Starting phenix.real_space_refine on Wed Mar 27 09:35:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4i_7341/03_2024/6c4i_7341_neut_updated.pdb" } resolution = 3.24 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= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4716 5.49 5 Mg 317 5.21 5 S 170 5.16 5 C 76387 2.51 5 N 28126 2.21 5 O 41728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 95": "NH1" <-> "NH2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 123": "NH1" <-> "NH2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "P GLU 112": "OE1" <-> "OE2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q GLU 34": "OE1" <-> "OE2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q GLU 102": "OE1" <-> "OE2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "T GLU 2": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V GLU 10": "OE1" <-> "OE2" Residue "V GLU 60": "OE1" <-> "OE2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V GLU 101": "OE1" <-> "OE2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Y GLU 76": "OE1" <-> "OE2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z GLU 13": "OE1" <-> "OE2" Residue "Z GLU 17": "OE1" <-> "OE2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 30": "NH1" <-> "NH2" Residue "0 GLU 37": "OE1" <-> "OE2" Residue "0 ARG 45": "NH1" <-> "NH2" Residue "0 GLU 58": "OE1" <-> "OE2" Residue "0 GLU 59": "OE1" <-> "OE2" Residue "1 GLU 11": "OE1" <-> "OE2" Residue "1 ARG 56": "NH1" <-> "NH2" Residue "1 ARG 59": "NH1" <-> "NH2" Residue "2 ARG 10": "NH1" <-> "NH2" Residue "2 ARG 16": "NH1" <-> "NH2" Residue "2 ARG 52": "NH1" <-> "NH2" Residue "3 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 28": "NH1" <-> "NH2" Residue "3 GLU 32": "OE1" <-> "OE2" Residue "3 GLU 35": "OE1" <-> "OE2" Residue "3 ARG 44": "NH1" <-> "NH2" Residue "4 ARG 3": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 33": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 13": "NH1" <-> "NH2" Residue "5 ARG 30": "NH1" <-> "NH2" Residue "5 ARG 40": "NH1" <-> "NH2" Residue "5 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 24": "NH1" <-> "NH2" Residue "b GLU 44": "OE1" <-> "OE2" Residue "b ARG 63": "NH1" <-> "NH2" Residue "b ARG 74": "NH1" <-> "NH2" Residue "b GLU 118": "OE1" <-> "OE2" Residue "b GLU 133": "OE1" <-> "OE2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b ARG 208": "NH1" <-> "NH2" Residue "b GLU 223": "OE1" <-> "OE2" Residue "b ARG 225": "NH1" <-> "NH2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "c PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c ARG 54": "NH1" <-> "NH2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c ARG 72": "NH1" <-> "NH2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c GLU 110": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c ARG 127": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 132": "NH1" <-> "NH2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c ARG 164": "NH1" <-> "NH2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d ARG 73": "NH1" <-> "NH2" Residue "d ARG 81": "NH1" <-> "NH2" Residue "d GLU 113": "OE1" <-> "OE2" Residue "d GLU 147": "OE1" <-> "OE2" Residue "d GLU 160": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "d GLU 202": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e ARG 45": "NH1" <-> "NH2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 69": "NH1" <-> "NH2" Residue "e ARG 93": "NH1" <-> "NH2" Residue "e GLU 101": "OE1" <-> "OE2" Residue "e GLU 145": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "g ARG 4": "NH1" <-> "NH2" Residue "g GLU 21": "OE1" <-> "OE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g ARG 53": "NH1" <-> "NH2" Residue "g GLU 58": "OE1" <-> "OE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g GLU 106": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h GLU 52": "OE1" <-> "OE2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h GLU 60": "OE1" <-> "OE2" Residue "h GLU 73": "OE1" <-> "OE2" Residue "h GLU 124": "OE1" <-> "OE2" Residue "i ARG 11": "NH1" <-> "NH2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i GLU 97": "OE1" <-> "OE2" Residue "i ARG 130": "NH1" <-> "NH2" Residue "j ARG 5": "NH1" <-> "NH2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 81": "OE1" <-> "OE2" Residue "j ARG 89": "NH1" <-> "NH2" Residue "k ARG 37": "NH1" <-> "NH2" Residue "k ARG 69": "NH1" <-> "NH2" Residue "k GLU 76": "OE1" <-> "OE2" Residue "k GLU 83": "OE1" <-> "OE2" Residue "k ARG 93": "NH1" <-> "NH2" Residue "k ARG 106": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 14": "NH1" <-> "NH2" Residue "l GLU 25": "OE1" <-> "OE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "m ARG 70": "NH1" <-> "NH2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "m ARG 109": "NH1" <-> "NH2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n ARG 59": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 65": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 85": "NH1" <-> "NH2" Residue "n GLU 92": "OE1" <-> "OE2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o ARG 17": "NH1" <-> "NH2" Residue "o GLU 26": "OE1" <-> "OE2" Residue "o ARG 72": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p GLU 34": "OE1" <-> "OE2" Residue "p GLU 45": "OE1" <-> "OE2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "q ARG 11": "NH1" <-> "NH2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q GLU 52": "OE1" <-> "OE2" Residue "q GLU 60": "OE1" <-> "OE2" Residue "q GLU 63": "OE1" <-> "OE2" Residue "q ARG 65": "NH1" <-> "NH2" Residue "q ARG 77": "NH1" <-> "NH2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r ARG 61": "NH1" <-> "NH2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s ARG 32": "NH1" <-> "NH2" Residue "s GLU 65": "OE1" <-> "OE2" Residue "t ARG 60": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "u GLU 8": "OE1" <-> "OE2" Residue "u GLU 24": "OE1" <-> "OE2" Residue "u GLU 31": "OE1" <-> "OE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u GLU 39": "OE1" <-> "OE2" Residue "u GLU 44": "OE1" <-> "OE2" Residue "u ARG 45": "NH1" <-> "NH2" Residue "u ARG 55": "NH1" <-> "NH2" Residue "u GLU 63": "OE1" <-> "OE2" Residue "u ARG 66": "NH1" <-> "NH2" Residue "u ARG 67": "NH1" <-> "NH2" Residue "u ARG 69": "NH1" <-> "NH2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v ARG 17": "NH1" <-> "NH2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 40": "OE1" <-> "OE2" Residue "v GLU 51": "OE1" <-> "OE2" Residue "v GLU 59": "OE1" <-> "OE2" Residue "v GLU 78": "OE1" <-> "OE2" Residue "v GLU 93": "OE1" <-> "OE2" Residue "v GLU 94": "OE1" <-> "OE2" Residue "v GLU 102": "OE1" <-> "OE2" Residue "v GLU 108": "OE1" <-> "OE2" Residue "v GLU 122": "OE1" <-> "OE2" Residue "v GLU 149": "OE1" <-> "OE2" Residue "v ARG 154": "NH1" <-> "NH2" Residue "v ARG 159": "NH1" <-> "NH2" Residue "v GLU 167": "OE1" <-> "OE2" Residue "v GLU 168": "OE1" <-> "OE2" Residue "v GLU 172": "OE1" <-> "OE2" Residue "v ARG 200": "NH1" <-> "NH2" Residue "v ARG 212": "NH1" <-> "NH2" Residue "v ARG 240": "NH1" <-> "NH2" Residue "v GLU 299": "OE1" <-> "OE2" Residue "v GLU 306": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151446 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 62356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2904, 62356 Classifications: {'RNA': 2904} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1050} Link IDs: {'rna2p': 460, 'rna3p': 2443} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "0" 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: "1" 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: "2" 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: "3" 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: "4" 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: "5" 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: "6" 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: "a" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 751, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1326} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1191 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "h" 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: "i" 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: "j" 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: "k" 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: "l" 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: "m" 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: "n" 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: "o" 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: "p" 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: "q" 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: "r" 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: "s" 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: "t" 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: "u" 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: "v" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2869 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 7, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "x" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "z" 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: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 230 Unusual residues: {' MG': 230} Classifications: {'undetermined': 230} Link IDs: {None: 229} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Unusual residues: {' MG': 71} Classifications: {'undetermined': 71} Link IDs: {None: 70} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" 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 90077 SG CYS 1 16 28.359 178.422 117.645 1.00250.04 S ATOM 90089 SG CYS 1 18 27.170 180.186 114.754 1.00244.75 S ATOM 92305 SG CYS 6 11 117.251 150.912 56.865 1.00 91.41 S ATOM 92330 SG CYS 6 14 117.762 147.514 58.057 1.00 75.00 S ATOM 92433 SG CYS 6 27 120.535 149.352 56.217 1.00 87.27 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG A3119 " occ=0.50 Time building chain proxies: 60.91, per 1000 atoms: 0.40 Number of scatterers: 151446 At special positions: 0 Unit cell: (264, 280.8, 235.2, 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 4716 15.00 Mg 317 11.99 O 41728 8.00 N 28126 7.00 C 76387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 70.46 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 16 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" ND1 HIS 6 33 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 14 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 27 " Number of angles added : 3 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11732 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: 201 helices and 77 sheets defined 41.1% alpha, 19.2% beta 1559 base pairs and 2290 stacking pairs defined. Time for finding SS restraints: 82.24 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.607A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.570A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.780A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.667A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 3.842A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.163A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.816A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.941A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 5.257A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.415A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 4.143A pdb=" N ALA E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 165 removed outlier: 3.628A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 5.592A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 21 removed outlier: 5.384A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.713A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.681A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 