (tp) cc_final: 0.7075 (tp) REVERT: o 25 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.5800 (mm) REVERT: o 62 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7961 (mtt90) REVERT: p 126 LYS cc_start: 0.8025 (tptt) cc_final: 0.7601 (mtmt) REVERT: q 30 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8209 (mttm) REVERT: q 76 GLU cc_start: 0.8212 (mp0) cc_final: 0.7886 (tt0) REVERT: q 81 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8315 (mp) REVERT: r 3 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (mmm160) REVERT: r 75 MET cc_start: 0.7383 (tpp) cc_final: 0.7165 (mtp) REVERT: r 98 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7561 (ttm-80) REVERT: r 104 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8740 (p) REVERT: t 39 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8121 (mp) REVERT: u 18 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7625 (mm-40) REVERT: v 19 LYS cc_start: 0.7741 (mttt) cc_final: 0.7296 (mtmt) REVERT: w 12 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6152 (mmp-170) REVERT: w 24 LYS cc_start: 0.7693 (mppt) cc_final: 0.7277 (mppt) REVERT: w 30 LYS cc_start: 0.8122 (tttt) cc_final: 0.7573 (ttpp) REVERT: w 66 SER cc_start: 0.8633 (m) cc_final: 0.8282 (t) REVERT: x 44 MET cc_start: 0.7540 (mtp) cc_final: 0.7330 (mmm) REVERT: x 66 MET cc_start: 0.8280 (mtt) cc_final: 0.7877 (mtt) REVERT: y 24 ARG cc_start: 0.8185 (mmp80) cc_final: 0.7314 (mtp85) REVERT: y 33 LYS cc_start: 0.7816 (ttmm) cc_final: 0.7586 (mptt) REVERT: y 54 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7056 (ppp) REVERT: z 21 ARG cc_start: 0.4925 (tpt170) cc_final: 0.4049 (tpt170) REVERT: z 36 GLU cc_start: 0.8352 (tt0) cc_final: 0.7953 (tp30) outliers start: 373 outliers final: 293 residues processed: 1231 average time/residue: 1.3585 time to fit residues: 2865.5004 Evaluate side-chains 1297 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 958 time to evaluate : 6.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 24 LEU Chi-restraints excluded: chain 6 residue 31 LYS Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 41 GLU Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 59 ARG Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 182 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 199 VAL Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 223 VAL Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 242 ILE Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 271 ILE Chi-restraints excluded: chain 7 residue 290 LYS Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain 7 residue 354 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 71 GLN Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 39 LYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 77 HIS Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 81 MET Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 98 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 78 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 938 optimal weight: 9.9990 chunk 988 optimal weight: 4.9990 chunk 901 optimal weight: 7.9990 chunk 961 optimal weight: 0.8980 chunk 987 optimal weight: 9.9990 chunk 578 optimal weight: 6.9990 chunk 418 optimal weight: 10.0000 chunk 754 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 868 optimal weight: 0.9990 chunk 908 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN G 66 ASN G 135 HIS N 107 ASN O 38 GLN V 49 ASN b 5 GLN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 190 ASN h 3 GLN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN u 63 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 161626 Z= 0.221 Angle : 0.652 14.858 241162 Z= 0.344 Chirality : 0.035 0.400 30627 Planarity : 0.006 0.128 13343 Dihedral : 23.189 179.635 79450 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 6.72 % Allowed : 24.06 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.10), residues: 6207 helix: 1.43 (0.11), residues: 2222 sheet: -0.96 (0.15), residues: 1121 loop : -1.35 (0.11), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP k 42 HIS 0.007 0.001 HIS J 47 PHE 0.027 0.001 PHE k 8 TYR 0.017 0.002 TYR 7 333 ARG 0.013 0.000 ARG v 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 962 time to evaluate : 5.985 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: 6 27 GLN cc_start: 0.6740 (tt0) cc_final: 0.5818 (pt0) REVERT: 7 30 PHE cc_start: 0.1308 (OUTLIER) cc_final: 0.0854 (t80) REVERT: 7 43 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.4162 (tm-30) REVERT: 7 149 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7063 (tt) REVERT: 7 190 TYR cc_start: 0.7296 (t80) cc_final: 0.6899 (t80) REVERT: 7 239 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5640 (mm-30) REVERT: 7 336 ASP cc_start: 0.7989 (t0) cc_final: 0.7644 (t0) REVERT: B 35 GLU cc_start: 0.8174 (tt0) cc_final: 0.7737 (tp30) REVERT: B 146 MET cc_start: 0.8369 (mmm) cc_final: 0.7990 (mmm) REVERT: B 183 LYS cc_start: 0.8431 (tttt) cc_final: 0.8219 (mtpp) REVERT: D 168 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: D 195 GLN cc_start: 0.7946 (mt0) cc_final: 0.7665 (tp40) REVERT: E 133 ARG cc_start: 0.7111 (mpt-90) cc_final: 0.6657 (mpt180) REVERT: E 167 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5657 (tmt170) REVERT: F 141 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7324 (pp) REVERT: G 41 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4457 (pttp) REVERT: G 114 GLU cc_start: 0.4077 (OUTLIER) cc_final: 0.3542 (pp20) REVERT: J 13 ARG cc_start: 0.8291 (mtt90) cc_final: 0.7932 (mtt90) REVERT: J 23 LYS cc_start: 0.8235 (tptp) cc_final: 0.8011 (tptm) REVERT: J 32 LEU cc_start: 0.8400 (mt) cc_final: 0.8172 (mt) REVERT: J 36 LEU cc_start: 0.8928 (mt) cc_final: 0.8570 (mp) REVERT: J 75 TYR cc_start: 0.8871 (m-80) cc_final: 0.8415 (m-80) REVERT: J 95 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7393 (mtp85) REVERT: J 98 GLU cc_start: 0.8645 (mp0) cc_final: 0.8385 (mt-10) REVERT: J 118 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8069 (mmm) REVERT: K 8 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7696 (pp) REVERT: K 17 ARG cc_start: 0.8299 (mmp80) cc_final: 0.7400 (mtm-85) REVERT: K 53 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7503 (mmtt) REVERT: L 91 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7312 (t0) REVERT: M 17 ASN cc_start: 0.8938 (t0) cc_final: 0.8641 (t0) REVERT: N 30 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7494 (mtp85) REVERT: O 9 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6082 (ptt90) REVERT: O 13 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: O 80 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7202 (mm-30) REVERT: O 88 LYS cc_start: 0.6368 (tttt) cc_final: 0.5734 (mmtt) REVERT: P 16 ASP cc_start: 0.5125 (OUTLIER) cc_final: 0.4712 (p0) REVERT: P 112 GLU cc_start: 0.8418 (pt0) cc_final: 0.7981 (tp30) REVERT: Q 84 LYS cc_start: 0.6803 (mmtt) cc_final: 0.6504 (tttm) REVERT: R 37 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8356 (mt-10) REVERT: R 43 ASN cc_start: 0.6271 (t0) cc_final: 0.5715 (p0) REVERT: S 48 LYS cc_start: 0.8522 (tttt) cc_final: 0.8041 (ttpt) REVERT: S 66 ILE cc_start: 0.8313 (mm) cc_final: 0.7812 (tt) REVERT: S 78 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7497 (mm-30) REVERT: S 95 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7984 (ttm110) REVERT: T 9 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7755 (mttt) REVERT: T 33 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6928 (mtmt) REVERT: U 10 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: U 62 GLU cc_start: 0.7257 (pm20) cc_final: 0.6949 (pm20) REVERT: V 7 GLU cc_start: 0.7315 (mp0) cc_final: 0.7074 (mp0) REVERT: W 78 LYS cc_start: 0.8701 (mptt) cc_final: 0.7758 (mmtt) REVERT: W 83 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: X 6 GLN cc_start: 0.8749 (mt0) cc_final: 0.8530 (mt0) REVERT: X 8 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8239 (t) REVERT: Y 20 ASN cc_start: 0.7807 (m-40) cc_final: 0.7587 (m-40) REVERT: Z 45 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7588 (mmt90) REVERT: a 22 MET cc_start: 0.7198 (ptp) cc_final: 0.6717 (pmm) REVERT: b 32 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6198 (mtmm) REVERT: c 53 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.6981 (tptp) REVERT: d 1 MET cc_start: 0.8305 (mtm) cc_final: 0.7956 (mmm) REVERT: d 24 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8346 (p) REVERT: g 27 MET cc_start: 0.6141 (ttt) cc_final: 0.5755 (mtp) REVERT: g 28 LYS cc_start: 0.6777 (tttt) cc_final: 0.6182 (ptmm) REVERT: g 64 LYS cc_start: 0.7368 (mttp) cc_final: 0.7129 (ptmt) REVERT: g 132 LYS cc_start: 0.2846 (OUTLIER) cc_final: 0.2540 (mmtp) REVERT: g 137 ARG cc_start: 0.4997 (mmt-90) cc_final: 0.4760 (ptt180) REVERT: g 188 ASP cc_start: 0.7345 (t0) cc_final: 0.6446 (t0) REVERT: h 54 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6866 (mtp85) REVERT: h 136 