Starting phenix.real_space_refine on Tue Mar 26 02:33:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdw_3490/03_2024/5mdw_3490_updated.pdb" } resolution = 3.06 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= 0.025 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 438 5.21 5 S 170 5.16 5 C 75473 2.51 5 N 27762 2.21 5 O 41124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 ARG 26": "NH1" <-> "NH2" Residue "7 GLU 36": "OE1" <-> "OE2" Residue "7 GLU 40": "OE1" <-> "OE2" Residue "7 GLU 49": "OE1" <-> "OE2" Residue "7 GLU 51": "OE1" <-> "OE2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 GLU 85": "OE1" <-> "OE2" Residue "7 GLU 89": "OE1" <-> "OE2" Residue "7 GLU 94": "OE1" <-> "OE2" Residue "7 GLU 98": "OE1" <-> "OE2" Residue "7 GLU 102": "OE1" <-> "OE2" Residue "7 GLU 107": "OE1" <-> "OE2" Residue "7 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 122": "OE1" <-> "OE2" Residue "7 ARG 150": "NH1" <-> "NH2" Residue "7 GLU 157": "OE1" <-> "OE2" Residue "7 ARG 159": "NH1" <-> "NH2" Residue "7 GLU 168": "OE1" <-> "OE2" Residue "7 GLU 170": "OE1" <-> "OE2" Residue "7 ARG 200": "NH1" <-> "NH2" Residue "7 ARG 203": "NH1" <-> "NH2" Residue "7 ARG 212": "NH1" <-> "NH2" Residue "7 ARG 213": "NH1" <-> "NH2" Residue "7 ARG 240": "NH1" <-> "NH2" Residue "7 GLU 299": "OE1" <-> "OE2" Residue "7 GLU 358": "OE1" <-> "OE2" 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 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 2": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D ARG 21": "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 GLU 155": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" 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 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 "F GLU 173": "OE1" <-> "OE2" 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 87": "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 "I GLU 129": "OE1" <-> "OE2" 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 106": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" 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 "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N GLU 49": "OE1" <-> "OE2" 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 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "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 ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 11": "OE1" <-> "OE2" 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 "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 34": "OE1" <-> "OE2" Residue "R GLU 37": "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 GLU 5": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 6": "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 GLU 83": "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 ARG 74": "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 "Z GLU 58": "OE1" <-> "OE2" Residue "Z GLU 59": "OE1" <-> "OE2" Residue "a GLU 10": "OE1" <-> "OE2" Residue "a GLU 11": "OE1" <-> "OE2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "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 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 "g ARG 225": "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 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 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 4": "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 "l GLU 146": "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 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 "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 "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 "t GLU 6": "OE1" <-> "OE2" Residue "t GLU 26": "OE1" <-> "OE2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 88": "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 "u GLU 77": "OE1" <-> "OE2" 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 "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 GLU 44": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z GLU 63": "OE1" <-> "OE2" Residue "z ARG 66": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149607 Number of models: 1 Model: "" Number of chains: 67 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': 162, 'rna3p': 16, 'rna3p_pur': 1380, 'rna3p_pyr': 1052} Link IDs: {'rna2p': 454, 'rna3p': 2448} 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': 116, 'rna2p_pyr': 87, 'rna3p': 10, 'rna3p_pur': 753, 'rna3p_pyr': 566} Link IDs: {'rna2p': 203, 'rna3p': 1330} 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': 4, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 33, 'rna3p_pyr': 27} Link IDs: {'p': 1, 'rna2p': 12, 'rna3p': 62} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 261 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "7" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2706 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "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: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 295 Unusual residues: {' MG': 295} Classifications: {'undetermined': 295} Link IDs: {None: 294} Chain: "2" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Unusual residues: {' MG': 133} Classifications: {'undetermined': 133} Link IDs: {None: 132} Chain: "3" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "5" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0N2W SG CYS f 11 182.257 135.326 117.506 1.00 75.93 S ATOM A0N3L SG CYS f 14 180.666 132.318 117.306 1.00 78.17 S ATOM A0N6G SG CYS f 27 182.846 132.704 120.651 1.00 78.67 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13146 " occ=0.50 Time building chain proxies: 57.17, per 1000 atoms: 0.38 Number of scatterers: 149607 At special positions: 0 Unit cell: (246.48, 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 170 16.00 P 4638 15.00 Mg 438 11.99 O 41124 8.00 N 27762 7.00 C 75473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS a 16 " - pdb=" SG CYS a 18 " distance=1.78 Simple disulfide: pdb=" SG CYS a 16 " - pdb=" SG CYS a 37 " distance=2.39 Simple disulfide: pdb=" SG CYS a 16 " - pdb=" SG CYS a 40 " distance=1.89 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=1.89 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 40 " distance=2.37 Simple disulfide: pdb=" SG CYS a 37 " - pdb=" SG CYS a 40 " distance=1.77 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: 63.23 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " Number of angles added : 3 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11672 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: 199 helices and 73 sheets defined 41.1% alpha, 19.0% beta 1544 base pairs and 2366 stacking pairs defined. Time for finding SS restraints: 77.95 Creating SS restraints... Processing helix chain '6' and resid 15 through 22 removed outlier: 3.669A pdb=" N LEU 6 19 " --> pdb=" O ALA 6 15 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 26 removed outlier: 3.726A pdb=" N GLN 7 12 " --> pdb=" O ASN 7 8 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 44 Proline residue: 7 44 - end of helix Processing helix chain '7' and resid 45 through 50 removed outlier: 4.427A pdb=" N GLU 7 49 " --> pdb=" O ASP 7 45 " (cutoff:3.500A) Proline residue: 7 50 - end of helix No H-bonds generated for 'chain '7' and resid 45 through 50' Processing helix chain '7' and resid 51 through 91 removed outlier: 3.782A pdb=" N SER 7 62 " --> pdb=" O LYS 7 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP 7 91 " --> pdb=" O ALA 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 92 through 120 removed outlier: 3.574A pdb=" N PHE 7 96 " --> pdb=" O ASP 7 92 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU 7 103 " --> pdb=" O ALA 7 99 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP 7 104 " --> pdb=" O VAL 7 100 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA 7 105 " --> pdb=" O ALA 7 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU 7 106 " --> pdb=" O GLU 7 102 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER 7 120 " --> pdb=" O ARG 7 116 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 160 Processing helix chain '7' and resid 187 through 196 removed outlier: 5.299A pdb=" N THR 7 194 " --> pdb=" O GLY 7 190 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU 7 195 " --> pdb=" O TRP 7 191 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR 7 196 " --> pdb=" O LEU 7 192 " (cutoff:3.500A) Processing helix chain '7' and resid 235 through 240 removed outlier: 5.330A pdb=" N ARG 7 240 " --> pdb=" O PRO 7 236 " (cutoff:3.500A) Processing helix chain '7' and resid 279 through 308 removed outlier: 3.606A pdb=" N ASN 7 283 " --> pdb=" O SER 7 279 " (cutoff:3.500A) Processing helix chain '7' and resid 344 through 351 Processing helix chain '7' and resid 353 through 364 Processing helix chain 'B' and resid 10 through 17 removed outlier: 7.293A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.579A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.471A 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: 3.784A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.730A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.137A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.376A 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: 3.996A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.928A 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 97 through 103 removed outlier: 4.891A pdb=" N PHE C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.322A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 6.448A 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: 4.348A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 5.632A 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: 5.129A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 46 removed outlier: 4.860A pdb=" N ILE E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.542A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.744A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.702A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.845A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.812A 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: 3.673A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.187A 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 29 through 34 Processing helix chain 'G' and resid 40 through 50 removed outlier: 3.946A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 73 removed outlier: 4.010A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 4.428A 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: 3.599A pdb=" N ASP H 7 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA H 22 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.767A pdb=" N LYS H 37 " --> pdb=" O VAL H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 Proline residue: H 68 - end of helix removed outlier: 4.253A pdb=" N CYS H 71 " --> pdb=" O THR H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 removed outlier: 4.236A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.716A 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: 4.063A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 5.015A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 48 removed outlier: 3.923A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.445A 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 117 removed outlier: 3.645A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N THR I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.858A 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: 4.070A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.671A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.593A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 104 through 109 removed outlier: 3.912A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 4.028A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.514A 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: 4.157A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.902A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.933A 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 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.277A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.755A 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 37 through 58 removed outlier: 4.154A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.305A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.284A 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: 4.610A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.340A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.147A 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 14 removed outlier: 3.983A pdb=" N LYS P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.532A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.674A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.610A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 73 removed outlier: 3.736A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.560A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.595A 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: 4.195A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.646A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.935A 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: 3.682A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.938A 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: 3.551A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.549A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.742A 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 9 removed outlier: 4.009A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.061A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.657A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (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 46 through 52 removed outlier: 4.139A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA a 52 " --> pdb=" O GLN a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 64 removed outlier: 3.580A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.712A 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 25 removed outlier: 3.804A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.535A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.002A 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 54 through 63 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: 4.034A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix removed outlier: 5.652A 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: 3.646A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.296A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 3.515A pdb=" N VAL g 107 " --> pdb=" O ASN g 103 " (cutoff:3.500A) removed outlier: 3.869A 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 removed outlier: 3.512A pdb=" N VAL g 217 " --> pdb=" O TYR g 213 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.856A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 3.599A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 3.780A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.497A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.522A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.476A 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: 4.206A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.653A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.505A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.003A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 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: 4.407A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.776A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.852A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 4.995A 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: 3.591A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.270A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.124A 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: 5.575A 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: 3.665A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.293A 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: 3.726A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 Processing helix chain 'l' and resid 20 through 31 Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.766A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.612A pdb=" N ALA l 61 " --> pdb=" O SER l 57 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.650A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.674A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.622A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) 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: 4.317A 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: 3.563A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.974A 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: 3.889A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.985A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.887A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.891A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.705A 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: 3.675A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 4.156A 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: 3.545A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.614A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.114A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.548A 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 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: 3.915A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.726A 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: 3.629A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU w 16 " --> pdb=" O ARG w 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.637A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 5.161A 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: 3.622A 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: 4.298A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.078A 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 removed outlier: 3.517A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) 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 removed outlier: 3.715A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.636A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 68 removed outlier: 3.838A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '7' and resid 161 through 166 removed outlier: 6.566A pdb=" N THR 7 180 " --> pdb=" O ILE 7 166 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LYS 7 177 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS 7 128 " --> pdb=" O ILE 7 183 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP 7 127 " --> pdb=" O GLU 7 225 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE 7 217 " --> pdb=" O GLY 7 135 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG 7 324 " --> pdb=" O VAL 7 198 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL 7 340 " --> pdb=" O ASP 7 335 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '7' and resid 241 through 244 removed outlier: 3.518A pdb=" N TYR 7 244 " --> pdb=" O ALA 7 260 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA 7 260 " --> pdb=" O TYR 7 244 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '7' and resid 167 through 170 Processing sheet with id= 4, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.748A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.359A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.285A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 3 through 9 removed outlier: 4.259A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 13.379A pdb=" N GLY C 198 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N LYS C 114 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.753A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.658A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.436A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 1 through 5 removed outlier: 4.445A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 117 through 120 Processing sheet with id= 13, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.559A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 15, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 16, first strand: chain 'F' and resid 94 through 99 removed outlier: 3.638A pdb=" N VAL F 102 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN F 101 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.743A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS F 86 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG F 163 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL F 90 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 17 through 21 removed outlier: 