112 removed outlier: 4.827A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 5.819A pdb=" N ARG F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.547A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.992A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.982A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 removed outlier: 4.316A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.169A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.170A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 74 removed outlier: 4.501A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'I' and resid 3 through 22 removed outlier: 3.508A pdb=" N ASP I 7 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA I 22 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 48 Processing helix chain 'I' and resid 62 through 71 Proline residue: I 68 - end of helix removed outlier: 4.272A pdb=" N CYS I 71 " --> pdb=" O THR I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 79 removed outlier: 4.524A pdb=" N VAL I 77 " --> pdb=" O LYS I 73 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY I 78 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Proline residue: I 79 - end of helix No H-bonds generated for 'chain 'I' and resid 73 through 79' Processing helix chain 'I' and resid 94 through 106 removed outlier: 4.199A pdb=" N GLU I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE I 99 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA I 100 " --> pdb=" O PHE I 96 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE I 106 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 29 removed outlier: 4.661A pdb=" N LEU J 27 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 49 removed outlier: 4.070A pdb=" N PHE J 37 " --> pdb=" O ASN J 33 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS J 38 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER J 47 " --> pdb=" O ALA J 43 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE J 48 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU J 49 " --> pdb=" O THR J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 84 removed outlier: 3.738A pdb=" N LEU J 78 " --> pdb=" O PRO J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.808A pdb=" N THR J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS J 112 " --> pdb=" O ILE J 108 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 136 removed outlier: 3.597A pdb=" N MET J 124 " --> pdb=" O ASP J 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 88 through 96 Processing helix chain 'K' and resid 97 through 110 removed outlier: 3.991A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Proline residue: K 110 - end of helix Processing helix chain 'K' and resid 112 through 123 removed outlier: 3.856A pdb=" N LEU K 122 " --> pdb=" O MET K 118 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.560A pdb=" N LYS K 72 " --> pdb=" O ASN K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 72' Processing helix chain 'L' and resid 104 through 109 removed outlier: 3.996A pdb=" N ARG L 108 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER L 109 " --> pdb=" O ARG L 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 104 through 109' Processing helix chain 'L' and resid 112 through 120 Proline residue: L 120 - end of helix Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.975A pdb=" N ARG M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER M 42 " --> pdb=" O GLN M 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 37 through 42' Processing helix chain 'M' and resid 56 through 62 Proline residue: M 62 - end of helix Processing helix chain 'M' and resid 68 through 75 removed outlier: 3.837A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR M 74 " --> pdb=" O LYS M 70 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA M 75 " --> pdb=" O ALA M 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 68 through 75' Processing helix chain 'M' and resid 78 through 85 removed outlier: 3.923A pdb=" N LEU M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS M 84 " --> pdb=" O SER M 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 85' Processing helix chain 'M' and resid 91 through 99 Processing helix chain 'M' and resid 128 through 139 Processing helix chain 'N' and resid 42 through 58 Processing helix chain 'N' and resid 109 through 125 removed outlier: 4.129A pdb=" N LYS N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU N 124 " --> pdb=" O ALA N 120 " (cutoff:3.500A) Proline residue: N 125 - end of helix Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 58 removed outlier: 4.003A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix removed outlier: 4.265A pdb=" N THR O 57 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 88 removed outlier: 3.521A pdb=" N LEU O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) Proline residue: O 85 - end of helix Processing helix chain 'P' and resid 2 through 22 removed outlier: 4.314A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 63 removed outlier: 4.181A pdb=" N GLN P 61 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU P 62 " --> pdb=" O ILE P 58 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 86 Processing helix chain 'P' and resid 101 through 114 Processing helix chain 'Q' and resid 2 through 13 removed outlier: 3.527A pdb=" N GLU Q 11 " --> pdb=" O GLN Q 7 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN Q 12 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 104 removed outlier: 4.751A pdb=" N ARG Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU Q 102 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG Q 103 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR Q 104 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 97 through 104' Processing helix chain 'R' and resid 6 through 22 removed outlier: 3.643A pdb=" N ALA R 10 " --> pdb=" O ARG R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 31 removed outlier: 3.912A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 37 removed outlier: 3.719A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 73 removed outlier: 4.003A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 103 through 118 Processing helix chain 'T' and resid 13 through 25 removed outlier: 3.522A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 61 removed outlier: 3.907A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 11 removed outlier: 4.018A pdb=" N LEU U 11 " --> pdb=" O LEU U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 26 Processing helix chain 'U' and resid 39 through 50 Processing helix chain 'V' and resid 66 through 71 removed outlier: 3.671A pdb=" N VAL V 70 " --> pdb=" O GLN V 66 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA V 71 " --> pdb=" O VAL V 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 66 through 71' Processing helix chain 'W' and resid 13 through 24 removed outlier: 3.520A pdb=" N SER W 17 " --> pdb=" O GLY W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 53 removed outlier: 3.962A pdb=" N LYS W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 59 removed outlier: 3.823A pdb=" N SER W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 63 Processing helix chain 'Y' and resid 64 through 75 Processing helix chain 'Z' and resid 2 through 9 removed outlier: 4.282A pdb=" N GLU Z 8 " --> pdb=" O LYS Z 4 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS Z 9 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 35 removed outlier: 3.583A pdb=" N SER Z 34 " --> pdb=" O MET Z 30 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Z 35 " --> pdb=" O GLN Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 62 removed outlier: 4.594A pdb=" N LEU Z 43 " --> pdb=" O GLN Z 39 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY Z 62 " --> pdb=" O ASN Z 58 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 28 Processing helix chain '0' and resid 41 through 52 Processing helix chain '1' and resid 44 through 52 removed outlier: 5.349A pdb=" N GLN 1 48 " --> pdb=" O PHE 1 44 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG 1 49 " --> pdb=" O THR 1 45 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL 1 51 " --> pdb=" O LYS 1 47 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA 1 52 " --> pdb=" O GLN 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 55 through 64 removed outlier: 3.978A pdb=" N ARG 1 59 " --> pdb=" O GLY 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 19 removed outlier: 4.769A pdb=" N HIS 2 19 " --> pdb=" O MET 2 15 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 31 Proline residue: 3 31 - end of helix Processing helix chain '4' and resid 8 through 16 Processing helix chain '4' and resid 17 through 25 removed outlier: 3.702A pdb=" N THR 4 24 " --> pdb=" O ALA 4 20 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS 4 25 " --> pdb=" O ARG 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 38 Processing helix chain '5' and resid 7 through 14 Processing helix chain '5' and resid 32 through 37 removed outlier: 4.451A pdb=" N LYS 5 36 " --> pdb=" O ILE 5 32 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA 5 37 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 32 through 37' Processing helix chain '5' and resid 38 through 46 Proline residue: 5 46 - end of helix Processing helix chain '5' and resid 51 through 63 removed outlier: 4.572A pdb=" N GLY 5 56 " --> pdb=" O LYS 5 52 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU 5 57 " --> pdb=" O GLY 5 53 " (cutoff:3.500A) Proline residue: 5 63 - end of helix Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.198A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) Proline residue: b 29 - end of helix removed outlier: 5.767A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 32' Processing helix chain 'b' and resid 43 through 64 Proline residue: b 48 - end of helix removed outlier: 3.568A pdb=" N LYS b 64 " --> pdb=" O ILE b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.635A pdb=" N CYS b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 4.102A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.664A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.554A pdb=" N ALA c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.027A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.572A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 3.596A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.117A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.599A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.005A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 Processing helix chain 'd' and resid 146 through 151 removed outlier: 4.522A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 3.765A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.559A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 3.617A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 4.402A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.633A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 148 removed outlier: 5.601A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 165 removed outlier: 3.679A pdb=" N ILE e 164 " --> pdb=" O SER e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 33 removed outlier: 3.555A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.570A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.626A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 5.473A pdb=" N VAL g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.573A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.651A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.769A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA g 98 " --> pdb=" O VAL