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7213 (ptm-80) REVERT: h 144 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5623 (mt) REVERT: h 161 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: h 175 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8050 (mm) REVERT: h 178 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8921 (mt) REVERT: i 47 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7382 (mmt-90) REVERT: i 95 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: i 105 MET cc_start: 0.8188 (mtt) cc_final: 0.7976 (mtt) REVERT: i 116 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: i 121 LYS cc_start: 0.7993 (mttt) cc_final: 0.7278 (mtpt) REVERT: i 124 MET cc_start: 0.7581 (mtt) cc_final: 0.7106 (ttp) REVERT: k 9 MET cc_start: 0.7606 (mtp) cc_final: 0.6966 (mtm) REVERT: k 58 HIS cc_start: 0.8825 (t-170) cc_final: 0.8385 (t-170) REVERT: k 80 PHE cc_start: 0.5970 (m-80) cc_final: 0.5599 (m-80) REVERT: k 102 MET cc_start: 0.6167 (ptp) cc_final: 0.5033 (mmm) REVERT: k 104 LYS cc_start: 0.4702 (tptp) cc_final: 0.4004 (pttp) REVERT: l 23 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6195 (mm) REVERT: l 68 ASN cc_start: 0.8532 (t0) cc_final: 0.7954 (t0) REVERT: l 78 ARG cc_start: 0.4077 (ttt180) cc_final: 0.3433 (mmt180) REVERT: l 90 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6649 (pm20) REVERT: l 139 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6673 (mt-10) REVERT: m 60 GLU cc_start: 0.7354 (tt0) cc_final: 0.6581 (tm-30) REVERT: m 83 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8353 (tp) REVERT: n 59 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5735 (tm-30) REVERT: n 130 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.3067 (ppt90) REVERT: o 8 ILE cc_start: 0.6570 (mt) cc_final: 0.6125 (pt) REVERT: o 17 LEU cc_start: 0.7512 (tp) cc_final: 0.7013 (tp) REVERT: o 25 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.5951 (mm) REVERT: o 62 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7963 (mtt90) REVERT: p 126 LYS cc_start: 0.7962 (tptt) cc_final: 0.7556 (mtmt) REVERT: q 30 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8191 (mttm) REVERT: q 70 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7406 (mt-10) REVERT: q 76 GLU cc_start: 0.8238 (mp0) cc_final: 0.7923 (tt0) REVERT: q 81 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8320 (mp) REVERT: r 3 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7887 (mmm160) REVERT: r 75 MET cc_start: 0.7455 (tpp) cc_final: 0.7160 (mtp) REVERT: r 98 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7575 (ttm-80) REVERT: t 39 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8066 (mp) REVERT: u 76 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7522 (ttmt) REVERT: v 26 GLU cc_start: 0.7534 (tp30) cc_final: 0.7172 (mm-30) REVERT: w 12 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6146 (mmp-170) REVERT: w 30 LYS cc_start: 0.8024 (tttt) cc_final: 0.7526 (ttpp) REVERT: w 66 SER cc_start: 0.8649 (m) cc_final: 0.8318 (t) REVERT: x 44 MET cc_start: 0.7584 (mtp) cc_final: 0.7362 (mmm) REVERT: x 66 MET cc_start: 0.8221 (mtt) cc_final: 0.7814 (mtt) REVERT: y 24 ARG cc_start: 0.8171 (mmp80) cc_final: 0.7456 (mtt180) REVERT: y 33 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7594 (mptt) REVERT: y 54 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7292 (ppp) REVERT: z 21 ARG cc_start: 0.4832 (tpt170) cc_final: 0.3979 (tpt170) REVERT: z 36 GLU cc_start: 0.8323 (tt0) cc_final: 0.7931 (tp30) outliers start: 347 outliers final: 276 residues processed: 1198 average time/residue: 1.4754 time to fit residues: 3039.8062 Evaluate side-chains 1271 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 952 time to evaluate : 6.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 24 LEU Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 41 GLU Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 182 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 199 VAL Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 223 VAL Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 240 LEU Chi-restraints excluded: chain 7 residue 242 ILE Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 271 ILE Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 354 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 39 LYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 11 CYS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 190 ASN Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 