5.105A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.454A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.977A pdb=" N LEU H 23 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL H 27 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.519A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.356A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 5 through 9 removed outlier: 3.891A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.957A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.646A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 30 through 36 removed outlier: 8.065A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 33 through 36 removed outlier: 4.909A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.722A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.673A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER P 85 " --> pdb=" O GLU P 27 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 49 through 52 removed outlier: 7.644A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.614A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.431A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 35, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.319A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.833A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.540A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.396A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 40 through 45 removed outlier: 4.705A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 82 through 86 removed outlier: 7.253A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.699A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.419A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 44, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.729A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 46, first strand: chain 'Z' and resid 33 through 39 removed outlier: 3.993A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.023A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU a 32 " --> pdb=" O THR a 13 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.598A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 20 through 26 removed outlier: 6.945A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.449A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 14 through 19 Processing sheet with id= 52, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.346A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 89 through 92 Processing sheet with id= 54, first strand: chain 'h' and resid 54 through 59 Processing sheet with id= 55, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.335A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.762A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.831A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 83 through 88 removed outlier: 7.309A pdb=" N HIS j 83 " --> pdb=" O PRO j 98 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 33 through 41 removed outlier: 7.051A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.564A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL k 7 " --> pdb=" O MET k 88 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 43 through 46 Processing sheet with id= 62, first strand: chain 'l' and resid 73 through 79 removed outlier: 6.286A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.277A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.662A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 66, first strand: chain 'o' and resid 42 through 52 removed outlier: 5.141A pdb=" N LEU o 71 " --> pdb=" O PRO o 43 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 42 through 45 removed outlier: 3.509A pdb=" N GLY p 19 " --> pdb=" O ASN p 81 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 29 through 32 removed outlier: 4.932A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.073A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'u' and resid 4 through 10 removed outlier: 3.864A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.861A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'x' and resid 30 through 34 removed outlier: 4.825A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 2236 hydrogen bonds defined for protein. 6597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3888 hydrogen bonds 6156 hydrogen bond angles 0 basepair planarities 1544 basepair parallelities 2366 stacking parallelities Total time for adding SS restraints: 279.09 Time building geometry restraints manager: 68.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.45: 89233 1.45 - 1.73: 72242 1.73 - 2.00: 301 2.00 - 2.28: 0 2.28 - 2.55: 1 Bond restraints: 161777 Sorted by residual: bond pdb=" O3' C 12196 " pdb=" P U 12197 " ideal model delta sigma weight residual 1.607 2.554 -0.947 1.50e-02 4.44e+03 3.98e+03 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.442 0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.443 0.359 2.00e-02 2.50e+03 3.22e+02 bond pdb=" C4 5MU 5 54 " pdb=" C5 5MU 5 54 " ideal model delta sigma weight residual 1.802 1.444 0.358 2.00e-02 2.50e+03 3.20e+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 161772 not shown) Histogram of bond angle deviations from ideal: 73.12 - 87.92: 5 87.92 - 102.71: 10301 102.71 - 117.51: 139366 117.51 - 132.30: 91371 132.30 - 147.10: 320 Bond angle restraints: 241363 Sorted by residual: angle pdb=" O3' C 12196 " pdb=" P U 12197 " pdb=" O5' U 12197 " ideal model delta sigma weight residual 104.00 79.69 24.31 1.50e+00 4.44e-01 2.63e+02 angle pdb=" O5' 3TD 11915 " pdb=" C5' 3TD 11915 " pdb=" C4' 3TD 11915 " ideal model delta sigma weight residual 111.50 135.17 -23.67 1.50e+00 4.44e-01 2.49e+02 angle pdb=" C3' G7M 12069 " pdb=" C2' G7M 12069 " pdb=" O2' G7M 12069 " ideal model delta sigma weight residual 110.70 133.26 -22.56 1.50e+00 4.44e-01 2.26e+02 angle pdb=" C4' C 11914 " pdb=" C3' C 11914 " pdb=" O3' C 11914 " ideal model delta sigma weight residual 113.00 134.97 -21.97 1.50e+00 4.44e-01 2.14e+02 angle pdb=" C3' 2MA 12503 " pdb=" C2' 2MA 12503 " pdb=" C1' 2MA 12503 " ideal model delta sigma weight residual 101.50 87.69 13.81 1.00e+00 1.00e+00 1.91e+02 ... (remaining 241358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 90677 35.91 - 71.81: 11481 71.81 - 107.72: 1196 107.72 - 143.62: 26 143.62 - 179.53: 39 Dihedral angle restraints: 103419 sinusoidal: 85331 harmonic: 18088 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 82.17 64.83 1 8.00e+00 1.56e-02 8.62e+01 dihedral pdb=" C5' A 12225 " pdb=" C4' A 12225 " pdb=" C3' A 12225 " pdb=" O3' A 12225 " ideal model delta sinusoidal sigma weight residual 147.00 83.41 63.59 1 8.00e+00 1.56e-02 8.33e+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 41.29 158.71 1 1.50e+01 4.44e-03 8.24e+01 ... (remaining 103416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 30550 0.329 - 0.658: 73 0.658 - 0.987: 13 0.987 - 1.316: 5 1.316 - 1.645: 9 Chirality restraints: 30650 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 -1.11 -1.64 2.00e-01 2.50e+01 6.76e+01 chirality pdb=" C2* PSU 12580 " pdb=" C3* PSU 12580 " pdb=" O2* PSU 12580 " pdb=" C1* PSU 12580 " both_signs ideal model delta sigma weight residual False -2.75 -1.13 -1.62 2.00e-01 2.50e+01 6.57e+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 6.32e+01 ... (remaining 30647 not shown) Planarity restraints: 13379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " 0.139 2.00e-02 2.50e+03 7.79e-01 1.36e+04 pdb=" C4' 7MG 2 527 " 0.524 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.597 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.501 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.912 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " 0.029 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 1.387 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.076 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -1.338 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.008 2.00e-02 2.50e+03 6.31e-01 8.97e+03 pdb=" C4' 2MG 21207 " -0.466 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " -0.710 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " 0.625 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " 0.652 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " 0.192 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " -1.032 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " -0.217 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " 0.949 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' H2U 5 20 " -1.091 2.00e-02 2.50e+03 6.23e-01 8.74e+03 pdb=" C4' H2U 5 20 " 0.137 2.00e-02 2.50e+03 pdb=" O4' H2U 5 20 " 0.630 2.00e-02 2.50e+03 pdb=" C3' H2U 5 20 " 0.012 2.00e-02 2.50e+03 pdb=" O3' H2U 5 20 " 0.836 2.00e-02 2.50e+03 pdb=" C2' H2U 5 20 " -0.411 2.00e-02 2.50e+03 pdb=" O2' H2U 5 20 " -0.829 2.00e-02 2.50e+03 pdb=" C1' H2U 5 20 " 0.556 2.00e-02 2.50e+03 pdb=" N1 H2U 5 20 " 0.161 2.00e-02 2.50e+03 ... (remaining 13376 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 145 2.15 - 2.84: 42003 2.84 - 3.53: 217084 3.53 - 4.21: 491078 4.21 - 4.90: 645946 Nonbonded interactions: 1396256 Sorted by model distance: nonbonded pdb=" O4 U 11082 " pdb=" N1 A 11086 " model vdw 1.464 2.496 nonbonded pdb=" N1 A 12013 " pdb=" O4 U 12613 " model vdw 1.471 2.496 nonbonded pdb=" O4 U 11019 " pdb=" N1 A 11142 " model vdw 1.505 2.496 nonbonded pdb=" O4 U 2 827 " pdb=" N1 A 2 872 " model vdw 1.589 2.496 nonbonded pdb=" O4 U 21358 " pdb=" N1 A 21363 " model vdw 1.591 2.496 ... (remaining 1396251 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: 3.530 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: 0.140 Extract box with map and model: 17.710 Check model and map are aligned: 1.600 Set scattering table: 1.000 Process input model: 603.020 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 632.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.947 161777 Z= 0.549 Angle : 1.333 39.099 241363 Z= 0.892 Chirality : 0.106 1.645 30650 Planarity : 0.021 0.779 13379 Dihedral : 23.726 179.527 91729 Min Nonbonded Distance : 1.464 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.62 % Favored : 93.90 % Rotamer: Outliers : 7.69 % Allowed : 11.41 % Favored : 80.91 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 1.45 % 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: -1.97 (0.09), residues: 6232 helix: 0.11 (0.08), residues: 2215 sheet: -2.20 (0.13), residues: 1137 loop : -2.04 (0.10), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP Q 61 HIS 0.017 0.002 HIS J 47 PHE 0.060 0.004 PHE Q 106 TYR 0.031 0.004 TYR B 161 ARG 0.027 0.002 ARG Q 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1955 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 1556 time to evaluate : 6.467 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: 7 73 MET cc_start: 0.3779 (mmm) cc_final: 0.3356 (mmm) REVERT: 7 102 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4561 (tp30) REVERT: 7 123 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: 7 149 GLU cc_start: 0.8254 (tt0) cc_final: 0.7910 (tm-30) REVERT: 7 159 ARG cc_start: 0.6543 (mmm160) cc_final: 0.6221 (mmm-85) REVERT: 7 167 GLU cc_start: 0.7705 (tt0) cc_final: 0.7052 (tt0) REVERT: 7 168 GLU cc_start: 0.8250 (tt0) cc_final: 0.7048 (pm20) REVERT: 7 177 LYS cc_start: 0.8208 (tttt) cc_final: 0.7981 (tttm) REVERT: 7 180 THR cc_start: 0.7999 (m) cc_final: 0.7589 (p) REVERT: 7 218 SER cc_start: 0.8920 (t) cc_final: 0.8644 (m) REVERT: 7 225 GLU cc_start: 0.6283 (mt-10) cc_final: 0.5431 (mt-10) REVERT: 7 238 ASP cc_start: 0.6398 (m-30) cc_final: 0.5804 (t0) REVERT: 7 262 ARG cc_start: 0.6857 (ttm110) cc_final: 0.6454 (ttt180) REVERT: 7 264 THR cc_start: 0.8014 (m) cc_final: 0.7049 (p) REVERT: 7 342 THR cc_start: 0.7758 (t) cc_final: 0.7370 (p) REVERT: 7 343 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7556 (mpt180) REVERT: 7 346 GLN cc_start: 0.7955 (tp40) cc_final: 0.7642 (pt0) REVERT: 7 360 SER cc_start: 0.8724 (t) cc_final: 0.8294 (p) REVERT: 7 362 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6560 (tppp) REVERT: B 66 ASP cc_start: 0.8846 (t0) cc_final: 0.8513 (t0) REVERT: B 146 MET cc_start: 0.8820 (mtt) cc_final: 0.8510 (mtp) REVERT: B 171 TYR cc_start: 0.8719 (m-80) cc_final: 0.8228 (m-80) REVERT: B 174 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8919 (mt) REVERT: B 183 LYS cc_start: 0.9035 (mttt) cc_final: 0.8590 (mmtt) REVERT: B 269 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8000 (ttt-90) REVERT: B 270 ARG cc_start: 0.8446 (mmm160) cc_final: 0.7784 (ttt-90) REVERT: C 11 MET cc_start: 0.9229 (mtp) cc_final: 0.8992 (mtp) REVERT: C 13 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8655 (ptm160) REVERT: C 42 ASN cc_start: 0.8167 (t0) cc_final: 0.7815 (t0) REVERT: C 43 ASP cc_start: 0.8526 (m-30) cc_final: 0.8274 (m-30) REVERT: C 99 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8346 (tm-30) REVERT: C 128 ARG cc_start: 0.8968 (mtt90) cc_final: 0.8164 (mmt180) REVERT: C 174 SER cc_start: 0.9554 (m) cc_final: 0.8967 (t) REVERT: D 22 ASP cc_start: 0.8795 (m-30) cc_final: 0.8504 (m-30) REVERT: D 40 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7265 (ttm-80) REVERT: D 44 ARG cc_start: 0.8393 (ptt-90) cc_final: 0.8097 (ptt90) REVERT: D 108 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8338 (mt) REVERT: D 144 GLU cc_start: 0.8195 (tt0) cc_final: 0.7962 (tt0) REVERT: D 145 ASP cc_start: 0.8789 (t0) cc_final: 0.8302 (t0) REVERT: D 163 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8654 (t0) REVERT: D 176 ASP cc_start: 0.7846 (p0) cc_final: 0.7561 (p0) REVERT: D 184 ASP cc_start: 0.8553 (m-30) cc_final: 0.8111 (m-30) REVERT: E 11 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7299 (mm-30) REVERT: E 122 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: E 142 ASP cc_start: 0.7360 (t70) cc_final: 0.6518 (t0) REVERT: E 164 GLU cc_start: 0.7582 (tt0) cc_final: 0.7285 (mp0) REVERT: F 32 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: F 45 HIS cc_start: 0.6142 (t-170) cc_final: 0.5859 (t-170) REVERT: F 95 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7762 (ptp90) REVERT: F 104 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7441 (t0) REVERT: F 130 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8068 (mt-10) REVERT: F 176 LYS cc_start: 0.5070 (OUTLIER) cc_final: 0.3909 (ttpp) REVERT: G 3 VAL cc_start: 0.8130 (p) cc_final: 0.7915 (m) REVERT: G 15 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7923 (tt) REVERT: H 38 MET cc_start: 0.4554 (mtm) cc_final: 0.4338 (tmm) REVERT: H 86 MET cc_start: 0.2188 (mmm) cc_final: 0.1793 (mmm) REVERT: H 117 LEU cc_start: 0.3288 (OUTLIER) cc_final: 0.2730 (mt) REVERT: J 7 LYS cc_start: 0.7650 (mttt) cc_final: 0.7365 (mttt) REVERT: J 9 GLU cc_start: 0.8213 (mp0) cc_final: 0.8005 (pm20) REVERT: J 12 LYS cc_start: 0.8238 (pttt) cc_final: 0.8029 (tptt) REVERT: J 85 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8109 (mmtt) REVERT: J 96 ARG cc_start: 0.8154 (ttt-90) cc_final: 0.7601 (ptm160) REVERT: J 108 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: J 129 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: K 51 LYS cc_start: 0.7773 (mttt) cc_final: 0.7250 (mppt) REVERT: K 66 LYS cc_start: 0.8872 (tttt) cc_final: 0.8625 (mtpp) REVERT: K 91 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7553 (t) REVERT: K 93 GLN cc_start: 0.8939 (pt0) cc_final: 0.8381 (pm20) REVERT: K 106 GLU cc_start: 0.8269 (mp0) cc_final: 0.7694 (mp0) REVERT: K 113 MET cc_start: 0.7812 (tpt) cc_final: 0.7469 (mmm) REVERT: L 69 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8184 (mtp-110) REVERT: L 76 GLU cc_start: 0.8607 (pt0) cc_final: 0.8377 (pt0) REVERT: L 115 GLU cc_start: 0.8579 (pt0) cc_final: 0.8068 (tp30) REVERT: M 17 ASN cc_start: 0.9291 (t0) cc_final: 0.9079 (t0) REVERT: M 18 ARG cc_start: 0.8755 (ptm-80) cc_final: 0.8551 (ptm160) REVERT: M 22 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8270 (mm-40) REVERT: M 40 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7596 (ptp-170) REVERT: M 58 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8344 (mmtp) REVERT: M 60 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7679 (mm-40) REVERT: N 6 SER cc_start: 0.9038 (t) cc_final: 0.8643 (p) REVERT: N 11 ASN cc_start: 0.9156 (m-40) cc_final: 0.8771 (m-40) REVERT: N 59 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8119 (p) REVERT: N 86 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7955 (mtp180) REVERT: N 106 ASP cc_start: 0.8973 (p0) cc_final: 0.8526 (p0) REVERT: N 117 ASP cc_start: 0.8387 (m-30) cc_final: 0.7928 (p0) REVERT: P 109 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8571 (mtm-85) REVERT: Q 72 ASN cc_start: 0.8692 (m-40) cc_final: 0.8431 (m110) REVERT: R 23 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8308 (mm-30) REVERT: R 34 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8152 (mt-10) REVERT: R 60 LYS cc_start: 0.8165 (mttt) cc_final: 0.7931 (mttm) REVERT: R 66 HIS cc_start: 0.8493 (m-70) cc_final: 0.8185 (m-70) REVERT: R 73 LYS cc_start: 0.8865 (mmtp) cc_final: 0.8644 (mtpp) REVERT: R 97 LYS cc_start: 0.8318 (tttt) cc_final: 0.8084 (ttpp) REVERT: S 28 LYS cc_start: 0.8388 (mttp) cc_final: 0.8146 (mmmt) REVERT: S 34 ASP cc_start: 0.8179 (m-30) cc_final: 0.7770 (m-30) REVERT: S 67 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7324 (p0) REVERT: T 1 MET cc_start: 0.4912 (OUTLIER) cc_final: 0.4679 (tpt) REVERT: T 33 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7737 (tttt) REVERT: T 61 LEU cc_start: 0.9034 (pp) cc_final: 0.8823 (pt) REVERT: T 69 ARG cc_start: 0.8430 (mtp85) cc_final: 0.7985 (mtp-110) REVERT: U 46 GLN cc_start: 0.8145 (mt0) cc_final: 0.7796 (tt0) REVERT: U 47 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8039 (mtpt) REVERT: U 62 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7172 (pt0) REVERT: U 81 ASP cc_start: 0.8736 (m-30) cc_final: 0.8481 (m-30) REVERT: U 88 GLU cc_start: 0.7305 (tt0) cc_final: 0.6747 (mm-30) REVERT: U 99 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7687 (p0) REVERT: U 102 THR cc_start: 0.9013 (m) cc_final: 0.8587 (t) REVERT: V 2 PHE cc_start: 0.7642 (m-80) cc_final: 0.7258 (m-80) REVERT: V 83 LYS cc_start: 0.8462 (mttt) cc_final: 0.8110 (mttt) REVERT: V 85 LYS cc_start: 0.8132 (mttt) cc_final: 0.7809 (mtpp) REVERT: V 90 ASP cc_start: 0.8598 (m-30) cc_final: 0.8270 (m-30) REVERT: W 11 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7652 (mtt-85) REVERT: W 38 VAL cc_start: 0.9312 (t) cc_final: 0.8939 (m) REVERT: W 39 ARG cc_start: 0.9164 (mtp-110) cc_final: 0.8650 (mtp85) REVERT: W 40 GLN cc_start: 0.9051 (pt0) cc_final: 0.8766 (pt0) REVERT: W 44 LYS cc_start: 0.8876 (tttt) cc_final: 0.8390 (tttm) REVERT: W 53 CYS cc_start: 0.9230 (t) cc_final: 0.8966 (t) REVERT: W 78 LYS cc_start: 0.8868 (mptt) cc_final: 0.8655 (mttp) REVERT: X 65 ASP cc_start: 0.8014 (m-30) cc_final: 0.7766 (m-30) REVERT: Y 5 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7505 (mp0) REVERT: Y 6 LEU cc_start: 0.8043 (mt) cc_final: 0.7405 (tp) REVERT: Y 49 ASP cc_start: 0.8432 (m-30) cc_final: 0.8190 (m-30) REVERT: Z 32 ILE cc_start: 0.9131 (pt) cc_final: 0.8818 (mt) REVERT: a 47 LYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4239 (mmtt) REVERT: a 61 ASN cc_start: 0.7592 (m-40) cc_final: 0.7037 (m110) REVERT: a 63 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6173 (ppt170) REVERT: b 40 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8078 (mmt180) REVERT: c 5 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7396 (mt) REVERT: c 48 ILE cc_start: 0.8368 (mt) cc_final: 0.8058 (mp) REVERT: c 49 TYR cc_start: 0.9278 (m-80) cc_final: 0.9032 (m-80) REVERT: d 3 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8503 (mmt-90) REVERT: e 19 LYS cc_start: 0.8721 (mttt) cc_final: 0.8443 (mtpt) REVERT: g 7 ARG cc_start: 0.6904 (mpp-170) cc_final: 0.6494 (ptm160) REVERT: g 27 MET cc_start: 0.8019 (mmm) cc_final: 0.7808 (mmm) REVERT: g 35 ARG cc_start: 0.7156 (mmt-90) cc_final: 0.6550 (mtp-110) REVERT: g 105 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7780 (mmtm) REVERT: g 132 LYS cc_start: 0.5035 (OUTLIER) cc_final: 0.4639 (ptpt) REVERT: g 135 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.5964 (tp) REVERT: g 136 MET cc_start: 0.6916 (mtp) cc_final: 0.6452 (mmt) REVERT: g 139 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.7174 (mtp85) REVERT: h 25 ASN cc_start: 0.8367 (m-40) cc_final: 0.7986 (m-40) REVERT: h 27 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7864 (tptp) REVERT: h 45 LYS cc_start: 0.8819 (tttt) cc_final: 0.8449 (tmtt) REVERT: h 58 GLU cc_start: 0.8016 (tt0) cc_final: 0.7642 (tt0) REVERT: h 89 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7507 (ttmt) REVERT: h 122 SER cc_start: 0.8191 (m) cc_final: 0.7903 (p) REVERT: h 154 SER cc_start: 0.9322 (m) cc_final: 0.9033 (t) REVERT: h 162 ILE cc_start: 0.9004 (mm) cc_final: 0.8802 (tt) REVERT: h 179 ARG cc_start: 0.8644 (ptt-90) cc_final: 0.8053 (ptt90) REVERT: h 196 ILE