g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.700A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 56 Proline residue: i 51 - end of helix removed outlier: 3.505A pdb=" N ASP i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 91 Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.921A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 4.346A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 4.033A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 3.830A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 76 removed outlier: 4.956A pdb=" N GLU k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 104 removed outlier: 3.944A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.776A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.720A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 64 removed outlier: 4.070A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 52 Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.040A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.952A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 82 Processing helix chain 'r' and resid 11 through 17 removed outlier: 3.988A pdb=" N ALA r 15 " --> pdb=" O CYS r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.506A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.794A pdb=" N GLN r 54 " --> pdb=" O LYS r 50 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.521A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 41 Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.689A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 37 removed outlier: 4.621A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing helix chain 'v' and resid 4 through 26 removed outlier: 3.594A pdb=" N GLU v 16 " --> pdb=" O GLN v 12 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 44 removed outlier: 3.617A pdb=" N GLN v 43 " --> pdb=" O ALA v 39 " (cutoff:3.500A) Proline residue: v 44 - end of helix Processing helix chain 'v' and resid 45 through 50 removed outlier: 4.330A pdb=" N GLU v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) Proline residue: v 50 - end of helix No H-bonds generated for 'chain 'v' and resid 45 through 50' Processing helix chain 'v' and resid 51 through 88 removed outlier: 3.895A pdb=" N SER v 62 " --> pdb=" O LYS v 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU v 63 " --> pdb=" O GLU v 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU v 78 " --> pdb=" O LYS v 74 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU v 86 " --> pdb=" O GLY v 82 " (cutoff:3.500A) Processing helix chain 'v' and resid 92 through 120 removed outlier: 3.630A pdb=" N SER v 120 " --> pdb=" O ARG v 116 " (cutoff:3.500A) Processing helix chain 'v' and resid 138 through 160 Processing helix chain 'v' and resid 187 through 193 Processing helix chain 'v' and resid 235 through 240 removed outlier: 3.772A pdb=" N LEU v 239 " --> pdb=" O ASN v 235 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG v 240 " --> pdb=" O PRO v 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 235 through 240' Processing helix chain 'v' and resid 251 through 257 removed outlier: 3.769A pdb=" N ASN v 255 " --> pdb=" O GLY v 251 " (cutoff:3.500A) Processing helix chain 'v' and resid 279 through 322 removed outlier: 3.614A pdb=" N ILE v 317 " --> pdb=" O ASN v 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY v 318 " --> pdb=" O LYS v 314 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TRP v 319 " --> pdb=" O SER v 315 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY v 320 " --> pdb=" O ASP v 316 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER v 321 " --> pdb=" O ILE v 317 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN v 322 " --> pdb=" O GLY v 318 " (cutoff:3.500A) Processing helix chain 'v' and resid 344 through 351 Processing helix chain 'v' and resid 353 through 364 removed outlier: 4.075A pdb=" N ALA v 359 " --> pdb=" O GLN v 355 " (cutoff:3.500A) Processing helix chain 'w' and resid 14 through 23 removed outlier: 3.518A pdb=" N ALA w 18 " --> pdb=" O ASN w 14 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP w 22 " --> pdb=" O ALA w 18 " (cutoff:3.500A) Proline residue: w 23 - end of helix Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.894A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 162 through 165 removed outlier: 6.610A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.442A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 7 removed outlier: 7.008A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.460A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 79 through 84 removed outlier: 5.467A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.132A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 1 through 6 removed outlier: 3.837A pdb=" N MET E 1 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 117 through 120 Processing sheet with id= 11, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.406A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 13, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 14, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 15, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.818A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 17 through 21 removed outlier: 4.496A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 76 through 82 removed outlier: 6.251A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 23 through 28 removed outlier: 4.206A pdb=" N LEU I 23 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 25 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 6 through 13 removed outlier: 4.265A pdb=" N VAL J 69 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR J 59 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR J 67 " --> pdb=" O THR J 59 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 52 through 57 removed outlier: 4.721A pdb=" N ASP K 19 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 74 through 78 removed outlier: 7.547A pdb=" N GLY K 83 " --> pdb=" O THR K 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 5 through 9 removed outlier: 4.057A pdb=" N THR L 6 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP L 37 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS L 59 " --> pdb=" O LEU L 87 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'N' and resid 37 through 40 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'N' and resid 62 through 65 removed outlier: 3.645A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU N 33 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS N 100 " --> pdb=" O ALA N 35 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 30 through 36 removed outlier: 8.039A pdb=" N SER N 30 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS N 127 " --> pdb=" O VAL N 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 33 through 37 removed outlier: 5.482A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N TYR O 94 " --> pdb=" O VAL O 116 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.656A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Q' and resid 38 through 45 removed outlier: 6.770A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 49 through 53 removed outlier: 3.546A pdb=" N ALA Q 49 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ARG Q 53 " --> pdb=" O HIS Q 56 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N SER Q 57 " --> pdb=" O THR Q 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 11 through 15 removed outlier: 6.872A pdb=" N LEU S 39 " --> pdb=" O GLY S 50 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN S 43 " --> pdb=" O GLU S 46 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU S 46 " --> pdb=" O ASN S 43 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 18 through 23 removed outlier: 4.485A pdb=" N GLN S 18 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP S 95 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS S 60 " --> pdb=" O THR S 99 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 57 through 60 Processing sheet with id= 33, first strand: chain 'S' and resid 65 through 68 Processing sheet with id= 34, first strand: chain 'S' and resid 71 through 78 removed outlier: 4.033A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 1 through 8 removed outlier: 6.396A pdb=" N MET T 1 " --> pdb=" O ASP T 109 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP T 109 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL T 106 " --> pdb=" O THR T 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 73 through 78 Processing sheet with id= 37, first strand: chain 'T' and resid 79 through 88 removed outlier: 4.300A pdb=" N THR T 100 " --> pdb=" O PRO T 80 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG T 92 " --> pdb=" O ARG T 88 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 28 through 33 removed outlier: 6.256A pdb=" N ASN U 28 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS U 66 " --> pdb=" O ARG U 77 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP U 79 " --> pdb=" O LYS U 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS U 64 " --> pdb=" O ASP U 79 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS U 81 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL U 62 " --> pdb=" O LYS U 81 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA U 83 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR U 60 " --> pdb=" O ALA U 83 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL U 85 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL U 58 " --> pdb=" O VAL U 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 40 through 44 removed outlier: 5.423A pdb=" N ASN V 40 " --> pdb=" O ALA V 63 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 83 through 87 Processing sheet with id= 41, first strand: chain 'W' and resid 69 through 72 removed outlier: 6.766A pdb=" N ALA W 39 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 51 through 54 removed outlier: 4.351A pdb=" N THR X 58 " --> pdb=" O GLY X 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 66 through 71 Processing sheet with id= 44, first strand: chain 'Y' and resid 12 through 19 removed outlier: 3.678A pdb=" N SER Y 19 " --> pdb=" O ASN Y 23 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Y' and resid 35 through 41 Processing sheet with id= 46, first strand: chain '0' and resid 33 through 39 removed outlier: 4.240A pdb=" N HIS 0 34 " --> pdb=" O GLN 0 9 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N MET 0 54 " --> pdb=" O THR 0 10 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '1' and resid 20 through 25 removed outlier: 4.716A pdb=" N ASN 1 20 " --> pdb=" O CYS 1 16 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS 1 16 " --> pdb=" O ASN 1 20 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '2' and resid 29 through 32 removed outlier: 4.352A pdb=" N GLU 2 36 " --> pdb=" O ASP 2 31 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '3' and resid 20 through 25 removed outlier: 6.952A pdb=" N ILE 3 48 " --> pdb=" O SER 3 14 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU 3 34 " --> pdb=" O GLU 3 51 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '5' and resid 22 through 25 removed outlier: 5.591A pdb=" N PHE 5 22 " --> pdb=" O VAL 5 50 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '6' and resid 13 through 19 removed outlier: 8.623A pdb=" N ASN 6 13 " --> pdb=" O SER 6 28 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER 6 28 " --> pdb=" O ASN 6 13 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'b' and resid 15 through 18 removed outlier: 5.136A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N HIS b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.604A pdb=" N ALA b 185 " --> pdb=" O PHE b 198 