161 GLU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 49 SER Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 149 SER Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 30 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 77 HIS Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 98 ARG Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain v residue 78 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 957 optimal weight: 0.7980 chunk 631 optimal weight: 0.5980 chunk 1016 optimal weight: 5.9990 chunk 620 optimal weight: 10.0000 chunk 482 optimal weight: 1.9990 chunk 706 optimal weight: 7.9990 chunk 1065 optimal weight: 0.9990 chunk 981 optimal weight: 3.9990 chunk 848 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 655 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 337 HIS E 127 ASN G 66 ASN K 29 HIS N 107 ASN S 15 GLN V 49 ASN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 190 ASN h 3 GLN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN u 63 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 161626 Z= 0.146 Angle : 0.613 15.927 241162 Z= 0.327 Chirality : 0.033 0.498 30627 Planarity : 0.006 0.124 13343 Dihedral : 23.168 179.704 79434 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 5.07 % Allowed : 25.59 % Favored : 69.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 6207 helix: 1.69 (0.11), residues: 2223 sheet: -0.71 (0.15), residues: 1123 loop : -1.24 (0.11), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP k 42 HIS 0.007 0.001 HIS J 47 PHE 0.028 0.001 PHE k 8 TYR 0.018 0.001 TYR k 4 ARG 0.011 0.001 ARG v 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12414 Ramachandran restraints generated. 6207 Oldfield, 0 Emsley, 6207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 953 time to evaluate : 6.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 27 GLN cc_start: 0.6687 (tt0) cc_final: 0.5849 (pt0) REVERT: 7 30 PHE cc_start: 0.1314 (OUTLIER) cc_final: 0.0905 (t80) REVERT: 7 43 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.4225 (tm-30) REVERT: 7 149 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6966 (tt) REVERT: 7 190 TYR cc_start: 0.7265 (t80) cc_final: 0.6862 (t80) REVERT: 7 239 GLU cc_start: 0.5791 (mm-30) cc_final: 0.5576 (mm-30) REVERT: 7 336 ASP cc_start: 0.7925 (t0) cc_final: 0.7661 (t0) REVERT: 7 338 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.5108 (ptt-90) REVERT: B 35 GLU cc_start: 0.8238 (tt0) cc_final: 0.7739 (tp30) REVERT: B 146 MET cc_start: 0.8292 (mmm) cc_final: 0.7919 (mmm) REVERT: B 183 LYS cc_start: 0.8389 (tttt) cc_final: 0.8159 (mtpp) REVERT: D 12 LEU cc_start: 0.6507 (tp) cc_final: 0.6272 (tp) REVERT: D 168 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: D 195 GLN cc_start: 0.7892 (mt0) cc_final: 0.7632 (tp40) REVERT: E 7 TYR cc_start: 0.8325 (t80) cc_final: 0.7869 (t80) REVERT: E 133 ARG cc_start: 0.6898 (mpt-90) cc_final: 0.6569 (mpt180) REVERT: E 140 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5364 (mm-30) REVERT: E 150 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.4129 (mtt180) REVERT: E 167 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5627 (tmt170) REVERT: F 141 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7188 (pp) REVERT: G 41 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4466 (pttp) REVERT: G 114 GLU cc_start: 0.4098 (OUTLIER) cc_final: 0.3505 (pp20) REVERT: J 13 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7919 (mtt90) REVERT: J 23 LYS cc_start: 0.8173 (tptp) cc_final: 0.7960 (tptm) REVERT: J 32 LEU cc_start: 0.8384 (mt) cc_final: 0.8153 (mt) REVERT: J 75 TYR cc_start: 0.8810 (m-80) cc_final: 0.8348 (m-80) REVERT: J 95 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7395 (mtp85) REVERT: J 98 GLU cc_start: 0.8593 (mp0) cc_final: 0.8238 (mt-10) REVERT: J 136 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: K 8 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7541 (pp) REVERT: K 53 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7462 (mmtt) REVERT: L 91 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7257 (t0) REVERT: M 17 ASN cc_start: 0.8799 (t0) cc_final: 0.8494 (t0) REVERT: N 30 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7495 (mtp85) REVERT: O 9 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6092 (ptt90) REVERT: O 13 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7808 (ttm170) REVERT: O 80 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7154 (mm-30) REVERT: O 88 