cc_start: 0.9149 (mt) cc_final: 0.8825 (mm) REVERT: i 33 LYS cc_start: 0.7555 (mttp) cc_final: 0.7234 (mmtt) REVERT: i 45 LYS cc_start: 0.8092 (mttm) cc_final: 0.7809 (tppt) REVERT: i 83 LYS cc_start: 0.8308 (mttp) cc_final: 0.7981 (mmtm) REVERT: i 124 MET cc_start: 0.8069 (mtt) cc_final: 0.7751 (mtm) REVERT: i 128 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7777 (mtt-85) REVERT: i 147 GLU cc_start: 0.7944 (tp30) cc_final: 0.7666 (tp30) REVERT: i 151 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7853 (ptmm) REVERT: i 166 GLU cc_start: 0.8274 (tt0) cc_final: 0.7724 (tp30) REVERT: i 185 LYS cc_start: 0.8773 (ptmm) cc_final: 0.8302 (mtpt) REVERT: i 187 GLU cc_start: 0.7387 (tt0) cc_final: 0.7142 (mm-30) REVERT: j 13 GLU cc_start: 0.8624 (pt0) cc_final: 0.8093 (pt0) REVERT: j 26 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8385 (ttmm) REVERT: j 45 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8161 (mmm160) REVERT: j 60 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7624 (mt) REVERT: j 68 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7958 (mtt90) REVERT: j 96 MET cc_start: 0.9174 (ptm) cc_final: 0.8968 (ptm) REVERT: j 115 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8605 (mt) REVERT: j 130 SER cc_start: 0.8763 (t) cc_final: 0.8363 (p) REVERT: k 36 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.7861 (mt) REVERT: k 56 LYS cc_start: 0.8360 (mttt) cc_final: 0.7986 (mmtt) REVERT: k 62 MET cc_start: 0.8184 (ttp) cc_final: 0.7976 (mtm) REVERT: l 17 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8238 (ttmt) REVERT: l 18 PHE cc_start: 0.7633 (m-80) cc_final: 0.7081 (m-80) REVERT: l 56 LYS cc_start: 0.8461 (mttt) cc_final: 0.8011 (mtmm) REVERT: l 67 GLU cc_start: 0.8314 (tp30) cc_final: 0.7831 (mt-10) REVERT: l 129 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7866 (tm-30) REVERT: l 130 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8136 (t0) REVERT: l 135 VAL cc_start: 0.8166 (m) cc_final: 0.7783 (t) REVERT: l 138 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7451 (ttp80) REVERT: l 146 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: m 5 ASP cc_start: 0.8899 (t0) cc_final: 0.8435 (t70) REVERT: m 22 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8342 (mttp) REVERT: m 31 LYS cc_start: 0.8321 (ttpm) cc_final: 0.7843 (mmmm) REVERT: m 94 LYS cc_start: 0.8276 (mttm) cc_final: 0.7881 (mtpp) REVERT: m 117 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7952 (mtt90) REVERT: n 19 VAL cc_start: 0.8704 (t) cc_final: 0.8340 (p) REVERT: n 27 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7122 (mmtt) REVERT: n 63 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8050 (pp) REVERT: n 98 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6885 (mp) REVERT: n 124 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8713 (ttm-80) REVERT: o 44 THR cc_start: 0.8975 (m) cc_final: 0.8769 (t) REVERT: o 66 GLU cc_start: 0.8979 (pt0) cc_final: 0.8773 (pt0) REVERT: o 72 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7528 (mpt180) REVERT: p 57 LYS cc_start: 0.8682 (pttt) cc_final: 0.8457 (pttp) REVERT: p 85 MET cc_start: 0.8242 (mtt) cc_final: 0.7866 (mtp) REVERT: q 44 LYS cc_start: 0.8971 (mptm) cc_final: 0.8748 (mmmt) REVERT: q 54 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7765 (tpt170) REVERT: q 73 ASN cc_start: 0.8488 (p0) cc_final: 0.8202 (p0) REVERT: q 108 LYS cc_start: 0.8631 (mttt) cc_final: 0.8221 (mptt) REVERT: r 41 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7405 (mp0) REVERT: r 93 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7534 (mpt-90) REVERT: s 100 SER cc_start: 0.8485 (p) cc_final: 0.8160 (t) REVERT: t 10 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7697 (mtpt) REVERT: t 67 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8183 (mt) REVERT: t 70 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8347 (tp) REVERT: t 74 ASP cc_start: 0.7201 (t0) cc_final: 0.6924 (t70) REVERT: u 48 GLU cc_start: 0.8823 (pt0) cc_final: 0.7900 (pm20) REVERT: u 50 THR cc_start: 0.9048 (m) cc_final: 0.8691 (t) REVERT: u 79 ASN cc_start: 0.7863 (m-40) cc_final: 0.7441 (m110) REVERT: v 15 ASP cc_start: 0.7525 (p0) cc_final: 0.7198 (p0) REVERT: v 25 ILE cc_start: 0.8773 (mt) cc_final: 0.8552 (mt) REVERT: v 30 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8497 (ttpp) REVERT: w 30 LYS cc_start: 0.8226 (tttt) cc_final: 0.7938 (mttt) REVERT: x 65 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7203 (mm-30) REVERT: y 10 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8371 (tpt170) REVERT: y 24 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (mtp85) REVERT: y 48 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7601 (tp-100) REVERT: z 33 ARG cc_start: 0.8250 (tmt170) cc_final: 0.7483 (mtm-85) REVERT: z 47 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7804 (mtm110) outliers start: 399 outliers final: 135 residues processed: 1837 average time/residue: 1.4894 time to fit residues: 4550.2959 Evaluate side-chains 1431 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1242 time to evaluate : 6.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU Chi-restraints excluded: chain 6 residue 18 THR Chi-restraints excluded: chain 6 residue 20 LEU Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 123 TYR Chi-restraints excluded: chain 7 residue 272 THR Chi-restraints excluded: chain 7 residue 273 GLN Chi-restraints excluded: chain 7 residue 279 SER Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 324 ARG Chi-restraints excluded: chain 7 residue 337 ARG Chi-restraints excluded: chain 7 residue 340 VAL Chi-restraints excluded: chain 7 residue 343 ARG Chi-restraints excluded: chain 7 residue 354 ASP Chi-restraints excluded: chain 7 residue 362 LYS Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 122 PHE 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 F residue 32 GLU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 38 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 109 ARG Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 99 ASN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 41 ARG Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 63 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 128 LYS Chi-restraints excluded: chain g residue 132 LYS Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 97 ASN Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain w residue 54 GLN Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 10 ARG Chi-restraints excluded: chain y residue 24 ARG Chi-restraints excluded: chain y residue 48 GLN Chi-restraints excluded: chain z residue 28 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 0.9980 chunk 812 optimal weight: 20.0000 chunk 450 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 548 optimal weight: 1.9990 chunk 434 optimal weight: 10.0000 chunk 840 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 510 optimal weight: 4.9990 chunk 625 optimal weight: 3.9990 chunk 973 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 27 GLN B 90 ASN C 32 ASN D 41 GLN D 94 GLN E 63 GLN F 88 GLN F 116 GLN G 11 ASN J 58 ASN J 67 ASN K 29 HIS N 18 GLN N 81 ASN O 104 GLN P 115 ASN R 82 HIS T 59 ASN V 12 GLN V 75 GLN X 6 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN i 131 ASN i 136 GLN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 73 ASN j 89 HIS j 132 ASN l 97 ASN n 5 GLN o 15 HIS o 64 GLN ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN w 54 GLN x 14 HIS y 48 GLN y 55 GLN z 56 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 161777 Z= 0.329 Angle : 0.724 16.260 241363 Z= 0.385 Chirality : 0.042 0.412 30650 Planarity : 0.007 0.133 13379 Dihedral : 23.540 179.784 79694 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 5.97 % Allowed : 15.65 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 6232 helix: 2.67 (0.11), residues: 2231 sheet: -1.67 (0.13), residues: 1156 loop : -1.48 (0.10), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP h 201 HIS 0.008 0.001 HIS V 88 PHE 0.022 0.002 PHE a 60 TYR 0.019 0.002 TYR L 58 ARG 0.008 0.001 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1673 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1363 time to evaluate : 6.497 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: 6 24 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8003 (tt) REVERT: 7 45 ASP cc_start: 0.5971 (m-30) cc_final: 0.5726 (t0) REVERT: 7 102 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.4257 (tp30) REVERT: 7 149 GLU cc_start: 0.8423 (tt0) cc_final: 0.7896 (tm-30) REVERT: 7 153 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8305 (mm) REVERT: 7 168 GLU cc_start: 0.8303 (tt0) cc_final: 0.7198 (pm20) REVERT: 7 177 LYS cc_start: 0.8204 (tttt) cc_final: 0.7998 (mttm) REVERT: 7 225 GLU cc_start: 0.5904 (mt-10) cc_final: 0.5637 (mt-10) REVERT: 7 238 ASP cc_start: 0.6099 (m-30) cc_final: 0.5766 (t0) REVERT: 7 262 ARG cc_start: 0.6797 (ttm110) cc_final: 0.6439 (ttt90) REVERT: 7 264 THR cc_start: 0.8405 (m) cc_final: 0.7675 (p) REVERT: 7 271 VAL cc_start: 0.8289 (m) cc_final: 0.8074 (m) REVERT: 7 342 THR cc_start: 0.7893 (t) cc_final: 0.7533 (p) REVERT: 7 346 GLN cc_start: 0.8031 (tp40) cc_final: 0.7770 (pm20) REVERT: 7 352 SER cc_start: 0.7776 (t) cc_final: 0.7530 (m) REVERT: B 183 LYS cc_start: 0.8807 (mttt) cc_final: 0.8356 (mmtt) REVERT: B 269 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7978 (ttt-90) REVERT: B 270 ARG cc_start: 0.8490 (mmm160) cc_final: 0.7684 (ttt-90) REVERT: B 271 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7904 (ptt-90) REVERT: C 13 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8960 (ptm160) REVERT: C 42 ASN cc_start: 0.8164 (t0) cc_final: 0.7686 (t0) REVERT: C 43 ASP cc_start: 0.8544 (m-30) cc_final: 0.8257 (m-30) REVERT: C 97 SER cc_start: 0.8557 (t) cc_final: 0.8291 (p) REVERT: C 99 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8200 (tm-30) REVERT: C 128 ARG cc_start: 0.8750 (mtt90) cc_final: 0.7977 (mmt180) REVERT: D 1 MET cc_start: 0.7671 (tpp) cc_final: 0.7416 (ttt) REVERT: D 12 LEU cc_start: 0.7312 (tt) cc_final: 0.7075 (tt) REVERT: D 16 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7905 (mm-30) REVERT: D 22 ASP cc_start: 0.8716 (m-30) cc_final: 0.8490 (m-30) REVERT: D 69 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7420 (ptp-170) REVERT: D 145 ASP cc_start: 0.8302 (t70) cc_final: 0.7718 (t0) REVERT: D 184 ASP cc_start: 0.8137 (m-30) cc_final: 0.7551 (m-30) REVERT: E 10 ASP cc_start: 0.8218 (p0) cc_final: 0.8012 (m-30) REVERT: E 11 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7085 (mm-30) REVERT: E 67 ILE cc_start: 0.8664 (mt) cc_final: 0.8419 (mm) REVERT: E 133 ARG cc_start: 0.7838 (mpp80) cc_final: 0.7277 (mpp80) REVERT: F 95 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7723 (ptp90) REVERT: F 130 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7880 (mt-10) REVERT: F 176 LYS cc_start: 0.5073 (OUTLIER) cc_final: 0.4584 (mttt) REVERT: G 15 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7928 (tt) REVERT: H 37 LYS cc_start: 0.3271 (OUTLIER) cc_final: 0.3064 (tttm) REVERT: H 38 MET cc_start: 0.4519 (mtm) cc_final: 0.4055 (tmm) REVERT: I 124 MET cc_start: 0.4165 (mtt) cc_final: 0.3711 (tpt) REVERT: J 9 GLU cc_start: 0.8160 (mp0) cc_final: 0.7851 (pm20) REVERT: J 85 LYS cc_start: 0.8365 (mmmm) cc_final: 0.7979 (mmtt) REVERT: J 96 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7587 (ptm160) REVERT: J 108 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.7772 (mtt) REVERT: J 129 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: K 66 LYS cc_start: 0.8909 (tttt) cc_final: 0.8694 (mtpp) REVERT: K 93 GLN cc_start: 0.8778 (pt0) cc_final: 0.8215 (mp10) REVERT: K 104 THR cc_start: 0.8766 (p) cc_final: 0.8222 (p) REVERT: K 106 GLU cc_start: 0.8471 (mp0) cc_final: 0.7680 (mp0) REVERT: K 113 MET cc_start: 0.7713 (tpt) cc_final: 0.7229 (mmm) REVERT: K 114 LYS cc_start: 0.8016 (tttp) cc_final: 0.7688 (tptm) REVERT: L 7 SER cc_start: 0.8981 (t) cc_final: 0.8717 (m) REVERT: L 115 GLU cc_start: 0.8645 (pt0) cc_final: 0.8060 (tp30) REVERT: M 10 ARG cc_start: 0.8987 (mtp85) cc_final: 0.8507 (mmm160) REVERT: M 22 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8104 (mm110) REVERT: M 30 SER cc_start: 0.8441 (t) cc_final: 0.8152 (t) REVERT: M 58 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8390 (mttp) REVERT: M 60 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7514 (mm110) REVERT: N 6 SER cc_start: 0.9007 (t) cc_final: 0.8784 (p) REVERT: N 23 ASN cc_start: 0.8583 (m-40) cc_final: 0.8228 (m110) REVERT: N 59 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8412 (p) REVERT: N 106 ASP cc_start: 0.9020 (p0) cc_final: 0.8614 (p0) REVERT: N 110 MET cc_start: 0.8742 (mmm) cc_final: 0.8423 (mmt) REVERT: O 83 LEU cc_start: 0.7865 (mt) cc_final: 0.7652 (mt) REVERT: Q 3 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8920 (tpt90) REVERT: Q 87 SER cc_start: 0.8948 (t) cc_final: 0.8601 (p) REVERT: R 23 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8517 (mm-30) REVERT: R 29 THR cc_start: 0.8622 (p) cc_final: 0.8404 (t) REVERT: R 73 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8499 (mtpp) REVERT: R 97 LYS cc_start: 0.8456 (tttt) cc_final: 0.8182 (ttpp) REVERT: S 2 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8216 (mp0) REVERT: S 28 LYS cc_start: 0.8008 (mttp) cc_final: 0.7754 (mmmt) REVERT: S 67 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7272 (p0) REVERT: T 12 ARG cc_start: 0.8432 (mmm160) cc_final: 0.8213 (mmm160) REVERT: T 33 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7822 (tttt) REVERT: T 69 ARG cc_start: 0.8387 (mtp85) cc_final: 0.7858 (mtp-110) REVERT: U 46 GLN cc_start: 0.8096 (mt0) cc_final: 0.7768 (tt0) REVERT: U 47 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7907 (mtpt) REVERT: U 81 ASP cc_start: 0.8744 (m-30) cc_final: 0.8520 (m-30) REVERT: U 88 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6742 (mm-30) REVERT: U 102 THR cc_start: 0.8874 (m) cc_final: 0.8443 (t) REVERT: V 59 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7488 (mt-10) REVERT: V 75 GLN cc_start: 0.8845 (tp40) cc_final: 0.8447 (tp40) REVERT: V 82 TYR cc_start: 0.9048 (p90) cc_final: 0.8631 (p90) REVERT: V 83 LYS cc_start: 0.8364 (mttt) cc_final: 0.8017 (mttt) REVERT: V 85 LYS cc_start: 0.8120 (mttt) cc_final: 0.7773 (mtpp) REVERT: W 11 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7916 (ptp-170) REVERT: W 39 ARG cc_start: 0.9149 (mtp-110) cc_final: 0.8548 (mtp85) REVERT: W 40 GLN cc_start: 0.8983 (pt0) cc_final: 0.8767 (pt0) REVERT: W 44 LYS cc_start: 0.8895 (tttt) cc_final: 0.8670 (tttm) REVERT: W 70 GLU cc_start: 0.8587 (pt0) cc_final: 0.8353 (pt0) REVERT: X 65 ASP cc_start: 0.8293 (m-30) cc_final: 0.8053 (m-30) REVERT: Y 6 LEU cc_start: 0.7917 (mt) cc_final: 0.7362 (tp) REVERT: Y 16 THR cc_start: 0.8623 (m) cc_final: 0.8334 (p) REVERT: Y 17 GLU cc_start: 0.8071 (tp30) cc_final: 0.7685 (tt0) REVERT: Y 45 GLN cc_start: 0.8484 (mt0) cc_final: 0.8083 (mt0) REVERT: Y 49 ASP cc_start: 0.8576 (m-30) cc_final: 0.8366 (m-30) REVERT: Z 36 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8622 (m) REVERT: a 15 SER cc_start: 0.7438 (t) cc_final: 0.7231 (p) REVERT: a 61 ASN cc_start: 0.7791 (m-40) cc_final: 0.7023 (m110) REVERT: b 40 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7818 (mmt180) REVERT: b 55 ILE cc_start: 0.8879 (tp) cc_final: 0.8639 (pt) REVERT: c 5 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7497 (mt) REVERT: c 7 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7702 (mt-10) REVERT: d 25 LYS cc_start: 0.8712 (tmmt) cc_final: 0.8064 (ttmm) REVERT: e 19 LYS cc_start: 0.8694 (mttt) cc_final: 0.8451 (mtpt) REVERT: g 35 ARG cc_start: 0.6982 (mmt-90) cc_final: 0.6342 (mtp85) REVERT: g 36 ASN cc_start: 0.7017 (t0) cc_final: 0.6511 (t0) REVERT: g 42 ASN cc_start: 0.7420 (t0) cc_final: 0.7191 (t0) REVERT: g 74 ARG cc_start: 0.7040 (ptt180) cc_final: 0.6276 (ptm-80) REVERT: g 78 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8060 (mm-30) REVERT: g 105 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7692 (mmmt) REVERT: g 112 LYS cc_start: 0.8044 (tppt) cc_final: 0.7785 (mtmm) REVERT: g 139 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7178 (mtp85) REVERT: g 165 ASP cc_start: 0.5903 (t0) cc_final: 0.5647 (t0) REVERT: g 169 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7854 (mm-30) REVERT: g 188 ASP cc_start: 0.6943 (t0) cc_final: 0.6724 (t0) REVERT: g 223 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7278 (tm-30) REVERT: h 89 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7943 (tppt) REVERT: h 110 GLU cc_start: 0.8760 (mp0) cc_final: 0.8358 (mp0) REVERT: h 162 ILE cc_start: 0.8945 (mm) cc_final: 0.8669 (tt) REVERT: h 196 ILE cc_start: 0.9283 (mt) cc_final: 0.8925 (mm) REVERT: i 33 LYS cc_start: 0.7444 (mttp) cc_final: 0.7115 (mmtt) REVERT: i 45 LYS cc_start: 0.8103 (mttm) cc_final: 0.7789 (tppt) REVERT: i 70 ARG cc_start: 0.8217 (tpp80) cc_final: 0.8004 (tpt-90) REVERT: i 73 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.7983 (ttp80) REVERT: i 124 MET cc_start: 0.8047 (mtt) cc_final: 0.7808 (mtm) REVERT: i 128 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7818 (mtp180) REVERT: i 151 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7939 (ptmm) REVERT: i 166 GLU cc_start: 0.8393 (tt0) cc_final: 0.7830 (tp30) REVERT: i 185 LYS cc_start: 0.8779 (ptmm) cc_final: 0.8360 (mtpt) REVERT: i 206 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6340 (ptpt) REVERT: j 14 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8763 (mttt) REVERT: j 26 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8430 (ttmm) REVERT: j 60 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7765 (mt) REVERT: j 115 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8711 (mt) REVERT: j 130 SER cc_start: 0.8557 (t) cc_final: 0.8331 (p) REVERT: k 1 MET cc_start: 0.6834 (mmm) cc_final: 0.6237 (mmt) REVERT: k 36 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8094 (mt) REVERT: k 38 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.6975 (ptp90) REVERT: k 91 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: l 56 LYS cc_start: 0.8465 (mttt) cc_final: 0.8118 (mtpp) REVERT: l 67 GLU cc_start: 0.8276 (tp30) cc_final: 0.7782 (mt-10) REVERT: l 79 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5317 (ppt90) REVERT: l 84 THR cc_start: 0.7330 (m) cc_final: 0.7050 (t) REVERT: l 110 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8381 (mtpt) REVERT: l 130 ASN cc_start: 0.8265 (t0) cc_final: 0.8028 (t0) REVERT: l 146 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: l 148 ASN cc_start: 0.7866 (m-40) cc_final: 0.7539 (m-40) REVERT: m 31 LYS cc_start: 0.8594 (ttpm) cc_final: 0.8053 (mmmm) REVERT: m 94 LYS cc_start: 0.8169 (mttm) cc_final: 0.7861 (mtpp) REVERT: m 117 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8235 (mtt90) REVERT: n 27 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7145 (mmtt) REVERT: n 119 ARG cc_start: 0.8401 (mtm110) cc_final: 0.8155 (mtm110) REVERT: o 66 GLU cc_start: 0.9007 (pt0) cc_final: 0.8783 (pt0) REVERT: o 68 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8305 (mtp85) REVERT: o 72 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7760 (mpt180) REVERT: p 15 GLN cc_start: 0.5765 (mm-40) cc_final: 0.5532 (mm-40) REVERT: p 85 MET cc_start: 0.8184 (mtt) cc_final: 0.7855 (mmm) REVERT: p 106 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7668 (ttp-170) REVERT: q 12 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7214 (mtt90) REVERT: q 44 LYS cc_start: 0.9010 (mptm) cc_final: 0.8742 (mmmt) REVERT: q 54 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7718 (tpt170) REVERT: q 73 ASN cc_start: 0.8670 (p0) cc_final: 0.8404 (p0) REVERT: q 108 LYS cc_start: 0.8619 (mttt) cc_final: 0.8248 (mptt) REVERT: r 41 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7455 (mp0) REVERT: r 73 ILE cc_start: 0.8443 (mm) cc_final: 0.8167 (mm) REVERT: s 100 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8358 (t) REVERT: t 10 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7755 (mtpt) REVERT: t 40 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: t 67 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8330 (mt) REVERT: t 74 ASP cc_start: 0.7185 (t0) cc_final: 0.6927 (t0) REVERT: u 48 GLU cc_start: 0.8833 (pt0) cc_final: 0.8511 (pt0) REVERT: v 15 ASP cc_start: 0.7614 (p0) cc_final: 0.7302 (p0) REVERT: v 60 GLU cc_start: 0.7939 (tt0) cc_final: 0.7707 (tm-30) REVERT: w 30 LYS cc_start: 0.8102 (tttt) cc_final: 0.7794 (mttt) REVERT: y 10 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8269 (tpt170) REVERT: y 21 ASN cc_start: 0.9233 (m-40) cc_final: 0.9002 (m110) REVERT: y 48 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7621 (mm-40) REVERT: y 52 ASN cc_start: 0.8601 (m-40) cc_final: 0.7920 (m110) REVERT: y 69 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8270 (mtpt) REVERT: y 80 THR cc_start: 0.8892 (m) cc_final: 0.8580 (m) REVERT: z 33 ARG cc_start: 0.8301 (tmt170) cc_final: 0.7493 (mtt180) outliers start: 310 outliers final: 172 residues processed: 1571 average time/residue: 1.4113 time to fit residues: 3750.4662 Evaluate side-chains 1476 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1265 time to evaluate : 6.