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'c' and resid 54 through 59 Processing sheet with id= 55, first strand: chain 'c' and resid 164 through 169 removed outlier: 5.779A pdb=" N ARG c 164 " --> pdb=" O GLY c 155 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'd' and resid 141 through 145 removed outlier: 3.630A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET d 178 " --> pdb=" O ILE d 145 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.825A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.571A pdb=" N ALA e 99 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'e' and resid 33 through 41 removed outlier: 6.882A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.782A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'f' and resid 43 through 47 removed outlier: 7.069A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'g' and resid 73 through 79 removed outlier: 6.596A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.374A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.580A pdb=" N SER h 74 " --> pdb=" O ALA h 130 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 66, first strand: chain 'j' and resid 37 through 42 removed outlier: 4.080A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG j 5 " --> pdb=" O GLY j 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 68, first strand: chain 'k' and resid 42 through 45 removed outlier: 3.720A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN k 109 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY k 88 " --> pdb=" O VAL k 113 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.397A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS l 96 " --> pdb=" O ARG l 83 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'l' and resid 36 through 41 removed outlier: 5.080A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'p' and resid 4 through 10 removed outlier: 4.020A pdb=" N PHE p 16 " --> pdb=" O HIS p 9 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'q' and resid 7 through 11 removed outlier: 6.956A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER q 72 " --> pdb=" O CYS q 64 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'q' and resid 19 through 30 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 's' and resid 30 through 34 removed outlier: 4.978A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'v' and resid 161 through 166 removed outlier: 6.646A pdb=" N THR v 180 " --> pdb=" O ILE v 166 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS v 177 " --> pdb=" O ALA v 134 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASP v 127 " --> pdb=" O GLU v 225 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE v 217 " --> pdb=" O GLY v 135 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG v 324 " --> pdb=" O VAL v 198 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL v 340 " --> pdb=" O ASP v 335 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'v' and resid 241 through 244 removed outlier: 3.910A pdb=" N ILE v 270 " --> pdb=" O HIS v 265 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'v' and resid 167 through 170 2270 hydrogen bonds defined for protein. 6690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3931 hydrogen bonds 6202 hydrogen bond angles 0 basepair planarities 1559 basepair parallelities 2290 stacking parallelities Total time for adding SS restraints: 286.24 Time building geometry restraints manager: 75.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14310 1.31 - 1.44: 68819 1.44 - 1.56: 71048 1.56 - 1.69: 9462 1.69 - 1.82: 304 Bond restraints: 163943 Sorted by residual: bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.635 1.336 0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" N1 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.635 1.340 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C5 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.155 1.392 -0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 163938 not shown) Histogram of bond angle deviations from ideal: 68.99 - 87.91: 2 87.91 - 106.83: 29943 106.83 - 125.74: 196421 125.74 - 144.66: 18314 144.66 - 163.57: 2 Bond angle restraints: 244682 Sorted by residual: angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" O5' A A2031 " ideal model delta sigma weight residual 104.00 68.99 35.01 1.50e+00 4.44e-01 5.45e+02 angle pdb=" C3' 6MZ A2030 " pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " ideal model delta sigma weight residual 120.20 152.65 -32.45 1.50e+00 4.44e-01 4.68e+02 angle pdb=" N1 3TD A1915 " pdb=" C6 3TD A1915 " pdb=" C5 3TD A1915 " ideal model delta sigma weight residual 119.91 163.57 -43.66 3.00e+00 1.11e-01 2.12e+02 angle pdb=" O2' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" C1' G7M A2069 " ideal model delta sigma weight residual 108.40 128.85 -20.45 1.50e+00 4.44e-01 1.86e+02 angle pdb=" C3' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" O2' G7M A2069 " ideal model delta sigma weight residual 110.70 127.85 -17.15 1.50e+00 4.44e-01 1.31e+02 ... (remaining 244677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 91699 35.94 - 71.87: 11686 71.87 - 107.81: 1407 107.81 - 143.75: 16 143.75 - 179.69: 42 Dihedral angle restraints: 104850 sinusoidal: 86663 harmonic: 18187 Sorted by residual: dihedral pdb=" C5' A A2225 " pdb=" C4' A A2225 " pdb=" C3' A A2225 " pdb=" O3' A A2225 " ideal model delta sinusoidal sigma weight residual 147.00 83.04 63.96 1 8.00e+00 1.56e-02 8.41e+01 dihedral pdb=" C5' C A2146 " pdb=" C4' C A2146 " pdb=" C3' C A2146 " pdb=" O3' C A2146 " ideal model delta sinusoidal sigma weight residual 147.00 83.58 63.42 1 8.00e+00 1.56e-02 8.29e+01 dihedral pdb=" O4' U a 467 " pdb=" C1' U a 467 " pdb=" N1 U a 467 " pdb=" C2 U a 467 " ideal model delta sinusoidal sigma weight residual 200.00 45.29 154.71 1 1.50e+01 4.44e-03 8.12e+01 ... (remaining 104847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 30943 0.303 - 0.606: 143 0.606 - 0.909: 7 0.909 - 1.212: 2 1.212 - 1.515: 1 Chirality restraints: 31096 Sorted by residual: chirality pdb=" C2' G7M A2069 " pdb=" C3' G7M A2069 " pdb=" O2' G7M A2069 " pdb=" C1' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.75 -1.24 -1.52 2.00e-01 2.50e+01 5.74e+01 chirality pdb=" C3' 6MZ A2030 " pdb=" C4' 6MZ A2030 " pdb=" O3' 6MZ A2030 " pdb=" C2' 6MZ A2030 " both_signs ideal model delta sigma weight residual False -2.74 -1.62 -1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" C1' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" N9 G7M A2069 " both_signs ideal model delta sigma weight residual False 2.46 1.51 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 31093 not shown) Planarity restraints: 13510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " 0.051 2.00e-02 2.50e+03 6.04e-01 8.20e+03 pdb=" C4' OMC A2498 " -0.495 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " -0.773 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " 0.553 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " 0.600 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " 0.224 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " -0.895 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " -0.201 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " 0.937 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " 0.073 2.00e-02 2.50e+03 5.94e-01 7.94e+03 pdb=" C4' 2MG A2445 " -0.503 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.840 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.546 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.531 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.259 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.782 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.231 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.948 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.063 2.00e-02 2.50e+03 5.80e-01 7.57e+03 pdb=" C4' OMG A2251 " -0.454 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " -0.763 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " 0.598 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " 0.545 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " 0.231 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " -0.848 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " -0.240 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " 0.868 2.00e-02 2.50e+03 ... (remaining 13507 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 291 2.42 - 3.04: 75668 3.04 - 3.66: 291190 3.66 - 4.28: 449735 4.28 - 4.90: 595271 Nonbonded interactions: 1412155 Sorted by model distance: nonbonded pdb=" OP1 G A2550 " pdb="MG MG A3117 " model vdw 1.796 2.170 nonbonded pdb=" OP1 A A1272 " pdb="MG MG A3030 " model vdw 1.836 2.170 nonbonded pdb=" OP1 A A1614 " pdb="MG MG A3017 " model vdw 1.845 2.170 nonbonded pdb=" O4 U A1602 " pdb="MG MG A3081 " model vdw 1.862 2.170 nonbonded pdb=" OP2 A A2518 " pdb="MG MG A3054 " model vdw 1.865 2.170 ... (remaining 1412150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'x' and ((resid 0 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N1 or name C2 or \ name O2 or name N3 or name C4 or name N4 or name C5 or name C6 )) or resid 1 thr \ ough 76)) selection = chain 'y' } 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 17.830 Check model and map are aligned: 1.700 Set scattering table: 1.010 Process input model: 634.320 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 664.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.321 163943 Z= 0.450 Angle : 1.193 43.661 244682 Z= 0.794 Chirality : 0.104 1.515 31096 Planarity : 0.018 0.604 13510 Dihedral : 23.938 179.686 93118 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.20 % Favored : 95.39 % Rotamer: Outliers : 9.75 % Allowed : 13.15 % Favored : 77.10 % Cbeta Deviations : 0.75 % 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: -0.69 (0.09), residues: 6269 helix: 1.29 (0.09), residues: 2252 sheet: -1.45 (0.13), residues: 1150 loop : -1.45 (0.10), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 201 HIS 0.013 0.002 HIS C 15 PHE 0.021 0.002 PHE R 57 TYR 0.024 0.002 TYR l 117 ARG 0.030 0.003 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2083 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 509 poor density : 1574 time to evaluate : 6.