LYS cc_start: 0.6388 (tttt) cc_final: 0.5733 (mmtt) REVERT: P 16 ASP cc_start: 0.5070 (OUTLIER) cc_final: 0.4663 (p0) REVERT: P 112 GLU cc_start: 0.8384 (pt0) cc_final: 0.7964 (tp30) REVERT: Q 84 LYS cc_start: 0.6770 (mmtt) cc_final: 0.6481 (tttm) REVERT: R 37 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8324 (mt-10) REVERT: R 43 ASN cc_start: 0.6180 (t0) cc_final: 0.5699 (p0) REVERT: S 66 ILE cc_start: 0.8364 (mm) cc_final: 0.7833 (tt) REVERT: S 78 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7431 (mm-30) REVERT: S 95 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.7975 (ttm110) REVERT: T 9 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7772 (mttt) REVERT: T 33 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6968 (mtmt) REVERT: T 69 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.6676 (mmt180) REVERT: U 10 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: U 62 GLU cc_start: 0.7278 (pm20) cc_final: 0.6985 (pm20) REVERT: W 78 LYS cc_start: 0.8654 (mptt) cc_final: 0.7755 (mmtt) REVERT: W 82 ILE cc_start: 0.8447 (mm) cc_final: 0.8090 (mm) REVERT: W 83 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: Y 20 ASN cc_start: 0.7868 (m-40) cc_final: 0.7623 (m-40) REVERT: Z 45 ARG cc_start: 0.7962 (mmt90) cc_final: 0.7613 (mmt90) REVERT: a 22 MET cc_start: 0.7212 (ptp) cc_final: 0.6747 (pmm) REVERT: b 32 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6048 (mtmm) REVERT: c 53 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7007 (tptp) REVERT: d 1 MET cc_start: 0.8226 (mtm) cc_final: 0.7945 (mmm) REVERT: f 30 GLU cc_start: 0.8383 (tp30) cc_final: 0.6746 (mm-30) REVERT: g 27 MET cc_start: 0.6118 (ttt) cc_final: 0.5826 (mtp) REVERT: g 28 LYS cc_start: 0.6809 (tttt) cc_final: 0.6184 (ptmm) REVERT: g 64 LYS cc_start: 0.7339 (mttp) cc_final: 0.7109 (ptmt) REVERT: g 132 LYS cc_start: 0.2774 (OUTLIER) cc_final: 0.2476 (mmtp) REVERT: h 54 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6779 (mtp85) REVERT: h 136 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7135 (ptm-80) REVERT: h 144 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5930 (mt) REVERT: h 175 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7922 (mm) REVERT: h 178 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8951 (mt) REVERT: h 179 ARG cc_start: 0.7663 (ptp90) cc_final: 0.7416 (ptp90) REVERT: h 206 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7292 (mt-10) REVERT: i 95 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: i 105 MET cc_start: 0.8138 (mtt) cc_final: 0.7933 (mtt) REVERT: i 116 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: i 121 LYS cc_start: 0.7904 (mttt) cc_final: 0.7186 (mtpt) REVERT: i 124 MET cc_start: 0.7575 (mtt) cc_final: 0.7090 (ttp) REVERT: i 128 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.7099 (mtp-110) REVERT: j 151 GLU cc_start: 0.8014 (mp0) cc_final: 0.7622 (mp0) REVERT: k 9 MET cc_start: 0.7578 (mtp) cc_final: 0.6918 (mtm) REVERT: k 58 HIS cc_start: 0.8790 (t-170) cc_final: 0.8294 (t-170) REVERT: k 80 PHE cc_start: 0.5933 (m-80) cc_final: 0.5559 (m-80) REVERT: k 102 MET cc_start: 0.5993 (ptp) cc_final: 0.4990 (mmm) REVERT: k 104 LYS cc_start: 0.4836 (tptp) cc_final: 0.3985 (pttp) REVERT: l 23 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.5972 (mm) REVERT: l 68 ASN cc_start: 0.8466 (t0) cc_final: 0.7892 (t0) REVERT: l 78 ARG cc_start: 0.3967 (ttt180) cc_final: 0.3331 (mmt180) REVERT: l 139 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6602 (mt-10) REVERT: m 60 GLU cc_start: 0.7490 (tt0) cc_final: 0.6610 (tm-30) REVERT: m 83 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8298 (tp) REVERT: n 57 MET cc_start: 0.7214 (mtp) cc_final: 0.6724 (mmm) REVERT: n 59 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5437 (tm-30) REVERT: n 60 LYS cc_start: 0.5906 (mptt) cc_final: 0.5591 (mptt) REVERT: n 130 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.3056 (ppt90) REVERT: o 17 LEU cc_start: 0.7519 (tp) cc_final: 0.7015 (tp) REVERT: o 25 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.5721 (mm) REVERT: o 62 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7954 (mtt90) REVERT: p 101 ASN cc_start: 0.5735 (t0) cc_final: 0.5533 (p0) REVERT: p 126 LYS cc_start: 0.7829 (tptt) cc_final: 0.7444 (mtmt) REVERT: q 70 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7411 (mt-10) REVERT: q 76 GLU cc_start: 0.8185 (mp0) cc_final: 0.7880 (tt0) REVERT: q 81 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8301 (mp) REVERT: r 3 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7872 (mmm160) REVERT: s 89 MET cc_start: 0.8849 (mmt) cc_final: 0.8463 (mmp) REVERT: t 39 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8015 (mp) REVERT: u 76 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7449 (ttmm) REVERT: v 26 GLU cc_start: 0.7570 (tp30) cc_final: 0.7206 (mm-30) REVERT: v 38 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7605 (tp) REVERT: v 49 GLU cc_start: 0.6310 (tt0) cc_final: 0.5355 (pm20) REVERT: w 12 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6202 (mmp-170) REVERT: w 30 LYS cc_start: 0.7928 (tttt) cc_final: 0.7445 (ttpp) REVERT: w 66 SER cc_start: 0.8569 (m) cc_final: 0.8202 (t) REVERT: x 44 MET cc_start: 0.7544 (mtp) cc_final: 0.7309 (mmm) REVERT: x 66 MET cc_start: 0.8163 (mtt) cc_final: 0.7814 (mtt) REVERT: y 24 ARG cc_start: 0.8130 (mmp80) cc_final: 0.7423 (mtt180) REVERT: y 33 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7550 (mptt) REVERT: z 21 ARG cc_start: 0.4684 (tpt170) cc_final: 0.3872 (tpt170) REVERT: z 36 GLU cc_start: 0.8273 (tt0) cc_final: 0.7960 (tp30) outliers start: 262 outliers final: 187 residues processed: 1135 average time/residue: 1.3768 time to fit residues: 2677.9581 Evaluate side-chains 1155 residues out of total 5167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 927 time to evaluate : 6.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 30 PHE Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 41 GLU Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 74 THR Chi-restraints excluded: chain 7 residue 111 LEU Chi-restraints excluded: chain 7 residue 130 ILE Chi-restraints excluded: chain 7 residue 149 LEU Chi-restraints excluded: chain 7 residue 160 GLN Chi-restraints excluded: chain 7 residue 177 ILE Chi-restraints excluded: chain 7 residue 183 LEU Chi-restraints excluded: chain 7 residue 199 VAL Chi-restraints excluded: chain 7 residue 211 SER Chi-restraints excluded: chain 7 residue 222 GLU Chi-restraints excluded: chain 7 residue 223 VAL Chi-restraints excluded: chain 7 residue 227 VAL Chi-restraints excluded: chain 7 residue 265 VAL Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 324 ILE Chi-restraints excluded: chain 7 residue 330 ASP Chi-restraints excluded: chain 7 residue 331 LYS Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 338 ARG Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 175 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 11 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 136 LYS Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 82 LEU Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 77 HIS Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 39 LEU Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 76 LYS Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain v residue 78 VAL Chi-restraints excluded: chain w residue 12 ARG Chi-restraints excluded: chain w residue 28 THR Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 81 ARG Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 520 optimal weight: 4.9990 chunk 674 optimal weight: 1.9990 chunk 904 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 782 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 850 optimal weight: 0.0970 chunk 355 optimal weight: 10.0000 chunk 873 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN N 107 ASN b 5 GLN ** g 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 190 ASN j 19 ASN j 73 ASN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN u 63 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.156737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.125706 restraints weight = 210682.396| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 0.90 r_work: 0.3118 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 161626 Z= 0.303 Angle : 0.690 14.833 241162 Z= 0.359 Chirality : 0.037 0.381 30627 Planarity : 0.006 0.134 13343 Dihedral : 23.149 179.565 79421 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 5.34 % Allowed : 25.59 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 6207 helix: 1.46 (0.11), residues: 2212 sheet: -0.86 (0.15), residues: 1122 loop : -1.33 (0.11), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP k 42 HIS 0.006 0.001 HIS B 230 PHE 0.028 0.002 PHE k 8 TYR 0.020 0.002 TYR 7 333 ARG 0.012 0.001 ARG v 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44291.44 seconds wall clock time: 771 minutes 9.44 seconds (46269.44 seconds total)