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU Chi-restraints excluded: chain 6 residue 18 THR 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 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 153 LEU Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 273 GLN Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 354 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 37 LYS 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 20 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 3 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 ILE 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 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 146 ASN Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 21 VAL 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 115 SER Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 40 GLN Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 10 ARG Chi-restraints excluded: chain y residue 69 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 810 optimal weight: 2.9990 chunk 662 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 chunk 975 optimal weight: 9.9990 chunk 1053 optimal weight: 0.6980 chunk 868 optimal weight: 8.9990 chunk 967 optimal weight: 7.9990 chunk 332 optimal weight: 10.0000 chunk 782 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 322 GLN B 128 ASN C 32 ASN D 41 GLN F 45 HIS F 73 ASN K 29 HIS L 38 GLN M 60 GLN O 29 HIS P 41 GLN T 70 HIS g 39 HIS g 177 ASN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 132 ASN ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 142 HIS ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 29 ASN ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN s 4 GLN y 20 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 161777 Z= 0.165 Angle : 0.601 15.309 241363 Z= 0.327 Chirality : 0.034 0.416 30650 Planarity : 0.006 0.126 13379 Dihedral : 23.295 179.867 79537 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 4.82 % Allowed : 18.07 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.47 (0.11), residues: 6232 helix: 2.77 (0.11), residues: 2242 sheet: -1.22 (0.14), residues: 1155 loop : -1.06 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 7 155 HIS 0.014 0.001 HIS 6 21 PHE 0.034 0.001 PHE K 100 TYR 0.019 0.001 TYR h 42 ARG 0.007 0.001 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1355 time to evaluate : 6.404 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: 7 128 CYS cc_start: 0.7772 (p) cc_final: 0.7394 (p) REVERT: 7 131 ASP cc_start: 0.7688 (t0) cc_final: 0.7293 (m-30) REVERT: 7 149 GLU cc_start: 0.8418 (tt0) cc_final: 0.7935 (tm-30) REVERT: 7 157 GLU cc_start: 0.8536 (tp30) cc_final: 0.7897 (mt-10) REVERT: 7 168 GLU cc_start: 0.8247 (tt0) cc_final: 0.7089 (pm20) REVERT: 7 225 GLU cc_start: 0.5956 (mt-10) cc_final: 0.5513 (mt-10) REVERT: 7 240 ARG cc_start: 0.5809 (mtm110) cc_final: 0.5551 (mtm-85) REVERT: 7 264 THR cc_start: 0.8464 (m) cc_final: 0.7672 (p) REVERT: 7 271 VAL cc_start: 0.8113 (m) cc_final: 0.7860 (m) REVERT: 7 297 GLU cc_start: 0.7669 (tp30) cc_final: 0.7196 (tp30) REVERT: 7 336 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7999 (mm) REVERT: 7 342 THR cc_start: 0.8029 (t) cc_final: 0.7630 (p) REVERT: 7 346 GLN cc_start: 0.8141 (tp40) cc_final: 0.7830 (pm20) REVERT: 7 352 SER cc_start: 0.7612 (t) cc_final: 0.7371 (m) REVERT: B 183 LYS cc_start: 0.8700 (mttt) cc_final: 0.8271 (mmtt) REVERT: B 269 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7986 (ttt-90) REVERT: B 270 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7557 (ttt-90) REVERT: C 42 ASN cc_start: 0.8162 (t0) cc_final: 0.7654 (t0) REVERT: C 43 ASP cc_start: 0.8499 (m-30) cc_final: 0.8227 (m-30) REVERT: C 128 ARG cc_start: 0.8597 (mtt90) cc_final: 0.7821 (mmt180) REVERT: D 5 LEU cc_start: 0.8122 (mp) cc_final: 0.7866 (mp) REVERT: D 12 LEU cc_start: 0.7145 (tt) cc_final: 0.6875 (tt) REVERT: D 16 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7538 (tp30) REVERT: D 22 ASP cc_start: 0.8575 (m-30) cc_final: 0.8366 (m-30) REVERT: D 111 GLU cc_start: 0.8516 (tp30) cc_final: 0.8299 (tp30) REVERT: E 11 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7008 (mm-30) REVERT: E 96 MET cc_start: 0.8874 (ttp) cc_final: 0.8673 (ttp) REVERT: E 112 ARG cc_start: 0.8274 (ptm160) cc_final: 0.8061 (ptm160) REVERT: F 77 ILE cc_start: 0.8151 (mm) cc_final: 0.7913 (mt) REVERT: F 95 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7673 (ptp90) REVERT: F 176 LYS cc_start: 0.5334 (OUTLIER) cc_final: 0.4852 (mttt) REVERT: G 15 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7860 (tt) REVERT: H 38 MET cc_start: 0.4519 (mtm) cc_final: 0.4065 (tmm) REVERT: H 117 LEU cc_start: 0.2685 (OUTLIER) cc_final: 0.2174 (mm) REVERT: J 9 GLU cc_start: 0.8186 (mp0) cc_final: 0.7833 (pm20) REVERT: J 61 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8290 (mmtm) REVERT: J 85 LYS cc_start: 0.8361 (mmmm) cc_final: 0.7995 (mmtt) REVERT: J 96 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7644 (ptm160) REVERT: J 102 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8380 (mt-10) REVERT: J 125 TYR cc_start: 0.8721 (m-80) cc_final: 0.8429 (m-80) REVERT: J 129 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: K 66 LYS cc_start: 0.8914 (tttt) cc_final: 0.8658 (mtpp) REVERT: K 93 GLN cc_start: 0.8590 (pt0) cc_final: 0.8052 (mp10) REVERT: K 113 MET cc_start: 0.7763 (tpt) cc_final: 0.7404 (mmm) REVERT: L 69 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8258 (mtp85) REVERT: L 115 GLU cc_start: 0.8644 (pt0) cc_final: 0.8087 (tp30) REVERT: M 10 ARG cc_start: 0.9002 (mtp85) cc_final: 0.8617 (mmm160) REVERT: M 16 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8690 (mmt180) REVERT: M 47 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: M 104 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8217 (mt-10) REVERT: N 23 ASN cc_start: 0.8519 (m-40) cc_final: 0.8195 (m110) REVERT: N 106 ASP cc_start: 0.8963 (p0) cc_final: 0.8678 (p0) REVERT: N 110 MET cc_start: 0.8714 (mmm) cc_final: 0.8492 (mmt) REVERT: Q 87 SER cc_start: 0.8907 (t) cc_final: 0.8594 (p) REVERT: R 73 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8482 (mtpp) REVERT: R 97 LYS cc_start: 0.8352 (tttt) cc_final: 0.8111 (ttpp) REVERT: S 2 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8241 (mp0) REVERT: S 3 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8131 (p) REVERT: S 28 LYS cc_start: 0.7944 (mttp) cc_final: 0.7674 (mmmt) REVERT: S 67 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7250 (p0) REVERT: T 12 ARG cc_start: 0.8364 (mmm160) cc_final: 0.8149 (mmp80) REVERT: T 33 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7826 (tttt) REVERT: T 49 LYS cc_start: 0.8670 (tptp) cc_final: 0.8393 (tttt) REVERT: T 69 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7771 (mtp-110) REVERT: U 46 GLN cc_start: 0.8099 (mt0) cc_final: 0.7749 (tt0) REVERT: U 47 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8040 (mtpt) REVERT: U 81 ASP cc_start: 0.8762 (m-30) cc_final: 0.8491 (m-30) REVERT: U 88 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6698 (mm-30) REVERT: U 102 THR cc_start: 0.8861 (m) cc_final: 0.8442 (t) REVERT: V 59 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7396 (mt-10) REVERT: V 82 TYR cc_start: 0.8993 (p90) cc_final: 0.8611 (p90) REVERT: V 83 LYS cc_start: 0.8267 (mttt) cc_final: 0.8040 (mtpt) REVERT: V 85 LYS cc_start: 0.8225 (mttt) cc_final: 0.7875 (mtpp) REVERT: W 11 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7739 (ptp-170) REVERT: W 29 GLU cc_start: 0.9160 (tt0) cc_final: 0.8638 (mt-10) REVERT: W 39 ARG cc_start: 0.8991 (mtp-110) cc_final: 0.8515 (mtp85) REVERT: W 40 GLN cc_start: 0.8843 (pt0) cc_final: 0.8571 (pt0) REVERT: W 44 LYS cc_start: 0.8789 (tttt) cc_final: 0.8570 (tttm) REVERT: W 70 GLU cc_start: 0.8598 (pt0) cc_final: 0.8320 (pt0) REVERT: X 65 ASP cc_start: 0.8350 (m-30) cc_final: 0.8086 (m-30) REVERT: Y 6 LEU cc_start: 0.8043 (mt) cc_final: 0.7583 (tp) REVERT: Y 13 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8140 (mt-10) REVERT: Y 16 THR cc_start: 0.8636 (m) cc_final: 0.8370 (p) REVERT: Y 45 GLN cc_start: 0.8537 (mt0) cc_final: 0.8033 (mt0) REVERT: Z 32 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8657 (mt) REVERT: a 61 ASN cc_start: 0.7863 (m-40) cc_final: 0.7252 (m110) REVERT: b 40 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7784 (mmt180) REVERT: b 50 ARG cc_start: 0.9060 (mtp180) cc_final: 0.8720 (mtp85) REVERT: b 55 ILE cc_start: 0.8939 (tp) cc_final: 0.8705 (pt) REVERT: c 5 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7422 (mt) REVERT: c 47 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8474 (m) REVERT: d 25 LYS cc_start: 0.8597 (tmmt) cc_final: 0.7937 (ttmm) REVERT: g 35 ARG cc_start: 0.6937 (mmt-90) cc_final: 0.6434 (mtp-110) REVERT: g 36 ASN cc_start: 0.6963 (t0) cc_final: 0.6356 (t0) REVERT: g 63 ARG cc_start: 0.6714 (ptp-110) cc_final: 0.6334 (ptt-90) REVERT: g 73 LYS cc_start: 0.7525 (mttm) cc_final: 0.7007 (mmmt) REVERT: g 74 ARG cc_start: 0.7181 (ptt180) cc_final: 0.6407 (ptm-80) REVERT: g 82 ASP cc_start: 0.8051 (m-30) cc_final: 0.7584 (t0) REVERT: g 139 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7150 (mtp85) REVERT: g 165 ASP cc_start: 0.6164 (t0) cc_final: 0.5695 (t0) REVERT: g 169 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7930 (mm-30) REVERT: g 179 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (mm) REVERT: g 188 ASP cc_start: 0.7412 (t0) cc_final: 0.7181 (t0) REVERT: g 223 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7639 (tm-30) REVERT: h 45 LYS cc_start: 0.8808 (tppt) cc_final: 0.8310 (tmtt) REVERT: h 83 ASP cc_start: 0.6594 (t0) cc_final: 0.6340 (t0) REVERT: h 89 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7832 (tppt) REVERT: h 135 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8274 (tptm) REVERT: h 162 ILE cc_start: 0.8836 (mm) cc_final: 0.8545 (tt) REVERT: i 33 LYS cc_start: 0.7415 (mttp) cc_final: 0.7069 (mmtt) REVERT: i 45 LYS cc_start: 0.8016 (mttm) cc_final: 0.7732 (tppt) REVERT: i 73 ARG cc_start: 0.8550 (tpp-160) cc_final: 0.7988 (ttp80) REVERT: i 124 MET cc_start: 0.8019 (mtt) cc_final: 0.7337 (mmm) REVERT: i 128 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7567 (mtp180) REVERT: i 151 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7850 (ptmm) REVERT: i 166 GLU cc_start: 0.8290 (tt0) cc_final: 0.7744 (tp30) REVERT: i 185 LYS cc_start: 0.8775 (ptmm) cc_final: 0.8377 (mtpt) REVERT: i 206 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6101 (ptpt) REVERT: j 13 GLU cc_start: 0.8353 (pt0) cc_final: 0.7889 (mt-10) REVERT: j 26 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8392 (ttmm) REVERT: k 1 MET cc_start: 0.7018 (mmm) cc_final: 0.6544 (mmt) REVERT: k 7 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8637 (t) REVERT: k 36 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8182 (mt) REVERT: k 38 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7041 (ptp90) REVERT: k 46 GLN cc_start: 0.7660 (tp40) cc_final: 0.7271 (tp-100) REVERT: k 86 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8061 (mtt-85) REVERT: l 67 GLU cc_start: 0.8331 (tp30) cc_final: 0.7815 (mt-10) REVERT: l 110 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8059 (mtpt) REVERT: l 123 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8144 (tp30) REVERT: l 146 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: m 31 LYS cc_start: 0.8596 (ttpm) cc_final: 0.8052 (mmmm) REVERT: m 94 LYS cc_start: 0.8137 (mttm) cc_final: 0.7781 (mtpp) REVERT: m 117 ARG cc_start: 0.8700 (ttp-170) cc_final: 0.8179 (mtt90) REVERT: n 27 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7084 (mmtt) REVERT: o 72 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7614 (mpt180) REVERT: p 18 ASP cc_start: 0.7936 (p0) cc_final: 0.7665 (p0) REVERT: p 37 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8188 (mmm-85) REVERT: p 69 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7472 (mtp85) REVERT: p 85 MET cc_start: 0.8113 (mtt) cc_final: 0.7772 (mmm) REVERT: p 106 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7789 (ttp80) REVERT: q 44 LYS cc_start: 0.9047 (mptm) cc_final: 0.8759 (mmmt) REVERT: q 54 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7757 (tpp80) REVERT: q 108 LYS cc_start: 0.8520 (mttt) cc_final: 0.8167 (mptt) REVERT: r 41 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7452 (mp0) REVERT: r 73 ILE cc_start: 0.8426 (mm) cc_final: 0.8147 (mm) REVERT: r 93 ARG cc_start: 0.7669 (mmt-90) cc_final: 0.7454 (mmm-85) REVERT: s 100 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8310 (t) REVERT: t 67 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8334 (mt) REVERT: u 48 GLU cc_start: 0.8719 (pt0) cc_final: 0.8395 (pt0) REVERT: v 15 ASP cc_start: 0.7586 (p0) cc_final: 0.6730 (t0) REVERT: v 34 TYR cc_start: 0.9358 (m-80) cc_final: 0.9045 (m-80) REVERT: v 61 ILE cc_start: 0.8672 (pt) cc_final: 0.8356 (pt) REVERT: w 30 LYS cc_start: 0.7939 (tttt) cc_final: 0.7722 (mttt) REVERT: x 21 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7483 (mmtm) REVERT: y 10 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7940 (tpt90) REVERT: y 21 ASN cc_start: 0.9246 (m-40) cc_final: 0.9007 (m110) REVERT: y 48 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7587 (mm-40) REVERT: y 52 ASN cc_start: 0.8552 (m-40) cc_final: 0.7830 (m110) REVERT: z 33 ARG cc_start: 0.8316 (tmt170) cc_final: 0.7520 (mtm180) outliers start: 250 outliers final: 145 residues processed: 1508 average time/residue: 1.4469 time to fit residues: 3713.3236 Evaluate side-chains 1436 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1261 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU Chi-restraints excluded: chain 6 residue 20 LEU Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 273 GLN Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 354 ASP Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL 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 Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 14 SER Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 10 ARG Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 3.9990 chunk 733 optimal weight: 0.9980 chunk 506 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 465 optimal weight: 5.9990 chunk 654 optimal weight: 7.9990 chunk 978 optimal weight: 10.0000 chunk 1036 optimal weight: 8.9990 chunk 511 optimal weight: 3.9990 chunk 927 optimal weight: 0.2980 chunk 279 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS 7 276 ASN 7 304 ASN 7 322 GLN B 115 GLN C 32 ASN D 41 GLN L 38 GLN Q 56 GLN g 42 ASN g 177 ASN i 74 ASN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN l 130 ASN l 142 HIS ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 29 ASN p 40 ASN p 101 ASN t 80 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 161777 Z= 0.284 Angle : 0.633 15.555 241363 Z= 0.338 Chirality : 0.037 0.394 30650 Planarity : 0.006 0.136 13379 Dihedral : 23.199 179.083 79454 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 5.20 % Allowed : 18.92 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.39 (0.11), residues: 6232 helix: 2.43 (0.11), residues: 2249 sheet: -1.05 (0.14), residues: 1165 loop : -0.96 (0.11), residues: 2818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 201 HIS 0.006 0.001 HIS V 88 PHE 0.025 0.002 PHE k 8 TYR 0.018 0.002 TYR S 38 ARG 0.009 0.001 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1566 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1296 time to evaluate : 6.548 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: 6 24 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8025 (tt) REVERT: 7 129 TYR cc_start: 0.8210 (m-80) cc_final: 0.7899 (m-10) REVERT: 7 131 ASP cc_start: 0.7686 (t0) cc_final: 0.7364 (m-30) REVERT: 7 149 GLU cc_start: 0.8444 (tt0) cc_final: 0.7641 (tm-30) REVERT: 7 151 MET cc_start: 0.8176 (ttt) cc_final: 0.7959 (ttm) REVERT: 7 153 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7656 (mp) REVERT: 7 168 GLU cc_start: 0.8287 (tt0) cc_final: 0.7091 (pm20) REVERT: 7 225 GLU cc_start: 0.5814 (mt-10) cc_final: 0.5343 (mt-10) REVERT: 7 240 ARG cc_start: 0.5907 (mtm110) cc_final: 0.5592 (mtm-85) REVERT: 7 264 THR cc_start: 0.8099 (m) cc_final: 0.7701 (p) REVERT: 7 297 GLU cc_start: 0.7462 (tp30) cc_final: 0.6794 (tp30) REVERT: 7 336 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8104 (mm) REVERT: 7 342 THR cc_start: 0.8150 (t) cc_final: 0.7748 (p) REVERT: 7 343 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6843 (mpt-90) REVERT: 7 346 GLN cc_start: 0.8133 (tp40) cc_final: 0.7840 (pm20) REVERT: 7 352 SER cc_start: 0.7797 (t) cc_final: 0.7545 (m) REVERT: B 183 LYS cc_start: 0.8775 (mttt) cc_final: 0.8335 (mmtt) REVERT: B 269 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7970 (ttt-90) REVERT: B 270 ARG cc_start: 0.8366 (mmm160) cc_final: 0.7651 (ttt-90) REVERT: B 271 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7903 (ptt-90) REVERT: C 42 ASN cc_start: 0.8194 (t0) cc_final: 0.7679 (t0) REVERT: C 43 ASP cc_start: 0.8490 (m-30) cc_final: 0.8160 (m-30) REVERT: C 128 ARG cc_start: 0.8712 (mtt90) cc_final: 0.7910 (mmt180) REVERT: D 16 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7597 (tp30) REVERT: D 153 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5592 (pp) REVERT: E 11 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7065 (mm-30) REVERT: E 20 PHE cc_start: 0.7999 (m-80) cc_final: 0.7722 (m-80) REVERT: E 42 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: E 85 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7937 (tp) REVERT: E 122 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: F 77 ILE cc_start: 0.8111 (mm) cc_final: 0.7864 (mt) REVERT: F 176 LYS cc_start: 0.4919 (OUTLIER) cc_final: 0.4521 (mttt) REVERT: G 15 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7844 (tt) REVERT: G 114 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.4493 (tp30) REVERT: H 38 MET cc_start: 0.4504 (mtm) cc_final: 0.3969 (tmm) REVERT: H 107 GLU cc_start: 0.2008 (OUTLIER) cc_final: 0.1804 (mt-10) REVERT: H 117 LEU cc_start: 0.2628 (OUTLIER) cc_final: 0.2213 (mm) REVERT: J 9 GLU cc_start: 0.8161 (mp0) cc_final: 0.7807 (pm20) REVERT: J 61 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8337 (mmtm) REVERT: J 85 LYS cc_start: 0.8376 (mmmm) cc_final: 0.7987 (mmtt) REVERT: J 96 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7664 (tpp80) REVERT: J 102 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8425 (mt-10) REVERT: J 129 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: K 66 LYS cc_start: 0.8890 (tttt) cc_final: 0.8656 (mtpp) REVERT: K 93 GLN cc_start: 0.8627 (pt0) cc_final: 0.8172 (mp10) REVERT: K 113 MET cc_start: 0.7669 (tpt) cc_final: 0.7206 (mmm) REVERT: L 69 ARG cc_start: 0.8649 (mtp-110) cc_final: 0.8368 (mtp85) REVERT: L 115 GLU cc_start: 0.8701 (pt0) cc_final: 0.8141 (tp30) REVERT: M 47 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: M 106 ASP cc_start: 0.8433 (t0) cc_final: 0.7977 (t0) REVERT: N 23 ASN cc_start: 0.8551 (m-40) cc_final: 0.8295 (m110) REVERT: N 106 ASP cc_start: 0.8994 (p0) cc_final: 0.8639 (p0) REVERT: N 110 MET cc_start: 0.8791 (mmm) cc_final: 0.8520 (mmt) REVERT: Q 87 SER cc_start: 0.8979 (t) cc_final: 0.8631 (p) REVERT: R 97 LYS cc_start: 0.8422 (tttt) cc_final: 0.8154 (ttpp) REVERT: S 2 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8241 (mp0) REVERT: S 3 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8111 (p) REVERT: S 28 LYS cc_start: 0.7943 (mttp) cc_final: 0.7665 (mmmt) REVERT: S 67 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7258 (p0) REVERT: T 1 MET cc_start: 0.4498 (OUTLIER) cc_final: 0.4181 (tpt) REVERT: T 12 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8206 (mmp80) REVERT: T 33 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7840 (tttt) REVERT: T 49 LYS cc_start: 0.8621 (tptp) cc_final: 0.8327 (tttt) REVERT: T 69 ARG cc_start: 0.8393 (mtp85) cc_final: 0.7771 (mtp-110) REVERT: U 46 GLN cc_start: 0.8134 (mt0) cc_final: 0.7766 (tt0) REVERT: U 47 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8051 (mtpt) REVERT: U 81 ASP cc_start: 0.8767 (m-30) cc_final: 0.8518 (m-30) REVERT: U 88 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6689 (mm-30) REVERT: U 102 THR cc_start: 0.8853 (m) cc_final: 0.8357 (t) REVERT: V 59 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7409 (mt-10) REVERT: V 82 TYR cc_start: 0.9083 (p90) cc_final: 0.8681 (p90) REVERT: V 83 LYS cc_start: 0.8213 (mttt) cc_final: 