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LYS cc_start: 0.8541 (mttt) cc_final: 0.8232 (mtmm) REVERT: C 24 LEU cc_start: 0.8764 (mt) cc_final: 0.8550 (mp) REVERT: C 26 LYS cc_start: 0.7104 (mttt) cc_final: 0.6649 (mtpp) REVERT: C 66 ASP cc_start: 0.8644 (t0) cc_final: 0.8121 (t0) REVERT: C 171 TYR cc_start: 0.7639 (m-80) cc_final: 0.7309 (m-80) REVERT: C 181 MET cc_start: 0.8451 (mmt) cc_final: 0.7986 (mmt) REVERT: C 192 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8222 (mt) REVERT: C 203 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8181 (ptp-170) REVERT: C 238 ARG cc_start: 0.8954 (mtt90) cc_final: 0.8571 (mtt180) REVERT: C 260 ASN cc_start: 0.8771 (t0) cc_final: 0.8480 (t0) REVERT: C 269 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7370 (ttt-90) REVERT: C 271 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7718 (ppt170) REVERT: D 74 GLU cc_start: 0.8492 (tt0) cc_final: 0.8220 (mm-30) REVERT: D 77 ARG cc_start: 0.8461 (ptt90) cc_final: 0.8066 (ptt-90) REVERT: D 81 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7746 (mt-10) REVERT: D 94 GLN cc_start: 0.6875 (tt0) cc_final: 0.6650 (tt0) REVERT: D 105 LYS cc_start: 0.7725 (mttt) cc_final: 0.7502 (mmtm) REVERT: D 106 LYS cc_start: 0.8917 (mttt) cc_final: 0.8555 (mttm) REVERT: D 179 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7779 (ttm-80) REVERT: D 204 LYS cc_start: 0.8284 (mtmt) cc_final: 0.8000 (mtmt) REVERT: E 3 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6560 (tp) REVERT: E 21 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7333 (ptm-80) REVERT: E 24 ASN cc_start: 0.8586 (t0) cc_final: 0.8181 (t0) REVERT: E 46 GLN cc_start: 0.9124 (mp10) cc_final: 0.8899 (mp10) REVERT: E 57 LYS cc_start: 0.5832 (ptmt) cc_final: 0.5340 (pttt) REVERT: E 130 LYS cc_start: 0.6918 (mmtm) cc_final: 0.6281 (mtpp) REVERT: E 132 LYS cc_start: 0.7923 (tttm) cc_final: 0.7542 (tppt) REVERT: E 153 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5953 (tp) REVERT: E 194 LYS cc_start: 0.7889 (tptt) cc_final: 0.7669 (tptp) REVERT: E 197 GLU cc_start: 0.6827 (tt0) cc_final: 0.6607 (tp30) REVERT: F 3 LYS cc_start: 0.6899 (tttt) cc_final: 0.6560 (tptt) REVERT: F 29 PRO cc_start: 0.8832 (Cg_exo) cc_final: 0.8548 (Cg_endo) REVERT: F 71 ARG cc_start: 0.6888 (ttp80) cc_final: 0.5822 (ptt180) REVERT: F 83 TYR cc_start: 0.8123 (m-80) cc_final: 0.7884 (m-80) REVERT: F 88 LYS cc_start: 0.7537 (tttt) cc_final: 0.7265 (ptmm) REVERT: F 105 THR cc_start: 0.6968 (OUTLIER) cc_final: 0.6558 (p) REVERT: F 114 PHE cc_start: 0.6242 (t80) cc_final: 0.5886 (t80) REVERT: F 130 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5731 (tpt) REVERT: F 140 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: G 87 LEU cc_start: 0.7683 (mp) cc_final: 0.7177 (mp) REVERT: G 89 LEU cc_start: 0.8697 (mp) cc_final: 0.8405 (mt) REVERT: H 11 ASN cc_start: 0.6322 (OUTLIER) cc_final: 0.5890 (t0) REVERT: H 27 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7799 (ptp90) REVERT: H 66 ASN cc_start: 0.5781 (OUTLIER) cc_final: 0.5023 (t0) REVERT: H 145 ASN cc_start: 0.5523 (t0) cc_final: 0.5186 (p0) REVERT: J 78 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4999 (mt) REVERT: J 117 THR cc_start: 0.5115 (OUTLIER) cc_final: 0.4888 (p) REVERT: J 137 LEU cc_start: 0.1115 (OUTLIER) cc_final: 0.0146 (pp) REVERT: K 10 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7643 (p) REVERT: K 14 ASP cc_start: 0.8334 (m-30) cc_final: 0.8020 (t0) REVERT: K 23 LYS cc_start: 0.7964 (mttt) cc_final: 0.7648 (mmtp) REVERT: K 31 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: K 41 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8040 (mttm) REVERT: K 60 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8036 (p0) REVERT: K 68 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7759 (mttp) REVERT: K 92 MET cc_start: 0.8489 (mmm) cc_final: 0.8258 (mmm) REVERT: K 123 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7395 (mmtt) REVERT: K 131 ASN cc_start: 0.8056 (m110) cc_final: 0.7825 (m110) REVERT: K 138 GLN cc_start: 0.8222 (mt0) cc_final: 0.7728 (mt0) REVERT: L 5 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8479 (mm-40) REVERT: L 30 ARG cc_start: 0.8773 (ttt180) cc_final: 0.8217 (ttt180) REVERT: M 1 MET cc_start: 0.7869 (ttp) cc_final: 0.7167 (ttp) REVERT: M 3 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8618 (tt) REVERT: M 12 SER cc_start: 0.9392 (t) cc_final: 0.9028 (p) REVERT: M 96 LYS cc_start: 0.7949 (mttt) cc_final: 0.7663 (mmtp) REVERT: M 123 ARG cc_start: 0.7187 (ttm-80) cc_final: 0.6140 (mtp85) REVERT: M 141 LYS cc_start: 0.6914 (tttt) cc_final: 0.6579 (ttmt) REVERT: M 143 GLU cc_start: 0.5823 (pt0) cc_final: 0.5127 (tt0) REVERT: N 12 MET cc_start: 0.8414 (ttt) cc_final: 0.8076 (ttm) REVERT: N 60 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6739 (tt0) REVERT: N 81 ARG cc_start: 0.8858 (mtt90) cc_final: 0.8572 (mtt90) REVERT: N 82 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8796 (mmm) REVERT: N 104 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8225 (mt-10) REVERT: O 1 MET cc_start: 0.8958 (ptp) cc_final: 0.8506 (ptp) REVERT: O 60 VAL cc_start: 0.7985 (t) cc_final: 0.7763 (p) REVERT: O 110 MET cc_start: 0.8699 (mmm) cc_final: 0.7818 (mmm) REVERT: P 19 GLN cc_start: 0.8777 (tm130) cc_final: 0.7881 (mm-40) REVERT: P 64 TYR cc_start: 0.5881 (t80) cc_final: 0.5431 (t80) REVERT: P 94 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6365 (ptt90) REVERT: P 116 GLN cc_start: 0.7024 (tt0) cc_final: 0.6359 (tm-30) REVERT: Q 7 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7274 (tp40) REVERT: Q 55 LEU cc_start: 0.9145 (tp) cc_final: 0.8940 (tp) REVERT: Q 71 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8279 (mt-10) REVERT: R 91 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8462 (p0) REVERT: S 19 THR cc_start: 0.8558 (m) cc_final: 0.8356 (t) REVERT: S 23 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8002 (mm-30) REVERT: S 46 GLU cc_start: 0.7567 (pt0) cc_final: 0.7298 (pt0) REVERT: S 78 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8352 (tpp-160) REVERT: T 1 MET cc_start: 0.7602 (ttt) cc_final: 0.6941 (ptp) REVERT: U 1 MET cc_start: 0.5810 (pmt) cc_final: 0.5600 (ttm) REVERT: U 28 ASN cc_start: 0.8051 (t0) cc_final: 0.7181 (t0) REVERT: U 33 LYS cc_start: 0.7654 (ttmt) cc_final: 0.7344 (tttp) REVERT: U 74 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7091 (tt) REVERT: U 77 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8473 (mtt180) REVERT: U 87 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8349 (mp) REVERT: V 27 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7573 (p0) REVERT: V 39 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8483 (mp) REVERT: V 46 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.6855 (mm-40) REVERT: V 59 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7525 (m) REVERT: V 73 PHE cc_start: 0.7739 (t80) cc_final: 0.7374 (t80) REVERT: V 88 GLU cc_start: 0.7995 (tt0) cc_final: 0.7727 (tp30) REVERT: W 5 ASN cc_start: 0.7672 (m110) cc_final: 0.7455 (m-40) REVERT: W 24 ASN cc_start: 0.7547 (t0) cc_final: 0.6631 (t0) REVERT: W 57 TYR cc_start: 0.8167 (m-80) cc_final: 0.7941 (m-80) REVERT: X 11 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6405 (mtp85) REVERT: X 15 ASP cc_start: 0.8307 (t0) cc_final: 0.8065 (t70) REVERT: X 35 SER cc_start: 0.9118 (m) cc_final: 0.8628 (m) REVERT: Y 16 ASN cc_start: 0.9196 (m-40) cc_final: 0.8878 (m110) REVERT: Z 39 GLN cc_start: 0.7077 (mt0) cc_final: 0.6105 (mp10) REVERT: 0 11 ARG cc_start: 0.8699 (mpt90) cc_final: 0.8184 (mpt90) REVERT: 0 31 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.7666 (ptp90) REVERT: 0 32 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7858 (pt) REVERT: 0 47 MET cc_start: 0.8638 (mtm) cc_final: 0.8300 (mtm) REVERT: 1 56 ARG cc_start: 0.5530 (mmm-85) cc_final: 0.5128 (mmm160) REVERT: 2 36 GLU cc_start: 0.8023 (pt0) cc_final: 0.7713 (tt0) REVERT: 3 33 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6721 (mmtm) REVERT: 3 50 LYS cc_start: 0.7028 (mtmp) cc_final: 0.6663 (mptt) REVERT: 4 42 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8715 (tm) REVERT: 4 43 THR cc_start: 0.8631 (p) cc_final: 0.8382 (p) REVERT: 5 15 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8100 (mmtm) REVERT: 6 15 LYS cc_start: 0.8247 (mttt) cc_final: 0.7534 (ptmm) REVERT: b 6 MET cc_start: 0.6474 (ttm) cc_final: 0.6259 (mtt) REVERT: b 23 TRP cc_start: 0.6815 (p-90) cc_final: 0.6523 (p-90) REVERT: b 24 ASN cc_start: 0.6038 (t0) cc_final: 0.5433 (t0) REVERT: b 27 MET cc_start: 0.7767 (mmm) cc_final: 0.7270 (mmm) REVERT: b 42 ASN cc_start: 0.5201 (t0) cc_final: 0.4882 (t0) REVERT: b 81 LYS cc_start: 0.6939 (tttt) cc_final: 0.6144 (mtpt) REVERT: c 8 ASN cc_start: 0.7064 (t0) cc_final: 0.6698 (m-40) REVERT: c 11 ARG cc_start: 0.6158 (mtm-85) cc_final: 0.5870 (mtt90) REVERT: c 40 ARG cc_start: 0.5657 (mtt-85) cc_final: 0.5373 (mtt180) REVERT: c 101 ILE cc_start: 0.5733 (mt) cc_final: 0.5376 (mp) REVERT: c 105 GLU cc_start: 0.4223 (tm-30) cc_final: 0.3299 (pm20) REVERT: c 108 LYS cc_start: 0.6874 (mttt) cc_final: 0.6518 (tttt) REVERT: c 129 MET cc_start: 0.6031 (mtt) cc_final: 0.5488 (mtt) REVERT: c 132 ARG cc_start: 0.5442 (ttm170) cc_final: 0.5231 (ttp-110) REVERT: c 135 LYS cc_start: 0.8176 (mttm) cc_final: 0.7852 (tptm) REVERT: c 173 VAL cc_start: 0.7815 (t) cc_final: 0.7571 (p) REVERT: d 56 ARG cc_start: 0.6340 (mmp80) cc_final: 0.5961 (mmm160) REVERT: d 60 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6735 (tttm) REVERT: d 105 MET cc_start: 0.5507 (mtt) cc_final: 0.5268 (mmt) REVERT: d 124 MET cc_start: 0.6283 (mtt) cc_final: 0.5600 (ppp) REVERT: d 171 LEU cc_start: 0.7150 (mt) cc_final: 0.6839 (mt) REVERT: d 183 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7495 (ttmt) REVERT: d 185 LYS cc_start: 0.7571 (ptmt) cc_final: 0.7024 (mtpp) REVERT: d 187 GLU cc_start: 0.7630 (tt0) cc_final: 0.6980 (mp0) REVERT: d 195 ILE cc_start: 0.7641 (mt) cc_final: 0.7386 (mt) REVERT: e 10 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5447 (mm-30) REVERT: e 13 GLU cc_start: 0.6429 (pt0) cc_final: 0.6093 (pt0) REVERT: e 15 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6291 (tp) REVERT: e 65 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: e 94 VAL cc_start: 0.6569 (OUTLIER) cc_final: 0.6335 (t) REVERT: f 9 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7461 (mtp) REVERT: f 14 GLN cc_start: 0.7381 (mm-40) cc_final: 0.6853 (mm-40) REVERT: g 59 LEU cc_start: 0.7289 (tp) cc_final: 0.6936 (tt) REVERT: g 68 ASN cc_start: 0.7262 (m-40) cc_final: 0.6851 (m-40) REVERT: g 78 ARG cc_start: 0.6097 (tpt170) cc_final: 0.4784 (tpp-160) REVERT: g 133 THR cc_start: 0.5768 (m) cc_final: 0.4975 (p) REVERT: h 15 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7038 (ttm110) REVERT: h 75 ILE cc_start: 0.7581 (tt) cc_final: 0.7206 (tt) REVERT: h 87 LYS cc_start: 0.7365 (mptt) cc_final: 0.6818 (mttm) REVERT: h 88 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6569 (mtm180) REVERT: i 109 ARG cc_start: 0.6590 (mtm180) cc_final: 0.5990 (mtm180) REVERT: j 48 ARG cc_start: 0.5558 (OUTLIER) cc_final: 0.5244 (mtt90) REVERT: k 68 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8050 (tp30) REVERT: k 86 VAL cc_start: 0.8006 (t) cc_final: 0.7800 (p) REVERT: k 93 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6865 (ttt-90) REVERT: k 119 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7018 (m110) REVERT: l 12 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.3641 (mtp85) REVERT: l 24 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8169 (mp) REVERT: l 25 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8157 (mt-10) REVERT: l 43 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6410 (pptt) REVERT: l 44 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8347 (mttt) REVERT: l 50 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6897 (mpt-90) REVERT: l 58 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7510 (m) REVERT: l 79 VAL cc_start: 0.8085 (t) cc_final: 0.7876 (p) REVERT: l 112 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: m 19 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6248 (mt) REVERT: m 21 SER cc_start: 0.7583 (m) cc_final: 0.7344 (p) REVERT: m 31 LYS cc_start: 0.7391 (mttt) cc_final: 0.6894 (mttt) REVERT: m 46 SER cc_start: 0.6215 (OUTLIER) cc_final: 0.5969 (p) REVERT: m 79 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7446 (ttt-90) REVERT: m 81 MET cc_start: 0.6677 (mmt) cc_final: 0.6384 (mmm) REVERT: m 93 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6913 (mpt180) REVERT: m 101 ARG cc_start: 0.7326 (ptp-110) cc_final: 0.6440 (ptp-110) REVERT: m 107 ARG cc_start: 0.6487 (mmp80) cc_final: 0.5898 (mmp80) REVERT: n 58 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7807 (p) REVERT: o 14 GLU cc_start: 0.7383 (tt0) cc_final: 0.7102 (tm-30) REVERT: o 80 GLN cc_start: 0.8244 (tt0) cc_final: 0.7989 (mm110) REVERT: p 28 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7209 (ttp80) REVERT: q 68 SER cc_start: 0.8517 (t) cc_final: 0.8116 (t) REVERT: s 21 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6781 (ptmt) REVERT: s 38 SER cc_start: 0.5066 (OUTLIER) cc_final: 0.4126 (m) REVERT: t 48 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7024 (tp-100) REVERT: t 52 ASN cc_start: 0.7912 (m-40) cc_final: 0.7648 (m-40) REVERT: t 54 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8434 (ppp) REVERT: t 67 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7402 (pt) REVERT: u 4 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6688 (mm) REVERT: u 7 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.5031 (ppt170) REVERT: u 21 ARG cc_start: 0.6220 (tpt170) cc_final: 0.5971 (mmm160) REVERT: v 124 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: v 133 GLN cc_start: 0.7343 (tp40) cc_final: 0.6653 (mt0) REVERT: v 142 GLN cc_start: 0.7749 (mt0) cc_final: 0.7388 (mm-40) REVERT: v 193 ARG cc_start: 0.6648 (ptt90) cc_final: 0.6329 (ptm-80) REVERT: v 201 LEU cc_start: 0.7345 (tp) cc_final: 0.7023 (tp) REVERT: v 245 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6843 (mtt180) REVERT: v 255 ASN cc_start: 0.7151 (m-40) cc_final: 0.6778 (m-40) REVERT: v 258 GLU cc_start: 0.7642 (pt0) cc_final: 0.7228 (pt0) REVERT: v 278 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7760 (mtt-85) REVERT: v 283 ASN cc_start: 0.7620 (m-40) cc_final: 0.7389 (m110) REVERT: v 323 ILE cc_start: 0.8015 (pt) cc_final: 0.7424 (tp) REVERT: v 346 GLN cc_start: 0.6783 (tp40) cc_final: 0.6474 (tp40) REVERT: w 11 ILE cc_start: 0.8125 (mt) cc_final: 0.7911 (mt) REVERT: w 30 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7097 (mt-10) outliers start: 509 outliers final: 95 residues processed: 1916 average time/residue: 1.4851 time to fit residues: 4669.3424 Evaluate side-chains 1381 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1219 time to evaluate : 6.