0.7926 (mtpt) REVERT: V 85 LYS cc_start: 0.8123 (mttt) cc_final: 0.7761 (mtpp) REVERT: W 11 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7699 (ptp-170) REVERT: W 39 ARG cc_start: 0.9074 (mtp-110) cc_final: 0.8558 (mtp85) REVERT: W 40 GLN cc_start: 0.8933 (pt0) cc_final: 0.8695 (pt0) REVERT: W 44 LYS cc_start: 0.8825 (tttt) cc_final: 0.8598 (tttm) REVERT: W 70 GLU cc_start: 0.8641 (pt0) cc_final: 0.8338 (pt0) REVERT: Y 6 LEU cc_start: 0.8017 (mt) cc_final: 0.7632 (tp) REVERT: Y 16 THR cc_start: 0.8630 (m) cc_final: 0.8332 (p) REVERT: a 45 THR cc_start: 0.6757 (m) cc_final: 0.6509 (t) REVERT: a 60 PHE cc_start: 0.7865 (t80) cc_final: 0.7632 (t80) REVERT: a 61 ASN cc_start: 0.7875 (m-40) cc_final: 0.7208 (m110) REVERT: b 40 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7945 (mmt180) REVERT: b 50 ARG cc_start: 0.9063 (mtp180) cc_final: 0.8710 (mtp85) REVERT: b 55 ILE cc_start: 0.8958 (tp) cc_final: 0.8730 (pt) REVERT: c 5 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7524 (mt) REVERT: c 47 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8386 (m) REVERT: d 25 LYS cc_start: 0.8693 (tmmt) cc_final: 0.7985 (ttmm) REVERT: g 18 HIS cc_start: 0.7851 (m90) cc_final: 0.7628 (m170) REVERT: g 35 ARG cc_start: 0.6868 (mmt-90) cc_final: 0.6511 (mtp-110) REVERT: g 36 ASN cc_start: 0.6939 (t0) cc_final: 0.6321 (t0) REVERT: g 73 LYS cc_start: 0.7482 (mttm) cc_final: 0.7136 (mmmt) REVERT: g 82 ASP cc_start: 0.7991 (m-30) cc_final: 0.7582 (t0) REVERT: g 135 LEU cc_start: 0.5969 (mt) cc_final: 0.5600 (tp) REVERT: g 137 ARG cc_start: 0.6741 (mmt-90) cc_final: 0.6420 (mmm-85) REVERT: g 139 ARG cc_start: 0.7729 (ttp-110) cc_final: 0.7157 (mtp85) REVERT: g 165 ASP cc_start: 0.6141 (t0) cc_final: 0.5644 (t0) REVERT: g 169 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7804 (mm-30) REVERT: g 179 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8047 (mm) REVERT: g 223 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7689 (tm-30) REVERT: h 45 LYS cc_start: 0.8786 (tppt) cc_final: 0.8290 (tmtt) REVERT: h 83 ASP cc_start: 0.6569 (t0) cc_final: 0.6255 (t0) REVERT: h 110 GLU cc_start: 0.8759 (mp0) cc_final: 0.8501 (mp0) REVERT: h 135 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (tptm) REVERT: h 162 ILE cc_start: 0.8880 (mm) cc_final: 0.8612 (tt) REVERT: h 196 ILE cc_start: 0.9236 (mt) cc_final: 0.8885 (mm) REVERT: i 33 LYS cc_start: 0.7483 (mttp) cc_final: 0.7114 (mmtt) REVERT: i 45 LYS cc_start: 0.8030 (mttm) cc_final: 0.7719 (tppt) REVERT: i 73 ARG cc_start: 0.8561 (tpp-160) cc_final: 0.8036 (ttp80) REVERT: i 124 MET cc_start: 0.7987 (mtt) cc_final: 0.7316 (mmm) REVERT: i 128 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7575 (mtp180) REVERT: i 151 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7932 (ptmm) REVERT: i 166 GLU cc_start: 0.8348 (tt0) cc_final: 0.7768 (tp30) REVERT: i 185 LYS cc_start: 0.8823 (ptmm) cc_final: 0.8428 (mtpt) REVERT: i 206 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6302 (ptpt) REVERT: j 26 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8531 (ttmm) REVERT: k 1 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.5659 (mmt) REVERT: k 36 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8123 (mt) REVERT: k 38 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7057 (ptp90) REVERT: k 46 GLN cc_start: 0.7650 (tp40) cc_final: 0.7252 (tp-100) REVERT: k 65 GLU cc_start: 0.8502 (tt0) cc_final: 0.7492 (tm-30) REVERT: k 86 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8078 (mtt-85) REVERT: l 67 GLU cc_start: 0.8397 (tp30) cc_final: 0.7899 (mt-10) REVERT: l 110 LYS cc_start: 0.8392 (mmmt) cc_final: 0.8098 (mtpt) REVERT: l 123 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8115 (tp30) REVERT: l 146 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: l 148 ASN cc_start: 0.8269 (m-40) cc_final: 0.7978 (m-40) REVERT: m 31 LYS cc_start: 0.8658 (ttpm) cc_final: 0.8136 (mmtt) REVERT: m 94 LYS cc_start: 0.8146 (mttm) cc_final: 0.7886 (mtpp) REVERT: m 117 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8217 (mtt90) REVERT: n 27 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7242 (mmtt) REVERT: o 68 ARG cc_start: 0.8596 (mtm180) cc_final: 0.8366 (mtp85) REVERT: p 69 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7490 (mtp85) REVERT: p 85 MET cc_start: 0.8165 (mtt) cc_final: 0.7812 (mtp) REVERT: p 106 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7637 (ttp80) REVERT: q 44 LYS cc_start: 0.9052 (mptm) cc_final: 0.8755 (mmmt) REVERT: q 54 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7826 (tpp80) REVERT: q 108 LYS cc_start: 0.8554 (mttt) cc_final: 0.8198 (mptt) REVERT: r 41 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7468 (mp0) REVERT: r 73 ILE cc_start: 0.8426 (mm) cc_final: 0.8145 (mm) REVERT: t 67 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8410 (mt) REVERT: t 79 THR cc_start: 0.8065 (m) cc_final: 0.7807 (p) REVERT: u 28 ARG cc_start: 0.8987 (ttp-170) cc_final: 0.8728 (ttp80) REVERT: u 48 GLU cc_start: 0.8706 (pt0) cc_final: 0.8272 (pt0) REVERT: v 15 ASP cc_start: 0.7536 (p0) cc_final: 0.6921 (t0) REVERT: v 34 TYR cc_start: 0.9449 (m-80) cc_final: 0.9174 (m-80) REVERT: w 30 LYS cc_start: 0.8026 (tttt) cc_final: 0.7777 (mttt) REVERT: x 21 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7528 (mmtm) REVERT: y 21 ASN cc_start: 0.9235 (m-40) cc_final: 0.9011 (m110) REVERT: y 48 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7656 (mm-40) REVERT: y 52 ASN cc_start: 0.8632 (m-40) cc_final: 0.7973 (m-40) REVERT: z 33 ARG cc_start: 0.8368 (tmt170) cc_final: 0.7542 (mtm180) outliers start: 270 outliers final: 190 residues processed: 1462 average time/residue: 1.3715 time to fit residues: 3410.5249 Evaluate side-chains 1480 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1255 time to evaluate : 8.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU Chi-restraints excluded: chain 6 residue 18 THR 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 40 MET Chi-restraints excluded: chain 7 residue 21 LEU Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 153 LEU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 169 SER Chi-restraints excluded: chain 7 residue 180 THR Chi-restraints excluded: chain 7 residue 273 GLN Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 343 ARG Chi-restraints excluded: chain 7 residue 354 ASP Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 40 ILE 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 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain j residue 146 ASN Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 161 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 54 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 5.9990 chunk 588 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 771 optimal weight: 8.9990 chunk 427 optimal weight: 10.0000 chunk 884 optimal weight: 0.1980 chunk 716 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 529 optimal weight: 0.0980 chunk 930 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS B 115 GLN D 41 GLN F 143 GLN Q 56 GLN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN l 130 ASN l 142 HIS ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 29 ASN p 40 ASN t 35 GLN x 69 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 161777 Z= 0.167 Angle : 0.598 15.496 241363 Z= 0.323 Chirality : 0.034 0.397 30650 Planarity : 0.006 0.128 13379 Dihedral : 23.228 179.538 79436 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 4.84 % Allowed : 19.85 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.47 (0.11), residues: 6232 helix: 2.36 (0.11), residues: 2245 sheet: -0.89 (0.14), residues: 1145 loop : -0.85 (0.11), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 155 HIS 0.009 0.001 HIS 6 21 PHE 0.026 0.001 PHE R 93 TYR 0.019 0.001 TYR h 42 ARG 0.011 0.000 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1286 time to evaluate : 6.528 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: 6 24 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8065 (tt) REVERT: 7 131 ASP cc_start: 0.7579 (t0) cc_final: 0.7302 (m-30) REVERT: 7 149 GLU cc_start: 0.8454 (tt0) cc_final: 0.7966 (tm-30) REVERT: 7 168 GLU cc_start: 0.8259 (tt0) cc_final: 0.7115 (pm20) REVERT: 7 264 THR cc_start: 0.8105 (m) cc_final: 0.7553 (p) REVERT: 7 280 GLN cc_start: 0.7107 (pp30) cc_final: 0.6878 (pp30) REVERT: 7 297 GLU cc_start: 0.7522 (tp30) cc_final: 0.7095 (tp30) REVERT: 7 336 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8106 (mm) REVERT: 7 342 THR cc_start: 0.8009 (t) cc_final: 0.7594 (p) REVERT: 7 343 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6883 (mpt-90) REVERT: 7 346 GLN cc_start: 0.8094 (tp40) cc_final: 0.7810 (pm20) REVERT: 7 352 SER cc_start: 0.7739 (t) cc_final: 0.7483 (m) REVERT: B 183 LYS cc_start: 0.8733 (mttt) cc_final: 0.8292 (mmtt) REVERT: B 269 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7955 (ttt-90) REVERT: B 270 ARG cc_start: 0.8317 (mmm160) cc_final: 0.7635 (ttt-90) REVERT: B 271 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8003 (ptt-90) REVERT: C 42 ASN cc_start: 0.8177 (t0) cc_final: 0.7638 (t0) REVERT: C 43 ASP cc_start: 0.8479 (m-30) cc_final: 0.8163 (m-30) REVERT: C 128 ARG cc_start: 0.8820 (mtt90) cc_final: 0.8032 (mmt180) REVERT: D 16 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7679 (tp30) REVERT: D 124 PHE cc_start: 0.8983 (t80) cc_final: 0.8772 (t80) REVERT: E 11 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7032 (mm-30) REVERT: E 19 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7600 (tm-30) REVERT: E 20 PHE cc_start: 0.7948 (m-80) cc_final: 0.7670 (m-80) REVERT: E 42 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: E 85 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7896 (tp) REVERT: E 164 GLU cc_start: 0.7591 (pm20) cc_final: 0.6877 (pm20) REVERT: E 165 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7386 (mp0) REVERT: F 77 ILE cc_start: 0.8115 (mm) cc_final: 0.7878 (mt) REVERT: F 176 LYS cc_start: 0.4922 (OUTLIER) cc_final: 0.4522 (mttt) REVERT: G 15 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7813 (tt) REVERT: G 114 GLU cc_start: 0.4821 (OUTLIER) cc_final: 0.4519 (tp30) REVERT: H 38 MET cc_start: 0.4349 (mtm) cc_final: 0.3838 (tmm) REVERT: H 107 GLU cc_start: 0.2030 (OUTLIER) cc_final: 0.1804 (mt-10) REVERT: H 117 LEU cc_start: 0.2613 (OUTLIER) cc_final: 0.2186 (mm) REVERT: I 124 MET cc_start: 0.4087 (mtt) cc_final: 0.3814 (tpt) REVERT: J 9 GLU cc_start: 0.8161 (mp0) cc_final: 0.7801 (pm20) REVERT: J 61 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8344 (mmtm) REVERT: J 85 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7981 (mmtt) REVERT: J 96 ARG cc_start: 0.7963 (ttt-90) cc_final: 0.7643 (tpp80) REVERT: J 102 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8383 (mt-10) REVERT: J 129 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: K 66 LYS cc_start: 0.8878 (tttt) cc_final: 0.8639 (mtpp) REVERT: K 93 GLN cc_start: 0.8573 (pt0) cc_final: 0.8094 (mp10) REVERT: K 113 MET cc_start: 0.7697 (tpt) cc_final: 0.7219 (mmm) REVERT: L 69 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8351 (mtp85) REVERT: L 115 GLU cc_start: 0.8680 (pt0) cc_final: 0.8129 (tp30) REVERT: M 16 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8682 (mmt180) REVERT: M 47 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: M 106 ASP cc_start: 0.8444 (t0) cc_final: 0.8018 (t0) REVERT: N 23 ASN cc_start: 0.8522 (m-40) cc_final: 0.8084 (m110) REVERT: N 106 ASP cc_start: 0.8988 (p0) cc_final: 0.8660 (p0) REVERT: N 110 MET cc_start: 0.8779 (mmm) cc_final: 0.8493 (mmt) REVERT: Q 87 SER cc_start: 0.8972 (t) cc_final: 0.8628 (p) REVERT: R 71 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8528 (ttmt) REVERT: R 97 LYS cc_start: 0.8373 (tttt) cc_final: 0.8100 (ttpp) REVERT: S 2 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8256 (mp0) REVERT: S 3 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8070 (p) REVERT: S 28 LYS cc_start: 0.7938 (mttp) cc_final: 0.7665 (mmmt) REVERT: S 67 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7243 (p0) REVERT: T 1 MET cc_start: 0.4456 (OUTLIER) cc_final: 0.4179 (tpt) REVERT: T 12 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8242 (mmp80) REVERT: T 33 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7926 (tttt) REVERT: T 49 LYS cc_start: 0.8679 (tptp) cc_final: 0.8370 (tttt) REVERT: T 69 ARG cc_start: 0.8374 (mtp85) cc_final: 0.7671 (mtp-110) REVERT: U 46 GLN cc_start: 0.8057 (mt0) cc_final: 0.7715 (tt0) REVERT: U 47 LYS cc_start: 0.8413 (ttmt) cc_final: 0.7981 (mtpt) REVERT: U 81 ASP cc_start: 0.8754 (m-30) cc_final: 0.8485 (m-30) REVERT: U 88 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6668 (mm-30) REVERT: U 102 THR cc_start: 0.8843 (m) cc_final: 0.8343 (t) REVERT: V 2 PHE cc_start: 0.7580 (m-80) cc_final: 0.7355 (m-80) REVERT: V 59 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7345 (mt-10) REVERT: V 82 TYR cc_start: 0.9039 (p90) cc_final: 0.8632 (p90) REVERT: V 83 LYS cc_start: 0.8273 (mttt) cc_final: 0.8008 (mtpt) REVERT: V 85 LYS cc_start: 0.8087 (mttt) cc_final: 0.7737 (mtpp) REVERT: W 11 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7677 (ptp-170) REVERT: W 39 ARG cc_start: 0.9031 (mtp-110) cc_final: 0.8521 (mtp85) REVERT: W 40 GLN cc_start: 0.8893 (pt0) cc_final: 0.8641 (pt0) REVERT: W 44 LYS cc_start: 0.8798 (tttt) cc_final: 0.8582 (tttm) REVERT: W 70 GLU cc_start: 0.8652 (pt0) cc_final: 0.8356 (pt0) REVERT: Y 6 LEU cc_start: 0.8048 (mt) cc_final: 0.7661 (tp) REVERT: Y 16 THR cc_start: 0.8661 (m) cc_final: 0.8380 (p) REVERT: a 60 PHE cc_start: 0.7895 (t80) cc_final: 0.7671 (t80) REVERT: a 61 ASN cc_start: 0.7872 (m-40) cc_final: 0.7212 (m110) REVERT: b 40 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8026 (mmt180) REVERT: b 50 ARG cc_start: 0.9064 (mtp180) cc_final: 0.8691 (mtp85) REVERT: b 55 ILE cc_start: 0.9020 (tp) cc_final: 0.8746 (pt) REVERT: c 5 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7501 (mt) REVERT: c 47 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8377 (m) REVERT: d 25 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8008 (ttmm) REVERT: g 18 HIS cc_start: 0.8135 (m90) cc_final: 0.7699 (m170) REVERT: g 35 ARG cc_start: 0.6827 (mmt-90) cc_final: 0.6553 (mtp-110) REVERT: g 73 LYS cc_start: 0.7353 (mttm) cc_final: 0.7039 (mmmt) REVERT: g 82 ASP cc_start: 0.8015 (m-30) cc_final: 0.7562 (t0) REVERT: g 135 LEU cc_start: 0.5929 (mt) cc_final: 0.5575 (tp) REVERT: g 137 ARG cc_start: 0.6740 (mmt-90) cc_final: 0.6419 (mmm-85) REVERT: g 139 ARG cc_start: 0.7734 (ttp-110) cc_final: 0.7154 (mtp85) REVERT: g 169 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7829 (mm-30) REVERT: g 179 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8078 (mm) REVERT: g 223 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7724 (tm-30) REVERT: h 45 LYS cc_start: 0.8792 (tppt) cc_final: 0.8329 (tmtt) REVERT: h 83 ASP cc_start: 0.6567 (t0) cc_final: 0.6242 (t0) REVERT: h 135 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8384 (tptm) REVERT: h 162 ILE cc_start: 0.8864 (mm) cc_final: 0.8605 (tt) REVERT: h 196 ILE cc_start: 0.9226 (mt) cc_final: 0.8878 (mm) REVERT: i 33 LYS cc_start: 0.7450 (mttp) cc_final: 0.7084 (mmtt) REVERT: i 45 LYS cc_start: 0.8017 (mttm) cc_final: 0.7707 (tppt) REVERT: i 73 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.8059 (ttp80) REVERT: i 124 MET cc_start: 0.8031 (mtt) cc_final: 0.7387 (mmm) REVERT: i 128 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7558 (mtp180) REVERT: i 151 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7943 (ptmm) REVERT: i 166 GLU cc_start: 0.8320 (tt0) cc_final: 0.7706 (tp30) REVERT: i 185 LYS cc_start: 0.8834 (ptmm) cc_final: 0.8454 (mtpt) REVERT: i 206 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6281 (ptpt) REVERT: j 26 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8521 (ttmm) REVERT: k 1 MET cc_start: 0.7011 (mmm) cc_final: 0.5600 (mmt) REVERT: k 36 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8134 (mt) REVERT: k 38 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6982 (ptp90) REVERT: k 65 GLU cc_start: 0.8468 (tt0) cc_final: 0.7375 (tm-30) REVERT: k 86 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8009 (mtt-85) REVERT: l 67 GLU cc_start: 0.8397 (tp30) cc_final: 0.7908 (mt-10) REVERT: l 110 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8036 (mtpt) REVERT: l 123 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8120 (tp30) REVERT: l 146 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: l 148 ASN cc_start: 0.8287 (m-40) cc_final: 0.8034 (m-40) REVERT: m 31 LYS cc_start: 0.8643 (ttpm) cc_final: 0.8129 (mmtt) REVERT: m 94 LYS cc_start: 0.8133 (mttm) cc_final: 0.7875 (mtpp) REVERT: m 117 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8215 (mtt90) REVERT: n 27 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7283 (mmtt) REVERT: n 63 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.7963 (mt) REVERT: o 72 ARG cc_start: 0.7889 (mmt-90) cc_final: 0.7494 (mpt180) REVERT: p 69 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7512 (mtp85) REVERT: p 85 MET cc_start: 0.8154 (mtt) cc_final: 0.7854 (mtp) REVERT: p 106 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7732 (ttp80) REVERT: q 44 LYS cc_start: 0.9048 (mptm) cc_final: 0.8753 (mmmt) REVERT: q 54 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7799 (tpp80) REVERT: q 108 LYS cc_start: 0.8535 (mttt) cc_final: 0.8188 (mptt) REVERT: r 73 ILE cc_start: 0.8414 (mm) cc_final: 0.8139 (mm) REVERT: t 67 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8383 (mt) REVERT: u 48 GLU cc_start: 0.8682 (pt0) cc_final: 0.8230 (pt0) REVERT: v 15 ASP cc_start: 0.7507 (p0) cc_final: 0.6882 (t0) REVERT: v 34 TYR cc_start: 0.9421 (m-80) cc_final: 0.9155 (m-80) REVERT: w 30 LYS cc_start: 0.8037 (tttt) cc_final: 0.7808 (mttt) REVERT: x 21 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7455 (mmtm) REVERT: y 21 ASN cc_start: 0.9231 (m-40) cc_final: 0.9011 (m110) REVERT: y 48 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7633 (mm-40) REVERT: y 52 ASN cc_start: 0.8624 (m-40) cc_final: 0.7949 (m-40) REVERT: z 33 ARG cc_start: 0.8362 (tmt170) cc_final: 0.7535 (mtm180) outliers start: 251 outliers final: 184 residues processed: 1440 average time/residue: 1.3816 time to fit residues: 3377.8721 Evaluate side-chains 1473 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1255 time to evaluate : 6.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU 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 40 MET Chi-restraints excluded: chain 7 residue 21 LEU Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 273 GLN Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 343 ARG Chi-restraints excluded: chain 7 residue 354 ASP Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 20 SER 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 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 58 SER 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 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 128 LYS Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain k residue 87 SER Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 68 ASN Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 3 ASN Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 8.9990 chunk 933 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 608 optimal weight: 50.0000 chunk 255 optimal weight: 7.9990 chunk 1037 optimal weight: 0.0970 chunk 861 optimal weight: 5.9990 chunk 480 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 544 optimal weight: 0.9980 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS 7 322 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 143 GLN Q 56 GLN S 60 HIS a 41 HIS e 26 HIS ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN l 142 HIS ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 29 ASN p 40 ASN t 35 GLN ** v 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 161777 Z= 0.318 Angle : 0.649 15.610 241363 Z= 0.345 Chirality : 0.038 0.409 30650 Planarity : 0.006 0.137 13379 Dihedral : 23.170 178.864 79432 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 5.63 % Allowed : 19.98 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.33 (0.10), residues: 6232 helix: 2.12 (0.11), residues: 2236 sheet: -0.79 (0.14), residues: 1167 loop : -0.87 (0.11), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 155 HIS 0.006 0.001 HIS V 88 PHE 0.025 0.002 PHE R 93 TYR 0.021 0.002 TYR h 42 ARG 0.011 0.001 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1575 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1283 time to evaluate : 5.814 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: 6 24 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8228 (tt) REVERT: 7 131 ASP cc_start: 0.7623 (t0) cc_final: 0.7328 (m-30) REVERT: 7 149 GLU cc_start: 0.8440 (tt0) cc_final: 0.7615 (tm-30) REVERT: 7 153 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7724 (mp) REVERT: 7 168 GLU cc_start: 0.8221 (tt0) cc_final: 0.7086 (pm20) REVERT: 7 176 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8617 (pp) REVERT: 7 200 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: 7 238 ASP cc_start: 0.6365 (m-30) cc_final: 0.6016 (t0) REVERT: 7 264 THR cc_start: 0.8006 (m) cc_final: 0.7640 (p) REVERT: 7 336 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8146 (mm) REVERT: 7 342 THR cc_start: 0.7986 (t) cc_final: 0.7546 (p) REVERT: 7 346 GLN cc_start: 0.8057 (tp40) cc_final: 0.7735 (pm20) REVERT: 7 352 SER cc_start: 0.7919 (t) cc_final: 0.7662 (m) REVERT: 7 360 SER cc_start: 0.8803 (m) cc_final: 0.8528 (p) REVERT: B 183 LYS cc_start: 0.8790 (mttt) cc_final: 0.8382 (mmtt) REVERT: B 214 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8280 (mtm-85) REVERT: B 269 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7920 (ttt-90) REVERT: B 270 ARG cc_start: 0.8341 (mmm160) cc_final: 0.7628 (ttt-90) REVERT: B 271 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7914 (ptt-90) REVERT: C 42 ASN cc_start: 0.8206 (t0) cc_final: 0.7734 (t0) REVERT: C 43 ASP cc_start: 0.8391 (m-30) cc_final: 0.8058 (m-30) REVERT: C 128 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8007 (mmt180) REVERT: D 40 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7674 (ttt180) REVERT: D 153 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5600 (pp) REVERT: D 171 ASP cc_start: 0.7976 (t0) cc_final: 0.7728 (t70) REVERT: D 184 ASP cc_start: 0.8442 (t0) cc_final: 0.8217 (t0) REVERT: E 11 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7102 (mm-30) REVERT: E 20 PHE cc_start: 0.7942 (m-80) cc_final: 0.7732 (m-80) REVERT: E 42 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: E 85 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7951 (tp) REVERT: E 122 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: E 142 ASP cc_start: 0.7460 (t70) cc_final: 0.6942 (t0) REVERT: E 144 ASP cc_start: 0.7935 (p0) cc_final: 0.7645 (p0) REVERT: E 165 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7379 (mp0) REVERT: F 77 ILE cc_start: 0.8132 (mm) cc_final: 0.7905 (mt) REVERT: F 176 LYS cc_start: 0.4921 (OUTLIER) cc_final: 0.4534 (mttt) REVERT: G 15 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7803 (tt) REVERT: G 114 GLU cc_start: 0.4932 (OUTLIER) cc_final: 0.4611 (tp30) REVERT: H 38 MET cc_start: 0.4524 (mtm) cc_final: 0.4003 (tmm) REVERT: H 107 GLU cc_start: 0.2170 (OUTLIER) cc_final: 0.1840 (mt-10) REVERT: H 117 LEU cc_start: 0.2859 (OUTLIER) cc_final: 0.2471 (mm) REVERT: I 124 MET cc_start: 0.4101 (mtt) cc_final: 0.3838 (tpt) REVERT: J 9 GLU cc_start: 0.8181 (mp0) cc_final: 0.7805 (pm20) REVERT: J 61 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8365 (mmtm) REVERT: J 85 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8008 (mmtt) REVERT: J 96 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.7628 (tpp80) REVERT: J 102 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8483 (mt-10) REVERT: J 129 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: K 66 LYS cc_start: 0.8909 (tttt) cc_final: 0.8669 (mtpp) REVERT: K 93 GLN cc_start: 0.8612 (pt0) cc_final: 0.8122 (mp10) REVERT: K 113 MET cc_start: 0.7720 (tpt) cc_final: 0.7218 (mmm) REVERT: L 69 ARG cc_start: 0.8729 (mtp-110) cc_final: 0.8478 (mtp85) REVERT: M 16 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8706 (mmt180) REVERT: M 47 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: N 23 ASN cc_start: 0.8592 (m-40) cc_final: 0.7991 (m-40) REVERT: N 106 ASP cc_start: 0.9026 (p0) cc_final: 0.8695 (p0) REVERT: N 110 MET cc_start: 0.8810 (mmm) cc_final: 0.8560 (mmt) REVERT: O 74 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8730 (p) REVERT: Q 87 SER cc_start: 0.8964 (t) cc_final: 0.8578 (p) REVERT: R 97 LYS cc_start: 0.8445 (tttt) cc_final: 0.8172 (ttpp) REVERT: S 2 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8236 (mp0) REVERT: S 3 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8097 (p) REVERT: S 28 LYS cc_start: 0.7940 (mttp) cc_final: 0.7661 (mmmt) REVERT: S 67 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7193 (p0) REVERT: T 1 MET cc_start: 0.4623 (OUTLIER) cc_final: 0.4223 (tpt) REVERT: T 12 ARG cc_start: 0.8461 (mmm160) cc_final: 0.8240 (mmp80) REVERT: T 33 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7791 (tttt) REVERT: T 49 LYS cc_start: 0.8720 (tptp) cc_final: 0.8403 (tttt) REVERT: T 69 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7668 (mtp-110) REVERT: U 46 GLN cc_start: 0.8104 (mt0) cc_final: 0.7704 (tt0) REVERT: U 47 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8105 (mttt) REVERT: U 81 ASP cc_start: 0.8712 (m-30) cc_final: 0.8478 (m-30) REVERT: U 88 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6844 (mm-30) REVERT: V 59 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7398 (mt-10) REVERT: V 82 TYR cc_start: 0.9115 (p90) cc_final: 0.8646 (p90) REVERT: V 83 LYS cc_start: 0.8230 (mttt) cc_final: 0.7937 (mtpt) REVERT: V 85 LYS cc_start: 0.8031 (mttt) cc_final: 0.7678 (mtpp) REVERT: W 11 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7743 (ptp-170) REVERT: W 39 ARG cc_start: 0.9113 (mtp-110) cc_final: 0.8538 (mtp85) REVERT: W 40 GLN cc_start: 0.8956 (pt0) cc_final: 0.8730 (pt0) REVERT: W 70 GLU cc_start: 0.8655 (pt0) cc_final: 0.8350 (pt0) REVERT: X 50 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8279 (ttt-90) REVERT: Y 6 LEU cc_start: 0.8077 (mt) cc_final: 0.7649 (tp) REVERT: Y 16 THR cc_start: 0.8666 (m) cc_final: 0.8351 (p) REVERT: Y 48 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6771 (mpt180) REVERT: a 60 PHE cc_start: 0.7881 (t80) cc_final: 0.7681 (t80) REVERT: a 61 ASN cc_start: 0.7764 (m-40) cc_final: 0.7035 (m110) REVERT: b 40 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8091 (mmt180) REVERT: b 50 ARG cc_start: 0.9138 (mtp180) cc_final: 0.8770 (mtp85) REVERT: b 55 ILE cc_start: 0.9028 (tp) cc_final: 0.8808 (pt) REVERT: c 47 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8357 (m) REVERT: d 25 LYS cc_start: 0.8742 (tmmt) cc_final: 0.7981 (ttmm) REVERT: g 18 HIS cc_start: 0.8136 (m90) cc_final: 0.7669 (m170) REVERT: g 35 ARG cc_start: 0.6877 (mmt-90) cc_final: 0.6641 (mtp85) REVERT: g 73 LYS cc_start: 0.7478 (mttm) cc_final: 0.7122 (mmmt) REVERT: g 82 ASP cc_start: 0.7995 (m-30) cc_final: 0.7567 (t0) REVERT: g 135 LEU cc_start: 0.6039 (mt) cc_final: 0.5680 (tp) REVERT: g 137 ARG cc_start: 0.6626 (mmt-90) cc_final: 0.6270 (mmm-85) REVERT: g 139 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7146 (mtp85) REVERT: g 169 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7776 (mm-30) REVERT: g 175 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7901 (mt-10) REVERT: g 179 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7999 (mm) REVERT: g 223 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7713 (tm-30) REVERT: h 28 GLU cc_start: 0.8508 (pm20) cc_final: 0.8278 (pm20) REVERT: h 45 LYS cc_start: 0.8722 (tppt) cc_final: 0.8246 (tmtt) REVERT: h 83 ASP cc_start: 0.6447 (t0) cc_final: 0.6137 (t0) REVERT: h 110 GLU cc_start: 0.8748 (mp0) cc_final: 0.8529 (mp0) REVERT: h 135 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8326 (tptm) REVERT: h 162 ILE cc_start: 0.8885 (mm) cc_final: 0.8648 (tt) REVERT: i 33 LYS cc_start: 0.7535 (mttp) cc_final: 0.7160 (mmtt) REVERT: i 45 LYS cc_start: 0.8039 (mttm) cc_final: 0.7754 (tppt) REVERT: i 73 ARG cc_start: 0.8567 (tpp-160) cc_final: 0.8060 (ttp80) REVERT: i 124 MET cc_start: 0.7945 (mtt) cc_final: 0.7527 (mmm) REVERT: i 128 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7663 (mtp180) REVERT: i 166 GLU cc_start: 0.8372 (tt0) cc_final: 0.7762 (tp30) REVERT: i 185 LYS cc_start: 0.8917 (ptmm) cc_final: 0.8538 (mtpt) REVERT: i 206 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6400 (ptpt) REVERT: j 26 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8539 (ttmm) REVERT: j 115 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8800 (mt) REVERT: k 1 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.5597 (mmt) REVERT: k 36 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8020 (mt) REVERT: k 38 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7104 (ptp90) REVERT: k 65 GLU cc_start: 0.8407 (tt0) cc_final: 0.7356 (tm-30) REVERT: l 63 GLU cc_start: 0.8466 (tt0) cc_final: 0.8226 (tm-30) REVERT: l 79 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5562 (ppt90) REVERT: l 110 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8070 (mtpt) REVERT: l 146 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: m 18 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8884 (mm-40) REVERT: m 31 LYS cc_start: 0.8675 (ttpm) cc_final: 0.8144 (mmtt) REVERT: m 94 LYS cc_start: 0.8126 (mttm) cc_final: 0.7864 (mtpp) REVERT: m 117 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8221 (mtt90) REVERT: n 61 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7331 (pp) REVERT: n 63 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.7982 (mt) REVERT: o 68 ARG cc_start: 0.8662 (mtm180) cc_final: 0.8363 (mtp85) REVERT: o 85 ASP cc_start: 0.6439 (OUTLIER) cc_final: 0.6092 (t0) REVERT: p 85 MET cc_start: 0.8285 (mtt) cc_final: 0.7936 (mtp) REVERT: p 106 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7683 (ttp80) REVERT: q 44 LYS cc_start: 0.9073 (mptm) cc_final: 0.8761 (mmmt) REVERT: q 54 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7827 (tpp80) REVERT: q 108 LYS cc_start: 0.8560 (mttt) cc_final: 0.8203 (mptt) REVERT: t 67 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8453 (mt) REVERT: t 79 THR cc_start: 0.8176 (m) cc_final: 0.7891 (p) REVERT: u 48 GLU cc_start: 0.8716 (pt0) cc_final: 0.7857 (pt0) REVERT: u 51 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.7895 (ttp80) REVERT: v 15 ASP cc_start: 0.7497 (p0) cc_final: 0.7206 (p0) REVERT: v 30 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8645 (tttp) REVERT: w 30 LYS cc_start: 0.8121 (tttt) cc_final: 0.7863 (mttt) REVERT: x 21 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7742 (ttpp) REVERT: y 21 ASN cc_start: 0.9230 (m-40) cc_final: 0.9028 (m110) REVERT: y 48 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7552 (mm-40) REVERT: y 52 ASN cc_start: 0.8598 (m-40) cc_final: 0.7919 (m-40) REVERT: z 33 ARG cc_start: 0.8396 (tmt170) cc_final: 0.7514 (mtt-85) outliers start: 292 outliers final: 210 residues processed: 1472 average time/residue: 1.3610 time to fit residues: 3397.5534 Evaluate side-chains 1502 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1247 time to evaluate : 6.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU 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 40 MET Chi-restraints excluded: chain 7 residue 21 LEU Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 153 LEU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 169 SER Chi-restraints excluded: chain 7 residue 176 ILE Chi-restraints excluded: chain 7 residue 180 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 232 ILE Chi-restraints excluded: chain 7 residue 273 GLN Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 354 ASP Chi-restraints excluded: chain 7 residue 358 GLU Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 20 SER 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 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 40 ILE 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 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 75 LYS Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 50 ARG Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 48 ARG Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 205 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 87 SER Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 26 GLU Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 590 optimal weight: 5.9990 chunk 757 optimal weight: 7.9990 chunk 586 optimal weight: 7.9990 chunk 873 optimal weight: 8.9990 chunk 579 optimal weight: 2.9990 chunk 1033 optimal weight: 7.9990 chunk 646 optimal weight: 0.8980 chunk 629 optimal weight: 6.9990 chunk 477 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 22 GLN I 11 GLN Q 56 GLN R 18 GLN U 66 GLN i 131 ASN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 142 HIS n 5 GLN p 40 ASN t 35 GLN u 59 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 161777 Z= 0.388 Angle : 0.692 15.884 241363 Z= 0.365 Chirality : 0.040 0.382 30650 Planarity : 0.007 0.139 13379 Dihedral : 23.203 179.991 79430 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.37 % Rotamer: Outliers : 6.11 % Allowed : 20.12 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.04 (0.10), residues: 6232 helix: 1.73 (0.11), residues: 2240 sheet: -0.80 (0.14), residues: 1174 loop : -0.98 (0.11), residues: 2818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 7 191 HIS 0.007 0.001 HIS V 88 PHE 0.023 0.002 PHE R 93 TYR 0.043 0.002 TYR h 42 ARG 0.013 0.001 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1283 time to evaluate : 6.536 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: 6 24 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8140 (tt) REVERT: 7 14 LEU cc_start: 0.4305 (tt) cc_final: 0.4071 (mp) REVERT: 7 123 TYR cc_start: 0.7244 (m-80) cc_final: 0.6600 (m-80) REVERT: 7 131 ASP cc_start: 0.7781 (t0) cc_final: 0.7434 (m-30) REVERT: 7 153 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8352 (mp) REVERT: 7 168 GLU cc_start: 0.8204 (tt0) cc_final: 0.7029 (pm20) REVERT: 7 200 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7509 (ttm170) REVERT: 7 336 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8162 (mm) REVERT: 7 342 THR cc_start: 0.7923 (t) cc_final: 0.7521 (p) REVERT: 7 343 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6771 (mpt-90) REVERT: 7 346 GLN cc_start: 0.7977 (tp40) cc_final: 0.7640 (pm20) REVERT: 7 352 SER cc_start: 0.8137 (t) cc_final: 0.7886 (m) REVERT: 7 360 SER cc_start: 0.8825 (m) cc_final: 0.8586 (p) REVERT: B 183 LYS cc_start: 0.8805 (mttt) cc_final: 0.8439 (mmtt) REVERT: B 214 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8333 (mtm-85) REVERT: B 269 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7937 (ttt-90) REVERT: B 270 ARG cc_start: 0.8410 (mmm160) cc_final: 0.7679 (ttt-90) REVERT: B 271 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8141 (ptt-90) REVERT: C 42 ASN cc_start: 0.8136 (t0) cc_final: 0.7752 (t0) REVERT: C 43 ASP cc_start: 0.8327 (m-30) cc_final: 0.8011 (m-30) REVERT: C 89 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8392 (mm-30) REVERT: C 128 ARG cc_start: 0.8815 (mtt90) cc_final: 0.7981 (mmt180) REVERT: D 40 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7706 (ttt180) REVERT: D 153 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5975 (pp) REVERT: D 171 ASP cc_start: 0.7990 (t0) cc_final: 0.7762 (t70) REVERT: D 184 ASP cc_start: 0.8425 (t0) cc_final: 0.8188 (t0) REVERT: E 11 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7151 (mm-30) REVERT: E 42 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: E 85 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8053 (tp) REVERT: E 122 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: F 77 ILE cc_start: 0.8177 (mm) cc_final: 0.7975 (mt) REVERT: G 15 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7917 (tt) REVERT: G 114 GLU cc_start: 0.4870 (OUTLIER) cc_final: 0.4556 (tp30) REVERT: H 38 MET cc_start: 0.4607 (mtm) cc_final: 0.4032 (tmm) REVERT: H 107 GLU cc_start: 0.2561 (OUTLIER) cc_final: 0.2152 (mt-10) REVERT: H 117 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2737 (mm) REVERT: I 11 GLN cc_start: 0.3355 (OUTLIER) cc_final: 0.2805 (pm20) REVERT: I 124 MET cc_start: 0.4176 (mtt) cc_final: 0.3968 (tpt) REVERT: J 9 GLU cc_start: 0.8127 (mp0) cc_final: 0.7862 (pm20) REVERT: J 61 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8424 (mmtm) REVERT: J 85 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8010 (mmtt) REVERT: J 96 ARG cc_start: 0.8116 (ttt-90) cc_final: 0.7682 (tpp80) REVERT: J 102 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8454 (mt-10) REVERT: J 129 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: K 66 LYS cc_start: 0.8929 (tttt) cc_final: 0.8711 (mtpp) REVERT: K 93 GLN cc_start: 0.8724 (pt0) cc_final: 0.8243 (mp10) REVERT: K 113 MET cc_start: 0.7617 (tpt) cc_final: 0.7126 (mmm) REVERT: L 69 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.8507 (mtp85) REVERT: M 10 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8566 (mtm-85) REVERT: M 16 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8383 (mmt90) REVERT: M 47 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: M 105 MET cc_start: 0.9130 (ttp) cc_final: 0.8916 (tpp) REVERT: N 23 ASN cc_start: 0.8572 (m-40) cc_final: 0.7929 (m-40) REVERT: N 106 ASP cc_start: 0.9024 (p0) cc_final: 0.8686 (p0) REVERT: N 110 MET cc_start: 0.8782 (mmm) cc_final: 0.8543 (mmt) REVERT: Q 87 SER cc_start: 0.8929 (t) cc_final: 0.8491 (p) REVERT: R 97 LYS cc_start: 0.8417 (tttt) cc_final: 0.8151 (ttpp) REVERT: S 2 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8226 (mp0) REVERT: S 3 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8042 (p) REVERT: S 28 LYS cc_start: 0.7916 (mttp) cc_final: 0.7628 (mmmt) REVERT: T 1 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4483 (tpt) REVERT: T 33 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7770 (tttt) REVERT: T 49 LYS cc_start: 0.8648 (tptp) cc_final: 0.8354 (tttt) REVERT: T 69 ARG cc_start: 0.8370 (mtp85) cc_final: 0.7661 (mtp-110) REVERT: U 46 GLN cc_start: 0.8007 (mt0) cc_final: 0.7666 (tt0) REVERT: U 81 ASP cc_start: 0.8685 (m-30) cc_final: 0.8461 (m-30) REVERT: V 46 LYS cc_start: 0.8446 (mmtp) cc_final: 0.7882 (mmtm) REVERT: V 59 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7418 (mt-10) REVERT: V 83 LYS cc_start: 0.8179 (mttt) cc_final: 0.7960 (mtpt) REVERT: V 85 LYS cc_start: 0.8022 (mttt) cc_final: 0.7665 (mtpp) REVERT: W 11 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7887 (ptp-170) REVERT: W 39 ARG cc_start: 0.9052 (mtp-110) cc_final: 0.8503 (mtp85) REVERT: W 70 GLU cc_start: 0.8663 (pt0) cc_final: 0.8390 (pt0) REVERT: X 50 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8294 (ttt-90) REVERT: Y 6 LEU cc_start: 0.8106 (mt) cc_final: 0.7704 (tp) REVERT: Y 16 THR cc_start: 0.8686 (m) cc_final: 0.8387 (p) REVERT: Y 48 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6768 (mpt180) REVERT: b 40 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8133 (mmt180) REVERT: b 50 ARG cc_start: 0.9153 (mtp180) cc_final: 0.8802 (mtp85) REVERT: c 47 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8338 (m) REVERT: d 25 LYS cc_start: 0.8743 (tmmt) cc_final: 0.8006 (ttmm) REVERT: g 18 HIS cc_start: 0.8111 (m90) cc_final: 0.7243 (m170) REVERT: g 35 ARG cc_start: 0.6926 (mmt-90) cc_final: 0.6619 (mtp-110) REVERT: g 36 ASN cc_start: 0.6780 (t0) cc_final: 0.6289 (p0) REVERT: g 73 LYS cc_start: 0.7421 (mttm) cc_final: 0.7085 (mmmt) REVERT: g 139 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7188 (mtp85) REVERT: g 179 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7996 (mm) REVERT: h 28 GLU cc_start: 0.8539 (pm20) cc_final: 0.8298 (pm20) REVERT: h 45 LYS cc_start: 0.8666 (tppt) cc_final: 0.8208 (tmtt) REVERT: h 135 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (tptm) REVERT: h 162 ILE cc_start: 0.8899 (mm) cc_final: 0.8691 (tt) REVERT: h 192 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8511 (t) REVERT: i 33 LYS cc_start: 0.7582 (mttp) cc_final: 0.7193 (mmtt) REVERT: i 45 LYS cc_start: 0.7998 (mttm) cc_final: 0.7755 (tppt) REVERT: i 124 MET cc_start: 0.7882 (mtt) cc_final: 0.7490 (mmm) REVERT: i 128 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7681 (mtp180) REVERT: i 166 GLU cc_start: 0.8386 (tt0) cc_final: 0.7738 (tp30) REVERT: i 177 LYS cc_start: 0.7153 (mttt) cc_final: 0.6854 (mmtp) REVERT: i 185 LYS cc_start: 0.8887 (ptmm) cc_final: 0.8537 (mtpt) REVERT: i 206 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6513 (ptpt) REVERT: j 26 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8545 (ttmm) REVERT: j 115 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8786 (mt) REVERT: k 1 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.5431 (mmt) REVERT: k 38 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7161 (ptp90) REVERT: k 65 GLU cc_start: 0.8465 (tt0) cc_final: 0.7325 (tm-30) REVERT: k 86 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8197 (mtt-85) REVERT: l 63 GLU cc_start: 0.8509 (tt0) cc_final: 0.8264 (tm-30) REVERT: l 79 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5727 (ppt90) REVERT: l 110 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8148 (mppt) REVERT: l 146 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: m 31 LYS cc_start: 0.8685 (ttpm) cc_final: 0.8168 (mmtt) REVERT: m 94 LYS cc_start: 0.8167 (mttm) cc_final: 0.7918 (mtpp) REVERT: m 117 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8235 (mtt90) REVERT: p 56 ARG cc_start: 0.8088 (mpt-90) cc_final: 0.7716 (mtt180) REVERT: p 85 MET cc_start: 0.8309 (mtt) cc_final: 0.8023 (mtp) REVERT: p 106 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7725 (ttp80) REVERT: q 44 LYS cc_start: 0.9094 (mptm) cc_final: 0.8777 (mmmt) REVERT: q 54 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7809 (tpp80) REVERT: q 56 ARG cc_start: 0.8726 (ttm-80) cc_final: 0.8420 (ttm-80) REVERT: q 62 GLU cc_start: 0.8786 (tt0) cc_final: 0.8414 (tt0) REVERT: q 108 LYS cc_start: 0.8615 (mttt) cc_final: 0.8247 (mptt) REVERT: t 74 ASP cc_start: 0.7150 (t0) cc_final: 0.6790 (t0) REVERT: t 79 THR cc_start: 0.8257 (m) cc_final: 0.7977 (p) REVERT: t 84 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7895 (ttp-170) REVERT: u 48 GLU cc_start: 0.8669 (pt0) cc_final: 0.7873 (pm20) REVERT: v 30 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8663 (tttp) REVERT: v 60 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8120 (tm-30) REVERT: w 30 LYS cc_start: 0.8190 (tttt) cc_final: 0.7928 (mttt) REVERT: x 21 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7739 (ttpp) REVERT: y 48 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7245 (mm-40) REVERT: y 52 ASN cc_start: 0.8593 (m-40) cc_final: 0.7834 (m-40) REVERT: z 33 ARG cc_start: 0.8495 (tmt170) cc_final: 0.7591 (mtt-85) REVERT: z 47 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7816 (mtm110) outliers start: 317 outliers final: 233 residues processed: 1491 average time/residue: 1.4002 time to fit residues: 3548.8875 Evaluate side-chains 1520 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1247 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU 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 40 MET Chi-restraints excluded: chain 7 residue 21 LEU Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 127 ASP Chi-restraints excluded: chain 7 residue 153 LEU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 169 SER Chi-restraints excluded: chain 7 residue 180 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 232 ILE Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 343 ARG Chi-restraints excluded: chain 7 residue 354 ASP Chi-restraints excluded: chain 7 residue 358 GLU Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 20 SER 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 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 50 ARG Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 48 ARG Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 128 LYS Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 205 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain k residue 87 SER Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 59 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 26 GLU Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 72 ASP Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 7.9990 chunk 412 optimal weight: 7.9990 chunk 617 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 656 optimal weight: 0.7980 chunk 703 optimal weight: 2.9990 chunk 510 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 812 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 143 GLN K 29 HIS P 3 ASN Q 56 GLN i 131 ASN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 142 HIS p 40 ASN t 35 GLN y 21 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 161777 Z= 0.325 Angle : 0.657 15.734 241363 Z= 0.348 Chirality : 0.038 0.377 30650 Planarity : 0.006 0.135 13379 Dihedral : 23.190 179.817 79422 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 5.70 % Allowed : 20.87 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 6232 helix: 1.77 (0.11), residues: 2236 sheet: -0.75 (0.14), residues: 1190 loop : -0.93 (0.11), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 7 155 HIS 0.007 0.001 HIS V 88 PHE 0.024 0.002 PHE g 16 TYR 0.028 0.002 TYR h 42 ARG 0.013 0.001 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1260 time to evaluate : 6.576 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: 6 24 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8143 (tt) REVERT: 7 14 LEU cc_start: 0.4210 (tt) cc_final: 0.3962 (mp) REVERT: 7 123 TYR cc_start: 0.7174 (m-80) cc_final: 0.6617 (m-80) REVERT: 7 131 ASP cc_start: 0.7652 (t0) cc_final: 0.7278 (m-30) REVERT: 7 153 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8376 (mp) REVERT: 7 168 GLU cc_start: 0.8156 (tt0) cc_final: 0.7080 (pm20) REVERT: 7 200 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7519 (ttm170) REVERT: 7 238 ASP cc_start: 0.6312 (m-30) cc_final: 0.5951 (t0) REVERT: 7 336 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8175 (mm) REVERT: 7 342 THR cc_start: 0.7915 (t) cc_final: 0.7541 (p) REVERT: 7 343 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.6854 (mpt-90) REVERT: 7 346 GLN cc_start: 0.7984 (tp40) cc_final: 0.7640 (pm20) REVERT: 7 352 SER cc_start: 0.8156 (t) cc_final: 0.7946 (m) REVERT: 7 360 SER cc_start: 0.8824 (m) cc_final: 0.8589 (p) REVERT: B 183 LYS cc_start: 0.8773 (mttt) cc_final: 0.8384 (mmtt) REVERT: B 214 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8323 (mtm-85) REVERT: B 269 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7946 (ttt-90) REVERT: B 270 ARG cc_start: 0.8342 (mmm160) cc_final: 0.7650 (ttt-90) REVERT: B 271 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8567 (ptt-90) REVERT: C 42 ASN cc_start: 0.8154 (t0) cc_final: 0.7827 (t0) REVERT: C 43 ASP cc_start: 0.8297 (m-30) cc_final: 0.7988 (m-30) REVERT: C 89 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8392 (mm-30) REVERT: C 128 ARG cc_start: 0.8843 (mtt90) cc_final: 0.8019 (mmt180) REVERT: D 40 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7606 (ttt180) REVERT: D 153 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6100 (pp) REVERT: D 171 ASP cc_start: 0.8008 (t0) cc_final: 0.7772 (t70) REVERT: D 184 ASP cc_start: 0.8422 (t0) cc_final: 0.8185 (t0) REVERT: E 42 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: E 85 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7975 (tp) REVERT: E 96 MET cc_start: 0.8935 (ttp) cc_final: 0.8701 (ttp) REVERT: E 122 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: G 15 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7844 (tt) REVERT: G 114 GLU cc_start: 0.4789 (OUTLIER) cc_final: 0.4460 (tp30) REVERT: H 38 MET cc_start: 0.4387 (mtm) cc_final: 0.3845 (tmm) REVERT: H 52 MET cc_start: -0.2470 (mmt) cc_final: -0.2848 (mmm) REVERT: H 117 LEU cc_start: 0.3205 (OUTLIER) cc_final: 0.2770 (mm) REVERT: I 124 MET cc_start: 0.4154 (mtt) cc_final: 0.3918 (tpt) REVERT: J 9 GLU cc_start: 0.8197 (mp0) cc_final: 0.7983 (pm20) REVERT: J 61 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8409 (mmtm) REVERT: J 85 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7968 (mmtt) REVERT: J 96 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7686 (tpp80) REVERT: J 102 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8453 (mt-10) REVERT: J 129 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: K 66 LYS cc_start: 0.8932 (tttt) cc_final: 0.8713 (mtpp) REVERT: K 93 GLN cc_start: 0.8661 (pt0) cc_final: 0.8171 (mp10) REVERT: K 113 MET cc_start: 0.7661 (tpt) cc_final: 0.7174 (mmm) REVERT: L 69 ARG cc_start: 0.8762 (mtp-110) cc_final: 0.8529 (mtp85) REVERT: M 10 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8536 (mtm-85) REVERT: M 16 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8700 (mmt180) REVERT: M 47 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: N 23 ASN cc_start: 0.8547 (m-40) cc_final: 0.7921 (m-40) REVERT: N 106 ASP cc_start: 0.9017 (p0) cc_final: 0.8676 (p0) REVERT: N 110 MET cc_start: 0.8788 (mmm) cc_final: 0.8541 (mmt) REVERT: Q 87 SER cc_start: 0.8922 (t) cc_final: 0.8507 (p) REVERT: R 97 LYS cc_start: 0.8420 (tttt) cc_final: 0.8135 (ttpp) REVERT: S 2 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8246 (mp0) REVERT: S 3 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8057 (p) REVERT: S 28 LYS cc_start: 0.7934 (mttp) cc_final: 0.7642 (mmmt) REVERT: T 1 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.4467 (tpt) REVERT: T 33 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7820 (tttt) REVERT: T 49 LYS cc_start: 0.8698 (tptp) cc_final: 0.8393 (tttt) REVERT: T 69 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7663 (mtp-110) REVERT: U 46 GLN cc_start: 0.8026 (mt0) cc_final: 0.7654 (tt0) REVERT: U 81 ASP cc_start: 0.8703 (m-30) cc_final: 0.8471 (m-30) REVERT: V 59 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7415 (mt-10) REVERT: V 68 LYS cc_start: 0.7138 (mtmt) cc_final: 0.6903 (mtpt) REVERT: V 83 LYS cc_start: 0.8214 (mttt) cc_final: 0.7997 (mtpt) REVERT: V 85 LYS cc_start: 0.8018 (mttt) cc_final: 0.7666 (mtpp) REVERT: W 11 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7873 (ptp-170) REVERT: W 39 ARG cc_start: 0.9041 (mtp-110) cc_final: 0.8495 (mtp85) REVERT: W 40 GLN cc_start: 0.8984 (pt0) cc_final: 0.8782 (pt0) REVERT: W 70 GLU cc_start: 0.8698 (pt0) cc_final: 0.8409 (pt0) REVERT: Y 6 LEU cc_start: 0.8165 (mt) cc_final: 0.7776 (tp) REVERT: Y 16 THR cc_start: 0.8617 (m) cc_final: 0.8307 (p) REVERT: Y 48 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.6737 (mpt180) REVERT: a 61 ASN cc_start: 0.7705 (m-40) cc_final: 0.6964 (m110) REVERT: b 40 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8209 (mmt180) REVERT: c 47 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8349 (m) REVERT: d 25 LYS cc_start: 0.8696 (tmmt) cc_final: 0.7994 (ttmm) REVERT: g 18 HIS cc_start: 0.8016 (m90) cc_final: 0.7141 (m170) REVERT: g 35 ARG cc_start: 0.6884 (mmt-90) cc_final: 0.6571 (mtp-110) REVERT: g 36 ASN cc_start: 0.6773 (t0) cc_final: 0.6284 (p0) REVERT: g 73 LYS cc_start: 0.7469 (mttm) cc_final: 0.7116 (mmmt) REVERT: g 139 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7186 (mtp85) REVERT: g 167 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6749 (p0) REVERT: g 175 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7893 (mt-10) REVERT: g 179 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7984 (mm) REVERT: h 28 GLU cc_start: 0.8544 (pm20) cc_final: 0.8311 (pm20) REVERT: h 45 LYS cc_start: 0.8676 (tppt) cc_final: 0.8230 (tmtt) REVERT: h 135 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8249 (tptm) REVERT: h 162 ILE cc_start: 0.8881 (mm) cc_final: 0.8670 (tt) REVERT: h 192 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8543 (t) REVERT: h 196 ILE cc_start: 0.9238 (mt) cc_final: 0.8884 (mm) REVERT: i 33 LYS cc_start: 0.7626 (mttp) cc_final: 0.7250 (mmtt) REVERT: i 124 MET cc_start: 0.7861 (mtt) cc_final: 0.7461 (mmm) REVERT: i 128 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7710 (mtp85) REVERT: i 166 GLU cc_start: 0.8366 (tt0) cc_final: 0.7724 (tp30) REVERT: i 177 LYS cc_start: 0.7087 (mttt) cc_final: 0.6812 (mmtp) REVERT: i 185 LYS cc_start: 0.8893 (ptmm) cc_final: 0.8565 (mtpt) REVERT: i 206 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6481 (ptpt) REVERT: j 26 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8537 (ttmm) REVERT: j 65 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8520 (mm-30) REVERT: k 1 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.5555 (mmt) REVERT: k 38 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7120 (ptp90) REVERT: k 65 GLU cc_start: 0.8466 (tt0) cc_final: 0.7367 (tm-30) REVERT: k 86 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8116 (mtt-85) REVERT: l 63 GLU cc_start: 0.8496 (tt0) cc_final: 0.8209 (tm-30) REVERT: l 79 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5661 (ppt90) REVERT: l 110 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8287 (mppt) REVERT: l 146 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: m 18 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8888 (mm-40) REVERT: m 31 LYS cc_start: 0.8672 (ttpm) cc_final: 0.8160 (mmtt) REVERT: m 38 ASN cc_start: 0.8880 (t0) cc_final: 0.8585 (t0) REVERT: m 94 LYS cc_start: 0.8176 (mttm) cc_final: 0.7926 (mtpp) REVERT: m 117 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8245 (mtt90) REVERT: o 68 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8348 (mtp85) REVERT: o 85 ASP cc_start: 0.6372 (OUTLIER) cc_final: 0.6142 (t0) REVERT: p 56 ARG cc_start: 0.8051 (mpt-90) cc_final: 0.7668 (mtt180) REVERT: p 85 MET cc_start: 0.8313 (mtt) cc_final: 0.8034 (mtp) REVERT: p 106 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7722 (ttp80) REVERT: q 44 LYS cc_start: 0.9074 (mptm) cc_final: 0.8764 (mmmt) REVERT: q 54 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7811 (tpp80) REVERT: q 56 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8349 (ttm-80) REVERT: q 62 GLU cc_start: 0.8765 (tt0) cc_final: 0.8348 (tt0) REVERT: q 108 LYS cc_start: 0.8607 (mttt) cc_final: 0.8245 (mptt) REVERT: t 74 ASP cc_start: 0.7084 (t0) cc_final: 0.6721 (t0) REVERT: t 79 THR cc_start: 0.8246 (m) cc_final: 0.7972 (p) REVERT: t 84 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7993 (ttp-170) REVERT: u 48 GLU cc_start: 0.8676 (pt0) cc_final: 0.7869 (pm20) REVERT: v 30 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8653 (tttp) REVERT: v 60 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8163 (tm-30) REVERT: w 10 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.5905 (p90) REVERT: w 30 LYS cc_start: 0.8180 (tttt) cc_final: 0.7933 (mttt) REVERT: x 21 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7725 (ttpp) REVERT: y 48 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7486 (mm-40) REVERT: y 52 ASN cc_start: 0.8587 (m-40) cc_final: 0.7929 (m-40) REVERT: z 33 ARG cc_start: 0.8511 (tmt170) cc_final: 0.7601 (mtt-85) outliers start: 296 outliers final: 232 residues processed: 1450 average time/residue: 1.4597 time to fit residues: 3622.4626 Evaluate side-chains 1505 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1234 time to evaluate : 6.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU 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 40 MET Chi-restraints excluded: chain 7 residue 21 LEU Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 153 LEU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 169 SER Chi-restraints excluded: chain 7 residue 180 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 264 THR Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 343 ARG Chi-restraints excluded: chain 7 residue 358 GLU Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 48 ARG Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 167 ASP Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 205 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain k residue 87 SER Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 68 ASN Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 59 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 26 GLU Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 10 PHE Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 72 ASP Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 3 ASN Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 10.0000 chunk 989 optimal weight: 3.9990 chunk 903 optimal weight: 5.9990 chunk 962 optimal weight: 2.9990 chunk 579 optimal weight: 2.9990 chunk 419 optimal weight: 10.0000 chunk 756 optimal weight: 4.9990 chunk 295 optimal weight: 8.9990 chunk 870 optimal weight: 7.9990 chunk 910 optimal weight: 6.9990 chunk 959 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 143 GLN P 3 ASN Q 56 GLN i 131 ASN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 142 HIS p 40 ASN t 35 GLN y 21 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 161777 Z= 0.361 Angle : 0.674 15.780 241363 Z= 0.355 Chirality : 0.039 0.384 30650 Planarity : 0.006 0.138 13379 Dihedral : 23.178 178.783 79416 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 5.66 % Allowed : 21.19 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.02 (0.10), residues: 6232 helix: 1.67 (0.11), residues: 2239 sheet: -0.76 (0.14), residues: 1192 loop : -0.98 (0.11), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 7 155 HIS 0.009 0.001 HIS V 88 PHE 0.019 0.002 PHE k 8 TYR 0.035 0.002 TYR h 42 ARG 0.012 0.001 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1528 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1234 time to evaluate : 6.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 24 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8210 (tt) REVERT: 7 14 LEU cc_start: 0.4167 (tt) cc_final: 0.3894 (mp) REVERT: 7 113 LEU cc_start: 0.5036 (tp) cc_final: 0.4755 (mt) REVERT: 7 123 TYR cc_start: 0.7283 (m-80) cc_final: 0.6698 (m-80) REVERT: 7 131 ASP cc_start: 0.7596 (t0) cc_final: 0.7262 (m-30) REVERT: 7 153 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8403 (mp) REVERT: 7 168 GLU cc_start: 0.8134 (tt0) cc_final: 0.7096 (pm20) REVERT: 7 200 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7536 (ttm170) REVERT: 7 238 ASP cc_start: 0.6310 (m-30) cc_final: 0.5854 (t0) REVERT: 7 336 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (mm) REVERT: 7 342 THR cc_start: 0.7918 (t) cc_final: 0.7535 (p) REVERT: 7 343 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.6974 (mpt-90) REVERT: 7 346 GLN cc_start: 0.7962 (tp40) cc_final: 0.7602 (pm20) REVERT: 7 352 SER cc_start: 0.8202 (t) cc_final: 0.7961 (m) REVERT: 7 360 SER cc_start: 0.8827 (m) cc_final: 0.8594 (p) REVERT: B 183 LYS cc_start: 0.8783 (mttt) cc_final: 0.8411 (mmtt) REVERT: B 214 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8269 (mtm-85) REVERT: B 269 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8021 (ttp80) REVERT: B 270 ARG cc_start: 0.8390 (mmm160) cc_final: 0.7736 (ttt-90) REVERT: C 42 ASN cc_start: 0.8134 (t0) cc_final: 0.7703 (t0) REVERT: C 43 ASP cc_start: 0.8322 (m-30) cc_final: 0.7993 (m-30) REVERT: C 89 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8416 (mm-30) REVERT: C 128 ARG cc_start: 0.8791 (mtt90) cc_final: 0.7948 (mmt180) REVERT: D 40 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7695 (ttt180) REVERT: D 153 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6275 (pp) REVERT: D 184 ASP cc_start: 0.8415 (t0) cc_final: 0.8194 (t0) REVERT: E 22 TYR cc_start: 0.7960 (m-80) cc_final: 0.7713 (m-80) REVERT: E 42 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: E 85 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8047 (tp) REVERT: E 122 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: G 15 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7915 (tt) REVERT: G 114 GLU cc_start: 0.4763 (OUTLIER) cc_final: 0.4404 (tp30) REVERT: H 38 MET cc_start: 0.4444 (mtm) cc_final: 0.3965 (tmm) REVERT: H 52 MET cc_start: -0.2477 (mmt) cc_final: -0.2851 (mmm) REVERT: H 117 LEU cc_start: 0.3496 (OUTLIER) cc_final: 0.3141 (mm) REVERT: J 61 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8417 (mmtm) REVERT: J 85 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8029 (mmtt) REVERT: J 96 ARG cc_start: 0.8095 (ttt-90) cc_final: 0.7684 (tpp80) REVERT: J 102 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8435 (mt-10) REVERT: J 129 GLU cc_start: 0.8126 (pm20) cc_final: 0.7691 (tm-30) REVERT: K 66 LYS cc_start: 0.8941 (tttt) cc_final: 0.8714 (mtpp) REVERT: K 93 GLN cc_start: 0.8687 (pt0) cc_final: 0.8180 (mp10) REVERT: K 113 MET cc_start: 0.7603 (tpt) cc_final: 0.7143 (mmm) REVERT: L 69 ARG cc_start: 0.8798 (mtp-110) cc_final: 0.8569 (mtp85) REVERT: M 10 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8547 (mtm-85) REVERT: M 16 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8714 (mmt180) REVERT: M 47 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: M 105 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8978 (ttm) REVERT: N 23 ASN cc_start: 0.8567 (m-40) cc_final: 0.7946 (m-40) REVERT: N 106 ASP cc_start: 0.9021 (p0) cc_final: 0.8671 (p0) REVERT: N 110 MET cc_start: 0.8787 (mmm) cc_final: 0.8540 (mmt) REVERT: Q 87 SER cc_start: 0.8932 (t) cc_final: 0.8505 (p) REVERT: R 97 LYS cc_start: 0.8410 (tttt) cc_final: 0.8122 (ttpp) REVERT: S 2 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8250 (mp0) REVERT: S 3 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8060 (p) REVERT: S 28 LYS cc_start: 0.7913 (mttp) cc_final: 0.7624 (mtpt) REVERT: T 1 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.4028 (tpt) REVERT: T 33 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7810 (tttt) REVERT: T 49 LYS cc_start: 0.8651 (tptp) cc_final: 0.8357 (tttt) REVERT: T 69 ARG cc_start: 0.8370 (mtp85) cc_final: 0.7672 (mtp-110) REVERT: U 46 GLN cc_start: 0.8000 (mt0) cc_final: 0.7642 (tt0) REVERT: U 81 ASP cc_start: 0.8706 (m-30) cc_final: 0.8467 (m-30) REVERT: V 46 LYS cc_start: 0.8419 (mmtp) cc_final: 0.7876 (mmtm) REVERT: V 59 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7416 (mt-10) REVERT: V 68 LYS cc_start: 0.7139 (mtmt) cc_final: 0.6910 (mtpt) REVERT: V 83 LYS cc_start: 0.8177 (mttt) cc_final: 0.7954 (mtpt) REVERT: V 85 LYS cc_start: 0.8018 (mttt) cc_final: 0.7660 (mtpp) REVERT: W 11 