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 48 ARG Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain U residue 74 ILE Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 46 GLN Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 14 ARG Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 66 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 60 LYS Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 21 GLU Chi-restraints excluded: chain h residue 88 ARG Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 50 ARG Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 112 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 59 GLU Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 6 LEU Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 67 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 7 ARG Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 124 ASP Chi-restraints excluded: chain v residue 166 ILE Chi-restraints excluded: chain v residue 230 ILE Chi-restraints excluded: chain v residue 245 ARG Chi-restraints excluded: chain v residue 247 SER Chi-restraints excluded: chain v residue 256 ARG Chi-restraints excluded: chain v residue 331 SER Chi-restraints excluded: chain v residue 333 ILE Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 913 optimal weight: 1.9990 chunk 820 optimal weight: 0.5980 chunk 455 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 553 optimal weight: 0.9980 chunk 438 optimal weight: 20.0000 chunk 848 optimal weight: 10.0000 chunk 328 optimal weight: 7.9990 chunk 515 optimal weight: 8.9990 chunk 631 optimal weight: 5.9990 chunk 982 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS C 143 ASN C 239 ASN D 36 GLN D 136 ASN E 156 ASN G 45 HIS H 18 GLN H 135 HIS I 4 ASN K 128 ASN M 99 ASN N 60 GLN O 9 GLN O 62 ASN P 98 GLN Q 75 GLN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 9 HIS V 40 ASN V 69 ASN X 76 ASN Y 34 HIS Z 15 ASN 3 26 ASN b 177 ASN b 178 ASN e 122 ASN f 81 ASN g 130 ASN h 4 GLN h 38 ASN i 50 GLN i 126 GLN j 35 GLN k 109 ASN m 105 ASN o 46 HIS ** v 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 290 GLN v 304 ASN v 355 GLN w 32 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 163943 Z= 0.268 Angle : 0.693 18.964 244682 Z= 0.367 Chirality : 0.039 0.564 31096 Planarity : 0.006 0.138 13510 Dihedral : 23.558 179.876 80959 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 5.73 % Allowed : 18.53 % Favored : 75.74 % 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: 0.48 (0.11), residues: 6269 helix: 2.67 (0.11), residues: 2261 sheet: -0.94 (0.14), residues: 1192 loop : -1.10 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP n 42 HIS 0.014 0.001 HIS I 88 PHE 0.021 0.002 PHE b 90 TYR 0.021 0.002 TYR l 38 ARG 0.008 0.001 ARG n 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1664 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1365 time to evaluate : 6.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 VAL cc_start: 0.8593 (m) cc_final: 0.8264 (t) REVERT: C 18 LYS cc_start: 0.8492 (mttt) cc_final: 0.8052 (mtmm) REVERT: C 26 LYS cc_start: 0.6960 (mttt) cc_final: 0.6376 (mtpp) REVERT: C 62 TYR cc_start: 0.8915 (t80) cc_final: 0.8509 (t80) REVERT: C 66 ASP cc_start: 0.8744 (t0) cc_final: 0.8282 (t0) REVERT: C 171 TYR cc_start: 0.7795 (m-80) cc_final: 0.7363 (m-80) REVERT: C 181 MET cc_start: 0.8194 (mmt) cc_final: 0.7789 (mmt) REVERT: C 182 ARG cc_start: 0.8323 (ttt-90) cc_final: 0.7979 (ttt-90) REVERT: C 192 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 269 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7098 (ttt-90) REVERT: C 271 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7847 (ptt-90) REVERT: D 33 ARG cc_start: 0.7382 (ptp90) cc_final: 0.7139 (mtm110) REVERT: D 74 GLU cc_start: 0.8548 (tt0) cc_final: 0.8112 (mm-30) REVERT: D 81 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8062 (mt-10) REVERT: D 94 GLN cc_start: 0.6954 (tt0) cc_final: 0.6749 (tt0) REVERT: D 105 LYS cc_start: 0.7543 (mttt) cc_final: 0.7255 (mmtm) REVERT: D 106 LYS cc_start: 0.8580 (mttt) cc_final: 0.8198 (mttm) REVERT: D 184 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7726 (ptt180) REVERT: E 3 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6539 (mp) REVERT: E 18 THR cc_start: 0.7552 (m) cc_final: 0.7236 (p) REVERT: E 22 ASP cc_start: 0.8186 (m-30) cc_final: 0.7276 (p0) REVERT: E 57 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5462 (pttt) REVERT: E 111 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: F 3 LYS cc_start: 0.6855 (tttt) cc_final: 0.6476 (tptt) REVERT: F 69 LYS cc_start: 0.8518 (mttt) cc_final: 0.8029 (mmtt) REVERT: F 78 LYS cc_start: 0.7044 (mttt) cc_final: 0.6690 (mmtm) REVERT: F 105 THR cc_start: 0.7238 (OUTLIER) cc_final: 0.6616 (p) REVERT: F 130 MET cc_start: 0.6656 (ptt) cc_final: 0.6314 (ptp) REVERT: F 140 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6881 (mm-30) REVERT: G 27 LYS cc_start: 0.6696 (mttt) cc_final: 0.5949 (tmtt) REVERT: G 95 ARG cc_start: 0.6718 (mtm110) cc_final: 0.6333 (ttm110) REVERT: G 130 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6069 (mp0) REVERT: H 17 ASP cc_start: 0.6226 (m-30) cc_final: 0.6019 (m-30) REVERT: H 27 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7800 (ptp90) REVERT: H 66 ASN cc_start: 0.5856 (OUTLIER) cc_final: 0.5067 (t0) REVERT: H 127 GLU cc_start: 0.5348 (OUTLIER) cc_final: 0.5028 (mp0) REVERT: H 129 GLU cc_start: 0.4195 (OUTLIER) cc_final: 0.3370 (mm-30) REVERT: I 3 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.3896 (mt) REVERT: J 78 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.5043 (mt) REVERT: K 14 ASP cc_start: 0.8529 (m-30) cc_final: 0.8073 (t0) REVERT: K 23 LYS cc_start: 0.8508 (mttt) cc_final: 0.7802 (tptp) REVERT: K 41 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8120 (mttm) REVERT: K 60 ASP cc_start: 0.8489 (p0) cc_final: 0.8253 (p0) REVERT: K 118 MET cc_start: 0.8563 (mtt) cc_final: 0.8349 (mtt) REVERT: K 123 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.6645 (mttt) REVERT: K 138 GLN cc_start: 0.8077 (mt0) cc_final: 0.7699 (mt0) REVERT: L 5 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8496 (mm-40) REVERT: L 29 HIS cc_start: 0.8843 (m-70) cc_final: 0.8628 (m170) REVERT: L 47 ILE cc_start: 0.8341 (pt) cc_final: 0.7854 (tp) REVERT: M 12 SER cc_start: 0.9255 (t) cc_final: 0.9001 (p) REVERT: M 78 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7841 (mmt-90) REVERT: M 96 LYS cc_start: 0.7924 (mttt) cc_final: 0.7592 (mmtp) REVERT: M 123 ARG cc_start: 0.7118 (ttm-80) cc_final: 0.6740 (mtt180) REVERT: M 141 LYS cc_start: 0.6797 (tttt) cc_final: 0.6444 (ttmt) REVERT: N 104 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8186 (mt-10) REVERT: O 42 LYS cc_start: 0.8609 (mttt) cc_final: 0.8309 (mttm) REVERT: O 60 VAL cc_start: 0.7846 (t) cc_final: 0.7610 (p) REVERT: O 63 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (mtt90) REVERT: O 110 MET cc_start: 0.8547 (mmm) cc_final: 0.7478 (mmm) REVERT: O 114 GLU cc_start: 0.8709 (pt0) cc_final: 0.8363 (pt0) REVERT: O 118 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6660 (ttp80) REVERT: P 19 GLN cc_start: 0.8726 (tm130) cc_final: 0.7820 (mm-40) REVERT: P 64 TYR cc_start: 0.6169 (t80) cc_final: 0.5214 (t80) REVERT: P 116 GLN cc_start: 0.7371 (tt0) cc_final: 0.6610 (pp30) REVERT: Q 7 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7109 (tm-30) REVERT: Q 55 LEU cc_start: 0.9095 (tp) cc_final: 0.8853 (tp) REVERT: R 44 GLN cc_start: 0.8924 (mt0) cc_final: 0.8654 (mt0) REVERT: R 51 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7957 (mmt-90) REVERT: R 78 LYS cc_start: 0.8111 (mttt) cc_final: 0.7873 (mttm) REVERT: R 117 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7072 (mp) REVERT: S 60 LYS cc_start: 0.7757 (mttt) cc_final: 0.7107 (ttmt) REVERT: S 78 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8346 (tpp-160) REVERT: S 85 LYS cc_start: 0.8589 (ttmt) cc_final: 0.7981 (ttmm) REVERT: S 86 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: T 1 MET cc_start: 0.7507 (ttt) cc_final: 0.6987 (ptp) REVERT: T 22 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: T 38 TYR cc_start: 0.8374 (m-80) cc_final: 0.7968 (m-80) REVERT: T 83 LYS cc_start: 0.9165 (ptpp) cc_final: 0.8932 (mttp) REVERT: U 1 MET cc_start: 0.6012 (pmt) cc_final: 0.5760 (ttm) REVERT: U 33 LYS cc_start: 0.7631 (ttmt) cc_final: 0.7422 (tttp) REVERT: U 77 ARG cc_start: 0.8760 (mtt-85) cc_final: 0.8404 (mmm-85) REVERT: U 92 ASN cc_start: 0.7618 (t0) cc_final: 0.7251 (p0) REVERT: V 27 ASN cc_start: 0.8027 (p0) cc_final: 0.7729 (p0) REVERT: V 73 PHE cc_start: 0.7641 (t80) cc_final: 0.7302 (t80) REVERT: V 88 GLU cc_start: 0.7647 (tt0) cc_final: 0.7418 (tp30) REVERT: W 24 ASN cc_start: 0.7515 (t0) cc_final: 0.7123 (t0) REVERT: X 11 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6171 (mtp85) REVERT: X 29 GLU cc_start: 0.8399 (tt0) cc_final: 0.8170 (tt0) REVERT: X 35 SER cc_start: 0.9207 (m) cc_final: 0.8799 (m) REVERT: X 39 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.7513 (mtt-85) REVERT: Y 16 ASN cc_start: 0.9188 (m-40) cc_final: 0.8908 (m110) REVERT: Y 59 ILE cc_start: 0.8188 (mt) cc_final: 0.7909 (mt) REVERT: Z 39 GLN cc_start: 0.7224 (mt0) cc_final: 0.5972 (mp10) REVERT: 0 11 ARG cc_start: 0.8745 (mpt90) cc_final: 0.8454 (mpt90) REVERT: 0 32 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.8006 (pt) REVERT: 0 47 MET cc_start: 0.8477 (mtm) cc_final: 0.8159 (mtm) REVERT: 0 49 ASN cc_start: 0.8622 (t0) cc_final: 0.8385 (t0) REVERT: 1 22 MET cc_start: 0.5939 (ttm) cc_final: 0.5518 (mpp) REVERT: 2 17 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8600 (mtt180) REVERT: 2 36 GLU cc_start: 0.7941 (pt0) cc_final: 0.7688 (tt0) REVERT: 4 42 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8590 (tm) REVERT: 5 15 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8233 (mmmm) REVERT: 5 30 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7796 (tpm170) REVERT: 6 15 LYS cc_start: 0.8244 (mttt) cc_final: 0.7663 (ptmt) REVERT: b 6 MET cc_start: 0.6752 (ttm) cc_final: 0.6281 (tmm) REVERT: b 81 LYS cc_start: 0.6962 (tttt) cc_final: 0.6119 (mtpt) REVERT: b 197 ASP cc_start: 0.5859 (m-30) cc_final: 0.5583 (m-30) REVERT: b 204 ASP cc_start: 0.3658 (p0) cc_final: 0.3245 (p0) REVERT: c 65 ARG cc_start: 0.6849 (ttm170) cc_final: 0.6357 (mtp180) REVERT: c 105 GLU cc_start: 0.4463 (tm-30) cc_final: 0.3324 (pm20) REVERT: c 129 MET cc_start: 0.5491 (mtt) cc_final: 0.5191 (mtt) REVERT: c 135 LYS cc_start: 0.8164 (mttm) cc_final: 0.7649 (tptp) REVERT: d 26 ARG cc_start: 0.5763 (ttt180) cc_final: 0.5151 (ttm-80) REVERT: d 31 LYS cc_start: 0.6037 (mtpp) cc_final: 0.5729 (mtmt) REVERT: d 57 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: d 78 GLU cc_start: 0.7537 (tp30) cc_final: 0.7245 (pp20) REVERT: d 95 GLU cc_start: 0.5860 (mm-30) cc_final: 0.5543 (mm-30) REVERT: d 105 MET cc_start: 0.5931 (mtt) cc_final: 0.5716 (mmt) REVERT: d 156 LYS cc_start: 0.6713 (mttt) cc_final: 0.6257 (pttt) REVERT: d 185 LYS cc_start: 0.7612 (ptmt) cc_final: 0.6918 (mtpp) REVERT: d 197 GLU cc_start: 0.7289 (pm20) cc_final: 0.6885 (mp0) REVERT: e 13 GLU cc_start: 0.6321 (pt0) cc_final: 0.5778 (pt0) REVERT: e 15 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6370 (tp) REVERT: g 78 ARG cc_start: 0.5685 (tpt170) cc_final: 0.4797 (tpp-160) REVERT: h 4 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7299 (mm-40) REVERT: h 87 LYS cc_start: 0.7512 (mptt) cc_final: 0.6853 (mttm) REVERT: h 124 GLU cc_start: 0.7385 (tt0) cc_final: 0.7180 (tt0) REVERT: j 9 ARG cc_start: 0.6001 (mtp-110) cc_final: 0.5540 (mtp180) REVERT: j 89 ARG cc_start: 0.5185 (ttm170) cc_final: 0.4890 (ptm160) REVERT: k 80 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7670 (mmtm) REVERT: k 83 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7100 (mt-10) REVERT: k 86 VAL cc_start: 0.8314 (t) cc_final: 0.8071 (m) REVERT: k 109 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7858 (m-40) REVERT: k 119 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7245 (m110) REVERT: l 6 GLN cc_start: 0.7723 (mt0) cc_final: 0.7209 (mt0) REVERT: l 58 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7394 (m) REVERT: l 79 VAL cc_start: 0.8407 (t) cc_final: 0.8186 (p) REVERT: l 108 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7780 (mtmm) REVERT: l 120 LYS cc_start: 0.7641 (mmmt) cc_final: 0.6859 (mppt) REVERT: m 31 LYS cc_start: 0.7502 (mttt) cc_final: 0.6885 (mttt) REVERT: m 46 SER cc_start: 0.5908 (m) cc_final: 0.5688 (p) REVERT: m 87 ARG cc_start: 0.6594 (mtm110) cc_final: 0.6307 (ttp-170) REVERT: m 92 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6340 (ptm-80) REVERT: m 101 ARG cc_start: 0.7401 (ptp-110) cc_final: 0.6739 (ptp-110) REVERT: m 107 ARG cc_start: 0.6523 (mmp80) cc_final: 0.6033 (mmp80) REVERT: n 63 ARG cc_start: 0.5643 (mtt-85) cc_final: 0.4875 (mtp85) REVERT: n 92 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6047 (mp0) REVERT: o 11 ILE cc_start: 0.6668 (mm) cc_final: 0.6253 (mp) REVERT: o 70 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7639 (tt) REVERT: o 80 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7865 (mm110) REVERT: o 81 LEU cc_start: 0.8212 (tp) cc_final: 0.7963 (tt) REVERT: s 21 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6771 (pptt) REVERT: t 48 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7057 (tp-100) REVERT: t 52 ASN cc_start: 0.7842 (m-40) cc_final: 0.7364 (m-40) REVERT: t 71 LYS cc_start: 0.7917 (tttp) cc_final: 0.7705 (tttp) REVERT: u 6 VAL cc_start: 0.7014 (t) cc_final: 0.6803 (t) REVERT: u 21 ARG cc_start: 0.6274 (tpt170) cc_final: 0.6069 (mmm160) REVERT: v 116 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7412 (ptt180) REVERT: v 142 GLN cc_start: 0.7830 (mt0) cc_final: 0.7383 (mm-40) REVERT: v 143 ASP cc_start: 0.8399 (t70) cc_final: 0.8133 (t70) REVERT: v 147 MET cc_start: 0.7523 (ttp) cc_final: 0.7278 (ptm) REVERT: v 164 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6606 (tt0) REVERT: v 184 SER cc_start: 0.5684 (t) cc_final: 0.5385 (m) REVERT: v 193 ARG cc_start: 0.6730 (ptt90) cc_final: 0.6055 (ptt180) REVERT: v 201 LEU cc_start: 0.7608 (tp) cc_final: 0.7185 (tp) REVERT: v 245 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6773 (mtt90) REVERT: v 286 GLN cc_start: 0.7409 (tp40) cc_final: 0.6836 (tp40) REVERT: v 316 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: v 326 TYR cc_start: 0.7828 (m-80) cc_final: 0.7430 (m-80) REVERT: w 30 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7074 (mt-10) outliers start: 299 outliers final: 150 residues processed: 1553 average time/residue: 1.4587 time to fit residues: 3805.8507 Evaluate side-chains 1423 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1232 time to evaluate : 6.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 57 ASN Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 112 LYS Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 57 GLU Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 21 GLU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 59 GLU Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 80 GLN Chi-restraints excluded: chain p residue 6 LEU Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 163 THR Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 245 ARG Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 333 ILE Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 546 optimal weight: 9.9990 chunk 304 optimal weight: 0.3980 chunk 817 optimal weight: 9.9990 chunk 669 optimal weight: 20.0000 chunk 271 optimal weight: 7.9990 chunk 984 optimal weight: 5.9990 chunk 1063 optimal weight: 8.9990 chunk 876 optimal weight: 30.0000 chunk 976 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 chunk 789 optimal weight: 10.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN E 62 GLN E 156 ASN G 64 GLN G 104 ASN G 111 HIS H 18 GLN J 110 GLN M 35 HIS S 66 HIS T 7 HIS V 69 ASN 3 26 ASN 5 26 HIS b 177 ASN c 41 GLN d 74 ASN e 73 ASN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN h 4 GLN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN h 38 ASN l 5 ASN ** o 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 52 HIS t 52 ASN ** v 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 276 ASN ** v 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 163943 Z= 0.291 Angle : 0.653 14.787 244682 Z= 0.351 Chirality : 0.038 0.544 31096 Planarity : 0.006 0.136 13510 Dihedral : 23.444 179.503 80753 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 6.29 % Allowed : 20.24 % Favored : 73.48 % 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: 0.35 (0.10), residues: 6269 helix: 2.24 (0.11), residues: 2287 sheet: -0.82 (0.14), residues: 1164 loop : -1.01 (0.11), residues: 2818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 201 HIS 0.011 0.001 HIS c 6 PHE 0.023 0.002 PHE p 38 TYR 0.027 0.002 TYR v 189 ARG 0.013 0.001 ARG 1 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1634 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1306 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LYS cc_start: 0.8242 (mttt) cc_final: 0.7989 (mtmm) REVERT: C 60 GLN cc_start: 0.9050 (mt0) cc_final: 0.8831 (mt0) REVERT: C 66 ASP cc_start: 0.8707 (t0) cc_final: 0.8291 (t0) REVERT: C 171 TYR cc_start: 0.7611 (m-80) cc_final: 0.7401 (m-80) REVERT: C 182 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7911 (ttt-90) REVERT: C 269 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7216 (ttt-90) REVERT: D 74 GLU cc_start: 0.8618 (tt0) cc_final: 0.8182 (mm-30) REVERT: D 81 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8038 (mt-10) REVERT: D 94 GLN cc_start: 0.6982 (tt0) cc_final: 0.6584 (tt0) REVERT: D 105 LYS cc_start: 0.7602 (mttt) cc_final: 0.7317 (mmtm) REVERT: D 106 LYS cc_start: 0.8535 (mttt) cc_final: 0.8136 (mttm) REVERT: D 114 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.7849 (mtmm) REVERT: E 3 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6526 (mp) REVERT: E 18 THR cc_start: 0.7494 (m) cc_final: 0.7132 (p) REVERT: E 22 ASP cc_start: 0.8185 (m-30) cc_final: 0.7261 (p0) REVERT: E 35 TYR cc_start: 0.8756 (t80) cc_final: 0.8540 (t80) REVERT: E 57 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.5294 (pttt) REVERT: E 111 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: E 194 LYS cc_start: 0.7793 (tptp) cc_final: 0.7278 (mttp) REVERT: F 3 LYS cc_start: 0.6850 (tttt) cc_final: 0.6465 (tptt) REVERT: F 69 LYS cc_start: 0.8371 (mttt) cc_final: 0.8139 (mtpt) REVERT: F 71 ARG cc_start: 0.7509 (ttp-170) cc_final: 0.6604 (ptt-90) REVERT: F 105 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6610 (p) REVERT: F 140 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6636 (mm-30) REVERT: G 76 VAL cc_start: 0.8024 (t) cc_final: 0.7590 (m) REVERT: G 130 GLU cc_start: 0.6355 (mm-30) cc_final: 0.5972 (mp0) REVERT: H 40 THR cc_start: 0.6326 (m) cc_final: 0.6105 (p) REVERT: H 66 ASN cc_start: 0.5794 (OUTLIER) cc_final: 0.4994 (t0) REVERT: H 114 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.4990 (tp30) REVERT: H 127 GLU cc_start: 0.5350 (OUTLIER) cc_final: 0.5128 (mp0) REVERT: H 129 GLU cc_start: 0.4312 (OUTLIER) cc_final: 0.3479 (mm-30) REVERT: I 3 LEU cc_start: 0.4211 (OUTLIER) cc_final: 0.3955 (mt) REVERT: J 78 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5280 (mp) REVERT: J 137 LEU cc_start: 0.0901 (OUTLIER) cc_final: 0.0052 (pp) REVERT: K 14 ASP cc_start: 0.8478 (m-30) cc_final: 0.7944 (t0) REVERT: K 23 LYS cc_start: 0.8623 (mttt) cc_final: 0.7965 (mmmt) REVERT: K 74 TYR cc_start: 0.8625 (m-80) cc_final: 0.8347 (m-80) REVERT: K 92 MET cc_start: 0.8372 (mmm) cc_final: 0.8124 (mmm) REVERT: K 99 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7831 (mmm160) REVERT: K 118 MET cc_start: 0.8616 (mtt) cc_final: 0.8329 (mtt) REVERT: K 123 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7525 (mmpt) REVERT: K 131 ASN cc_start: 0.8192 (m110) cc_final: 0.7749 (m-40) REVERT: K 138 GLN cc_start: 0.8005 (mt0) cc_final: 0.7592 (mt0) REVERT: L 5 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8504 (mm-40) REVERT: L 29 HIS cc_start: 0.8918 (m-70) cc_final: 0.8705 (m170) REVERT: L 47 ILE cc_start: 0.8390 (pt) cc_final: 0.8038 (tp) REVERT: M 10 GLU cc_start: 0.8494 (tp30) cc_final: 0.8240 (tp30) REVERT: M 12 SER cc_start: 0.9216 (t) cc_final: 0.9006 (p) REVERT: M 78 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7809 (mmt-90) REVERT: M 123 ARG cc_start: 0.7121 (ttm-80) cc_final: 0.6535 (mtt180) REVERT: M 141 LYS cc_start: 0.6602 (tttt) cc_final: 0.6292 (ttmt) REVERT: N 104 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8299 (mt-10) REVERT: O 60 VAL cc_start: 0.8353 (t) cc_final: 0.8075 (p) REVERT: O 110 MET cc_start: 0.8521 (mmm) cc_final: 0.7385 (mmm) REVERT: O 114 GLU cc_start: 0.8760 (pt0) cc_final: 0.8267 (pt0) REVERT: O 118 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6403 (ttp80) REVERT: P 9 ARG cc_start: 0.7629 (ttp80) cc_final: 0.7341 (ttp80) REVERT: P 25 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6727 (ptt-90) REVERT: P 64 TYR cc_start: 0.6143 (t80) cc_final: 0.5394 (t80) REVERT: P 106 LEU cc_start: 0.7988 (tt) cc_final: 0.7767 (tt) REVERT: P 116 GLN cc_start: 0.7551 (tt0) cc_final: 0.6678 (tm-30) REVERT: Q 55 LEU cc_start: 0.9162 (tp) cc_final: 0.8906 (tp) REVERT: R 117 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6917 (mp) REVERT: S 23 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7989 (mm-30) REVERT: S 60 LYS cc_start: 0.7627 (mttt) cc_final: 0.7080 (ttmt) REVERT: S 73 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7821 (ttpp) REVERT: S 78 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8553 (tpp-160) REVERT: S 85 LYS cc_start: 0.8602 (ttmt) cc_final: 0.7976 (ttmm) REVERT: T 1 MET cc_start: 0.7792 (ttt) cc_final: 0.7288 (ptp) REVERT: T 22 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: T 59 