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7884 (ptp-170) REVERT: W 39 ARG cc_start: 0.9057 (mtp-110) cc_final: 0.8500 (mtp85) REVERT: W 70 GLU cc_start: 0.8631 (pt0) cc_final: 0.8334 (pt0) REVERT: X 50 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8249 (ttt-90) REVERT: Y 6 LEU cc_start: 0.8145 (mt) cc_final: 0.7566 (tp) REVERT: Y 16 THR cc_start: 0.8618 (m) cc_final: 0.8310 (p) REVERT: Y 17 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: Y 48 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.6742 (mpt180) REVERT: b 40 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8185 (mmt180) REVERT: c 47 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (m) REVERT: d 25 LYS cc_start: 0.8695 (tmmt) cc_final: 0.8004 (ttmm) REVERT: g 18 HIS cc_start: 0.8052 (m90) cc_final: 0.7239 (m170) REVERT: g 35 ARG cc_start: 0.6780 (mmt-90) cc_final: 0.6519 (mtp-110) REVERT: g 36 ASN cc_start: 0.6762 (t0) cc_final: 0.6332 (p0) REVERT: g 73 LYS cc_start: 0.7478 (mttm) cc_final: 0.7099 (mmmt) REVERT: g 139 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7170 (mtp85) REVERT: g 167 ASP cc_start: 0.6953 (p0) cc_final: 0.6601 (p0) REVERT: g 179 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7979 (mm) REVERT: h 28 GLU cc_start: 0.8546 (pm20) cc_final: 0.8292 (pm20) REVERT: h 45 LYS cc_start: 0.8704 (tppt) cc_final: 0.8278 (tmtt) REVERT: h 162 ILE cc_start: 0.8890 (mm) cc_final: 0.8680 (tt) REVERT: h 192 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8529 (t) REVERT: i 33 LYS cc_start: 0.7651 (mttp) cc_final: 0.7247 (mmtt) REVERT: i 124 MET cc_start: 0.7842 (mtt) cc_final: 0.7436 (mmm) REVERT: i 128 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7693 (ttm110) REVERT: i 166 GLU cc_start: 0.8373 (tt0) cc_final: 0.7774 (tp30) REVERT: i 177 LYS cc_start: 0.7119 (mttt) cc_final: 0.6830 (mmtp) REVERT: i 185 LYS cc_start: 0.8900 (ptmm) cc_final: 0.8571 (mtpt) REVERT: i 206 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6534 (ptpt) REVERT: j 26 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8558 (ttmm) REVERT: j 65 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8523 (mm-30) REVERT: k 1 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.5517 (mmt) REVERT: k 38 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7116 (ptp90) REVERT: k 65 GLU cc_start: 0.8469 (tt0) cc_final: 0.7348 (tm-30) REVERT: l 17 LYS cc_start: 0.8452 (tppt) cc_final: 0.8010 (tttm) REVERT: l 79 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.5682 (ppt90) REVERT: l 110 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8282 (mtpt) REVERT: l 146 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: m 31 LYS cc_start: 0.8679 (ttpm) cc_final: 0.8165 (mmtt) REVERT: m 94 LYS cc_start: 0.8208 (mttm) cc_final: 0.7952 (mtpp) REVERT: m 117 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8256 (mtt90) REVERT: o 37 ARG cc_start: 0.6502 (tpm170) cc_final: 0.6013 (mmm160) REVERT: p 56 ARG cc_start: 0.8062 (mpt-90) cc_final: 0.7682 (mtt180) REVERT: p 85 MET cc_start: 0.8321 (mtt) cc_final: 0.8042 (mtp) REVERT: p 106 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7697 (ttp80) REVERT: q 44 LYS cc_start: 0.9069 (mptm) cc_final: 0.8748 (mmmt) REVERT: q 54 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7798 (tpp80) REVERT: q 56 ARG cc_start: 0.8744 (ttm-80) cc_final: 0.8526 (ttm-80) REVERT: q 62 GLU cc_start: 0.8763 (tt0) cc_final: 0.8441 (tt0) REVERT: q 108 LYS cc_start: 0.8610 (mttt) cc_final: 0.8245 (mptt) REVERT: t 74 ASP cc_start: 0.7120 (t0) cc_final: 0.6736 (t0) REVERT: t 79 THR cc_start: 0.8283 (m) cc_final: 0.8007 (p) REVERT: t 84 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7984 (ttp-170) REVERT: u 48 GLU cc_start: 0.8633 (pt0) cc_final: 0.7992 (pm20) REVERT: v 30 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8651 (tttp) REVERT: v 60 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8145 (tm-30) REVERT: w 10 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6209 (p90) REVERT: w 30 LYS cc_start: 0.8197 (tttt) cc_final: 0.7944 (mttt) REVERT: x 21 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7748 (ttpp) REVERT: y 48 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7479 (mm-40) REVERT: y 52 ASN cc_start: 0.8590 (m-40) cc_final: 0.7955 (m-40) REVERT: z 33 ARG cc_start: 0.8519 (tmt170) cc_final: 0.7587 (mtt-85) outliers start: 294 outliers final: 237 residues processed: 1421 average time/residue: 1.3801 time to fit residues: 3344.2531 Evaluate side-chains 1505 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1232 time to evaluate : 6.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU Chi-restraints excluded: chain 6 residue 18 THR 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 31 LYS Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 21 LEU Chi-restraints excluded: chain 7 residue 61 SER Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 127 ASP Chi-restraints excluded: chain 7 residue 153 LEU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 169 SER Chi-restraints excluded: chain 7 residue 180 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 232 ILE Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 343 ARG Chi-restraints excluded: chain 7 residue 358 GLU Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 41 PHE 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 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 50 ARG Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 48 ARG Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 205 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 68 ASN Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 59 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 26 GLU Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 10 PHE Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 72 ASP Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 7.9990 chunk 1018 optimal weight: 3.9990 chunk 621 optimal weight: 30.0000 chunk 483 optimal weight: 8.9990 chunk 707 optimal weight: 7.9990 chunk 1067 optimal weight: 5.9990 chunk 982 optimal weight: 1.9990 chunk 850 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 656 optimal weight: 5.9990 chunk 521 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 143 GLN Q 56 GLN i 131 ASN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 142 HIS p 40 ASN t 35 GLN y 21 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 161777 Z= 0.332 Angle : 0.666 15.736 241363 Z= 0.352 Chirality : 0.038 0.379 30650 Planarity : 0.006 0.137 13379 Dihedral : 23.183 178.776 79413 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 5.55 % Allowed : 21.39 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.03 (0.10), residues: 6232 helix: 1.66 (0.11), residues: 2239 sheet: -0.75 (0.14), residues: 1190 loop : -0.97 (0.11), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 155 HIS 0.008 0.001 HIS g 15 PHE 0.035 0.002 PHE a 60 TYR 0.032 0.002 TYR h 42 ARG 0.013 0.001 ARG r 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12464 Ramachandran restraints generated. 6232 Oldfield, 0 Emsley, 6232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1235 time to evaluate : 6.453 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: 6 24 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8238 (tt) REVERT: 7 14 LEU cc_start: 0.4028 (tt) cc_final: 0.3765 (mp) REVERT: 7 113 LEU cc_start: 0.5039 (tp) cc_final: 0.4756 (mt) REVERT: 7 123 TYR cc_start: 0.7301 (m-80) cc_final: 0.6708 (m-80) REVERT: 7 131 ASP cc_start: 0.7591 (t0) cc_final: 0.7255 (m-30) REVERT: 7 153 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8384 (mp) REVERT: 7 168 GLU cc_start: 0.8091 (tt0) cc_final: 0.7028 (pm20) REVERT: 7 200 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7535 (ttm170) REVERT: 7 238 ASP cc_start: 0.6301 (m-30) cc_final: 0.5831 (t0) REVERT: 7 336 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8171 (mm) REVERT: 7 342 THR cc_start: 0.7927 (t) cc_final: 0.7529 (p) REVERT: 7 343 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6982 (mpt-90) REVERT: 7 346 GLN cc_start: 0.7959 (tp40) cc_final: 0.7603 (pm20) REVERT: 7 352 SER cc_start: 0.8254 (t) cc_final: 0.8007 (m) REVERT: 7 360 SER cc_start: 0.8825 (m) cc_final: 0.8595 (p) REVERT: B 183 LYS cc_start: 0.8783 (mttt) cc_final: 0.8407 (mmtt) REVERT: B 214 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8340 (mtm-85) REVERT: B 269 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8035 (ttp80) REVERT: B 270 ARG cc_start: 0.8367 (mmm160) cc_final: 0.7728 (ttt-90) REVERT: C 42 ASN cc_start: 0.8164 (t0) cc_final: 0.7745 (t0) REVERT: C 43 ASP cc_start: 0.8315 (m-30) cc_final: 0.7985 (m-30) REVERT: C 89 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8406 (mm-30) REVERT: C 128 ARG cc_start: 0.8802 (mtt90) cc_final: 0.7965 (mmt180) REVERT: D 16 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7689 (tp30) REVERT: D 40 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7610 (ttt180) REVERT: D 153 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6299 (pp) REVERT: D 171 ASP cc_start: 0.7924 (t0) cc_final: 0.7493 (t70) REVERT: D 184 ASP cc_start: 0.8430 (t0) cc_final: 0.8209 (t0) REVERT: E 42 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: E 85 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8043 (tp) REVERT: E 122 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: G 15 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7919 (tt) REVERT: G 114 GLU cc_start: 0.4760 (OUTLIER) cc_final: 0.4398 (tp30) REVERT: H 38 MET cc_start: 0.4431 (mtm) cc_final: 0.3955 (tmm) REVERT: H 52 MET cc_start: -0.2494 (mmt) cc_final: -0.2863 (mmm) REVERT: H 117 LEU cc_start: 0.3498 (OUTLIER) cc_final: 0.3142 (mm) REVERT: J 61 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8420 (mmtm) REVERT: J 85 LYS cc_start: 0.8338 (mmmm) cc_final: 0.7974 (mmtt) REVERT: J 96 ARG cc_start: 0.8090 (ttt-90) cc_final: 0.7679 (tpp80) REVERT: J 102 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8417 (mt-10) REVERT: J 129 GLU cc_start: 0.8091 (pm20) cc_final: 0.7734 (tm-30) REVERT: K 66 LYS cc_start: 0.8942 (tttt) cc_final: 0.8718 (mtpp) REVERT: K 93 GLN cc_start: 0.8682 (pt0) cc_final: 0.8178 (mp10) REVERT: K 113 MET cc_start: 0.7603 (tpt) cc_final: 0.7138 (mmm) REVERT: L 69 ARG cc_start: 0.8797 (mtp-110) cc_final: 0.8571 (mtp85) REVERT: M 10 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8543 (mtm-85) REVERT: M 16 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8711 (mmt180) REVERT: M 47 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: N 23 ASN cc_start: 0.8560 (m-40) cc_final: 0.7946 (m-40) REVERT: N 106 ASP cc_start: 0.9039 (p0) cc_final: 0.8683 (p0) REVERT: N 110 MET cc_start: 0.8787 (mmm) cc_final: 0.8537 (mmt) REVERT: P 71 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: Q 87 SER cc_start: 0.8928 (t) cc_final: 0.8503 (p) REVERT: R 97 LYS cc_start: 0.8399 (tttt) cc_final: 0.8116 (ttpp) REVERT: S 2 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8251 (mp0) REVERT: S 3 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8061 (p) REVERT: S 28 LYS cc_start: 0.7931 (mttp) cc_final: 0.7640 (mmmt) REVERT: T 1 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.3828 (tpt) REVERT: T 33 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7815 (tttt) REVERT: T 49 LYS cc_start: 0.8654 (tptp) cc_final: 0.8357 (tttt) REVERT: T 69 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7666 (mtp-110) REVERT: U 46 GLN cc_start: 0.8008 (mt0) cc_final: 0.7654 (tt0) REVERT: U 81 ASP cc_start: 0.8702 (m-30) cc_final: 0.8468 (m-30) REVERT: V 46 LYS cc_start: 0.8415 (mmtp) cc_final: 0.7873 (mmtm) REVERT: V 59 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7423 (mt-10) REVERT: V 68 LYS cc_start: 0.7197 (mtmt) cc_final: 0.6926 (mtpt) REVERT: V 83 LYS cc_start: 0.8174 (mttt) cc_final: 0.7947 (mtpt) REVERT: V 85 LYS cc_start: 0.8010 (mttt) cc_final: 0.7651 (mtpp) REVERT: W 11 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7873 (ptp-170) REVERT: W 39 ARG cc_start: 0.9071 (mtp-110) cc_final: 0.8516 (mtp85) REVERT: W 70 GLU cc_start: 0.8651 (pt0) cc_final: 0.8335 (pt0) REVERT: X 50 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8256 (ttt-90) REVERT: Y 6 LEU cc_start: 0.8141 (mt) cc_final: 0.7553 (tp) REVERT: Y 16 THR cc_start: 0.8616 (m) cc_final: 0.8310 (p) REVERT: Y 17 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: Y 48 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.6717 (mpt180) REVERT: b 40 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8199 (mmt180) REVERT: c 47 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8351 (m) REVERT: d 25 LYS cc_start: 0.8687 (tmmt) cc_final: 0.7985 (ttmm) REVERT: g 18 HIS cc_start: 0.7990 (m90) cc_final: 0.7221 (m170) REVERT: g 35 ARG cc_start: 0.6897 (mmt-90) cc_final: 0.6652 (mtp-110) REVERT: g 36 ASN cc_start: 0.6765 (t0) cc_final: 0.6336 (p0) REVERT: g 73 LYS cc_start: 0.7468 (mttm) cc_final: 0.7092 (mmmt) REVERT: g 139 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7169 (mtp85) REVERT: g 167 ASP cc_start: 0.6958 (p0) cc_final: 0.6601 (p0) REVERT: g 175 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7868 (mt-10) REVERT: g 179 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7957 (mm) REVERT: h 28 GLU cc_start: 0.8549 (pm20) cc_final: 0.8308 (pm20) REVERT: h 45 LYS cc_start: 0.8703 (tppt) cc_final: 0.8280 (tmtt) REVERT: h 162 ILE cc_start: 0.8886 (mm) cc_final: 0.8673 (tt) REVERT: h 192 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8524 (t) REVERT: i 33 LYS cc_start: 0.7634 (mttp) cc_final: 0.7229 (mmtt) REVERT: i 124 MET cc_start: 0.7839 (mtt) cc_final: 0.7434 (mmm) REVERT: i 128 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7691 (ttm110) REVERT: i 166 GLU cc_start: 0.8370 (tt0) cc_final: 0.7762 (tp30) REVERT: i 177 LYS cc_start: 0.7120 (mttt) cc_final: 0.6838 (mmtp) REVERT: i 185 LYS cc_start: 0.8901 (ptmm) cc_final: 0.8572 (mtpt) REVERT: i 206 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6522 (ptpt) REVERT: j 13 GLU cc_start: 0.8273 (pt0) cc_final: 0.7416 (mt-10) REVERT: j 26 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8557 (ttmm) REVERT: j 65 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8531 (mm-30) REVERT: k 1 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.5516 (mmt) REVERT: k 38 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7173 (ptp90) REVERT: k 65 GLU cc_start: 0.8468 (tt0) cc_final: 0.7345 (tm-30) REVERT: l 79 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5755 (ppt90) REVERT: l 110 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8278 (mtpt) REVERT: l 146 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: m 18 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8885 (mm-40) REVERT: m 31 LYS cc_start: 0.8673 (ttpm) cc_final: 0.8162 (mmtt) REVERT: m 94 LYS cc_start: 0.8214 (mttm) cc_final: 0.7958 (mtpp) REVERT: m 117 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8244 (mtt90) REVERT: o 37 ARG cc_start: 0.6505 (tpm170) cc_final: 0.6125 (mmm160) REVERT: p 56 ARG cc_start: 0.8058 (mpt-90) cc_final: 0.7681 (mtt180) REVERT: p 85 MET cc_start: 0.8318 (mtt) cc_final: 0.8039 (mtp) REVERT: p 106 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7699 (ttp80) REVERT: q 44 LYS cc_start: 0.9067 (mptm) cc_final: 0.8744 (mmmt) REVERT: q 54 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7833 (tpp80) REVERT: q 56 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8523 (ttm-80) REVERT: q 62 GLU cc_start: 0.8771 (tt0) cc_final: 0.8452 (tt0) REVERT: q 108 LYS cc_start: 0.8604 (mttt) cc_final: 0.8242 (mptt) REVERT: t 74 ASP cc_start: 0.7092 (t0) cc_final: 0.6716 (t0) REVERT: t 79 THR cc_start: 0.8252 (m) cc_final: 0.7978 (p) REVERT: t 84 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7983 (ttp-170) REVERT: u 48 GLU cc_start: 0.8629 (pt0) cc_final: 0.7991 (pm20) REVERT: v 30 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8653 (tttp) REVERT: v 60 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8160 (tm-30) REVERT: w 10 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6215 (p90) REVERT: w 30 LYS cc_start: 0.8214 (tttt) cc_final: 0.7967 (mttt) REVERT: x 21 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7741 (ttpp) REVERT: y 48 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7287 (mm-40) REVERT: y 52 ASN cc_start: 0.8574 (m-40) cc_final: 0.7795 (m-40) REVERT: z 33 ARG cc_start: 0.8512 (tmt170) cc_final: 0.7582 (mtt-85) outliers start: 288 outliers final: 247 residues processed: 1418 average time/residue: 1.3384 time to fit residues: 3227.6920 Evaluate side-chains 1515 residues out of total 5191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1232 time to evaluate : 6.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 17 GLU 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 31 LYS Chi-restraints excluded: chain 6 residue 40 MET Chi-restraints excluded: chain 7 residue 21 LEU Chi-restraints excluded: chain 7 residue 61 SER Chi-restraints excluded: chain 7 residue 102 GLU Chi-restraints excluded: chain 7 residue 122 GLU Chi-restraints excluded: chain 7 residue 127 ASP Chi-restraints excluded: chain 7 residue 153 LEU Chi-restraints excluded: chain 7 residue 163 THR Chi-restraints excluded: chain 7 residue 169 SER Chi-restraints excluded: chain 7 residue 180 THR Chi-restraints excluded: chain 7 residue 196 THR Chi-restraints excluded: chain 7 residue 200 ARG Chi-restraints excluded: chain 7 residue 232 ILE Chi-restraints excluded: chain 7 residue 271 VAL Chi-restraints excluded: chain 7 residue 292 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 343 ARG Chi-restraints excluded: chain 7 residue 358 GLU Chi-restraints excluded: chain 7 residue 365 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 41 PHE 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 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 50 ARG Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 48 ARG Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 41 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 6 SER Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain g residue 128 LYS Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 53 SER Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain h residue 208 LEU Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 156 LYS Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 179 GLU Chi-restraints excluded: chain i residue 192 SER Chi-restraints excluded: chain i residue 206 LYS Chi-restraints excluded: chain j residue 11 LEU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 38 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain k residue 73 GLU Chi-restraints excluded: chain k residue 87 SER Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 68 ASN Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 79 ARG Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 146 GLU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain m residue 121 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 88 MET Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 59 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 18 ASP Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 26 GLU Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 55 ILE Chi-restraints excluded: chain v residue 58 VAL Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 10 PHE Chi-restraints excluded: chain w residue 43 ARG Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 72 ASP Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 3 ASN Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 4.9990 chunk 905 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 784 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 851 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 874 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 214 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 143 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 GLN ** j 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 142 HIS ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 ASN t 35 GLN y 21 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.085783 restraints weight = 221166.106| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.10 r_work: 0.2702 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 161777 Z= 0.466 Angle : 0.733 16.024 241363 Z= 0.382 Chirality : 0.042 0.381 30650 Planarity : 0.007 0.143 13379 Dihedral : 23.204 178.208 79413 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 5.84 % Allowed : 21.27 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.19 (0.10), residues: 6232 helix: 1.42 (0.11), residues: 2240 sheet: -0.79 (0.14), residues: 1194 loop : -1.06 (0.11), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 7 155 HIS 0.007 0.001 HIS g 15 PHE 0.029 0.002 PHE a 60 TYR 0.034 0.002 TYR h 42 ARG 0.012 0.001 ARG r 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50237.97 seconds wall clock time: 871 minutes 39.58 seconds (52299.58 seconds total)