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8519 (mm-30) REVERT: U 24 MET cc_start: 0.7694 (mtt) cc_final: 0.7336 (tpt) REVERT: U 33 LYS cc_start: 0.7535 (ttmt) cc_final: 0.7228 (tttm) REVERT: U 76 ARG cc_start: 0.8548 (ttt-90) cc_final: 0.7904 (ttm-80) REVERT: U 92 ASN cc_start: 0.7670 (t0) cc_final: 0.7179 (p0) REVERT: V 27 ASN cc_start: 0.8000 (p0) cc_final: 0.7727 (p0) REVERT: V 37 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7871 (tp30) REVERT: V 60 GLU cc_start: 0.7908 (tt0) cc_final: 0.7547 (pm20) REVERT: V 62 GLU cc_start: 0.8047 (mt-10) cc_final: 0.6806 (mt-10) REVERT: V 73 PHE cc_start: 0.7673 (t80) cc_final: 0.7285 (t80) REVERT: V 88 GLU cc_start: 0.7767 (tt0) cc_final: 0.7506 (tp30) REVERT: V 95 PHE cc_start: 0.7759 (p90) cc_final: 0.7525 (p90) REVERT: W 24 ASN cc_start: 0.7775 (t0) cc_final: 0.7392 (t0) REVERT: W 25 LYS cc_start: 0.8386 (mttt) cc_final: 0.8048 (mtpt) REVERT: X 11 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6141 (mtp85) REVERT: X 29 GLU cc_start: 0.8423 (tt0) cc_final: 0.8117 (tt0) REVERT: X 35 SER cc_start: 0.9173 (m) cc_final: 0.8753 (m) REVERT: Y 11 ARG cc_start: 0.8497 (mmm160) cc_final: 0.8046 (mpt180) REVERT: Y 16 ASN cc_start: 0.9193 (m-40) cc_final: 0.8895 (m110) REVERT: Y 59 ILE cc_start: 0.8258 (mt) cc_final: 0.8043 (mt) REVERT: Y 68 LEU cc_start: 0.8891 (mt) cc_final: 0.8682 (mt) REVERT: Z 29 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7071 (ptp-170) REVERT: Z 39 GLN cc_start: 0.7592 (mt0) cc_final: 0.7233 (mt0) REVERT: 0 11 ARG cc_start: 0.8653 (mpt90) cc_final: 0.8282 (mpt90) REVERT: 0 47 MET cc_start: 0.8491 (mtm) cc_final: 0.8174 (mtm) REVERT: 0 49 ASN cc_start: 0.8698 (t0) cc_final: 0.8437 (t0) REVERT: 1 22 MET cc_start: 0.6109 (ttm) cc_final: 0.5585 (mpp) REVERT: 2 36 GLU cc_start: 0.8094 (pt0) cc_final: 0.7852 (tt0) REVERT: 4 25 LYS cc_start: 0.8088 (tmmt) cc_final: 0.7303 (tttp) REVERT: 4 42 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8694 (tm) REVERT: 5 15 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8229 (mmmm) REVERT: 5 30 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.7539 (tpm170) REVERT: 6 15 LYS cc_start: 0.8286 (mttt) cc_final: 0.7679 (ptmt) REVERT: b 6 MET cc_start: 0.6668 (ttm) cc_final: 0.6169 (tmm) REVERT: b 23 TRP cc_start: 0.6554 (p-90) cc_final: 0.6329 (p-90) REVERT: b 24 ASN cc_start: 0.6069 (t0) cc_final: 0.5597 (t0) REVERT: b 27 MET cc_start: 0.7619 (mmm) cc_final: 0.7407 (mmm) REVERT: b 35 ARG cc_start: 0.6484 (mmt-90) cc_final: 0.6150 (mtm-85) REVERT: b 197 ASP cc_start: 0.6023 (m-30) cc_final: 0.5703 (m-30) REVERT: b 203 ASN cc_start: 0.6905 (t0) cc_final: 0.6622 (t0) REVERT: b 214 LEU cc_start: 0.6511 (mt) cc_final: 0.6202 (mt) REVERT: c 8 ASN cc_start: 0.6752 (t0) cc_final: 0.6425 (m-40) REVERT: c 65 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6417 (mtp180) REVERT: c 105 GLU cc_start: 0.5167 (OUTLIER) cc_final: 0.3906 (mp0) REVERT: c 108 LYS cc_start: 0.7052 (mttt) cc_final: 0.6320 (ptpp) REVERT: c 129 MET cc_start: 0.5620 (mtt) cc_final: 0.5368 (mtt) REVERT: c 135 LYS cc_start: 0.8248 (mttm) cc_final: 0.7764 (tptp) REVERT: d 57 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: d 58 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6799 (pttp) REVERT: d 60 LYS cc_start: 0.7403 (ttmt) cc_final: 0.6853 (tttt) REVERT: d 78 GLU cc_start: 0.7439 (tp30) cc_final: 0.7170 (pp20) REVERT: d 105 MET cc_start: 0.6202 (mtt) cc_final: 0.5940 (mmt) REVERT: d 117 LEU cc_start: 0.7596 (mt) cc_final: 0.7245 (mp) REVERT: d 128 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.7048 (ttp-110) REVERT: d 185 LYS cc_start: 0.7905 (ptmt) cc_final: 0.7258 (mtpp) REVERT: d 187 GLU cc_start: 0.7235 (tt0) cc_final: 0.6759 (mp0) REVERT: f 17 GLN cc_start: 0.7742 (mp10) cc_final: 0.7461 (mp10) REVERT: g 56 LYS cc_start: 0.6375 (mttt) cc_final: 0.5707 (tttp) REVERT: g 90 GLU cc_start: 0.7268 (tp30) cc_final: 0.6705 (pp20) REVERT: h 4 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.6262 (mt0) REVERT: h 15 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7294 (ptp-110) REVERT: h 56 LYS cc_start: 0.7237 (pttt) cc_final: 0.6987 (pttt) REVERT: h 101 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7796 (tp) REVERT: j 89 ARG cc_start: 0.5207 (ttm170) cc_final: 0.4736 (ptm160) REVERT: k 34 ILE cc_start: 0.8644 (mm) cc_final: 0.8277 (mp) REVERT: k 80 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7729 (mmtm) REVERT: k 83 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7293 (mt-10) REVERT: k 86 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.8042 (m) REVERT: k 108 THR cc_start: 0.7402 (m) cc_final: 0.6889 (p) REVERT: k 119 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7159 (m110) REVERT: l 6 GLN cc_start: 0.7670 (mt0) cc_final: 0.7299 (mt0) REVERT: l 58 THR cc_start: 0.7934 (m) cc_final: 0.7547 (m) REVERT: l 78 SER cc_start: 0.7947 (t) cc_final: 0.7609 (m) REVERT: l 79 VAL cc_start: 0.8425 (t) cc_final: 0.8187 (p) REVERT: l 108 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7879 (mtmm) REVERT: l 120 LYS cc_start: 0.7674 (mmmt) cc_final: 0.6937 (mppt) REVERT: m 31 LYS cc_start: 0.7626 (mttt) cc_final: 0.7073 (mtmt) REVERT: m 46 SER cc_start: 0.5832 (m) cc_final: 0.5562 (p) REVERT: m 87 ARG cc_start: 0.6358 (mtm110) cc_final: 0.5954 (ttp-170) REVERT: m 93 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6899 (mpt180) REVERT: m 101 ARG cc_start: 0.7469 (ptp-110) cc_final: 0.6841 (ptp-110) REVERT: n 92 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6309 (mt-10) REVERT: o 11 ILE cc_start: 0.6312 (mm) cc_final: 0.6038 (mm) REVERT: o 39 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8021 (tp) REVERT: o 47 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: o 63 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7618 (ttp-170) REVERT: o 74 ASP cc_start: 0.6939 (t0) cc_final: 0.5958 (m-30) REVERT: q 57 ASP cc_start: 0.6765 (t70) cc_final: 0.6219 (t0) REVERT: s 21 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6777 (pttt) REVERT: s 44 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7861 (mpt) REVERT: t 48 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7018 (tp-100) REVERT: t 52 ASN cc_start: 0.7730 (m110) cc_final: 0.7216 (m-40) REVERT: u 6 VAL cc_start: 0.7588 (t) cc_final: 0.7341 (t) REVERT: v 142 GLN cc_start: 0.7855 (mt0) cc_final: 0.7311 (mm-40) REVERT: v 143 ASP cc_start: 0.8370 (t70) cc_final: 0.8146 (t70) REVERT: v 147 MET cc_start: 0.7596 (ttp) cc_final: 0.7197 (ptm) REVERT: v 201 LEU cc_start: 0.7959 (tp) cc_final: 0.7656 (tp) REVERT: v 245 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6745 (mpp80) REVERT: v 273 GLN cc_start: 0.8339 (mt0) cc_final: 0.7668 (tt0) REVERT: v 295 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6983 (mm) REVERT: v 300 MET cc_start: 0.6716 (mmm) cc_final: 0.6439 (mmm) REVERT: v 316 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: w 30 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7475 (mt-10) outliers start: 328 outliers final: 197 residues processed: 1509 average time/residue: 1.4262 time to fit residues: 3623.3380 Evaluate side-chains 1469 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1230 time to evaluate : 6.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 57 ASN Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 116 MET Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 86 MET Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 54 MET Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 57 GLU Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 111 MET Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 59 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 245 ARG Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 325 SER Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 972 optimal weight: 20.0000 chunk 740 optimal weight: 20.0000 chunk 510 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 469 optimal weight: 10.0000 chunk 660 optimal weight: 20.0000 chunk 987 optimal weight: 6.9990 chunk 1045 optimal weight: 5.9990 chunk 516 optimal weight: 10.0000 chunk 936 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS G 30 ASN G 111 HIS G 115 HIS ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN K 135 GLN O 62 ASN P 19 GLN R 44 GLN V 69 ASN W 12 GLN W 78 GLN X 57 HIS 1 20 ASN 2 42 HIS 4 26 ASN b 39 HIS c 3 GLN c 8 ASN c 41 GLN d 59 GLN e 77 ASN h 4 GLN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN l 5 ASN m 52 GLN r 54 GLN t 48 GLN ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 6 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 163943 Z= 0.550 Angle : 0.841 15.339 244682 Z= 0.433 Chirality : 0.049 0.540 31096 Planarity : 0.008 0.142 13510 Dihedral : 23.543 179.678 80721 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 7.86 % Allowed : 20.89 % Favored : 71.25 % 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: -0.40 (0.10), residues: 6269 helix: 1.29 (0.11), residues: 2252 sheet: -0.98 (0.14), residues: 1165 loop : -1.20 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 96 HIS 0.015 0.002 HIS 5 43 PHE 0.033 0.003 PHE E 183 TYR 0.026 0.003 TYR M 58 ARG 0.012 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1694 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 1284 time to evaluate : 6.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LYS cc_start: 0.8165 (mttt) cc_final: 0.7909 (mtmm) REVERT: C 62 TYR cc_start: 0.8910 (t80) cc_final: 0.8663 (t80) REVERT: C 66 ASP cc_start: 0.8784 (t0) cc_final: 0.8309 (t0) REVERT: C 163 GLN cc_start: 0.8355 (mt0) cc_final: 0.8074 (mt0) REVERT: C 181 MET cc_start: 0.8352 (mmm) cc_final: 0.7822 (mmm) REVERT: C 183 LYS cc_start: 0.8056 (mttp) cc_final: 0.7793 (mtpt) REVERT: C 192 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 242 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8179 (mttm) REVERT: C 269 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7285 (ttt-90) REVERT: C 270 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8188 (mmm160) REVERT: C 271 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8069 (ptt-90) REVERT: D 17 GLU cc_start: 0.8411 (tt0) cc_final: 0.7987 (mp0) REVERT: D 64 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7846 (mt-10) REVERT: D 88 GLU cc_start: 0.6329 (mt-10) cc_final: 0.5516 (mt-10) REVERT: D 94 GLN cc_start: 0.7000 (tt0) cc_final: 0.6656 (tt0) REVERT: D 103 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: D 105 LYS cc_start: 0.7844 (mttt) cc_final: 0.7555 (mmtm) REVERT: D 106 LYS cc_start: 0.8509 (mttt) cc_final: 0.8128 (mttm) REVERT: E 3 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6579 (mp) REVERT: E 18 THR cc_start: 0.7384 (m) cc_final: 0.7027 (p) REVERT: E 22 ASP cc_start: 0.8215 (m-30) cc_final: 0.7180 (p0) REVERT: E 23 PHE cc_start: 0.8894 (t80) cc_final: 0.8520 (t80) REVERT: E 35 TYR cc_start: 0.8810 (t80) cc_final: 0.8509 (t80) REVERT: E 57 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5289 (pttt) REVERT: E 168 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: E 176 ASP cc_start: 0.8098 (p0) cc_final: 0.7430 (p0) REVERT: E 194 LYS cc_start: 0.7796 (tptp) cc_final: 0.7285 (mttp) REVERT: F 3 LYS cc_start: 0.7193 (tttt) cc_final: 0.6727 (tptt) REVERT: F 38 MET cc_start: 0.6885 (mtm) cc_final: 0.6467 (ptp) REVERT: F 69 LYS cc_start: 0.8478 (mttt) cc_final: 0.8206 (mtpt) REVERT: F 105 THR cc_start: 0.7244 (OUTLIER) cc_final: 0.6594 (p) REVERT: F 140 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: G 27 LYS cc_start: 0.6506 (mttt) cc_final: 0.5685 (ttpp) REVERT: G 58 TYR cc_start: 0.6662 (m-80) cc_final: 0.6400 (m-80) REVERT: G 76 VAL cc_start: 0.7885 (t) cc_final: 0.7666 (m) REVERT: G 95 ARG cc_start: 0.6883 (mtm110) cc_final: 0.6347 (ttm110) REVERT: G 130 GLU cc_start: 0.6315 (mm-30) cc_final: 0.6036 (mp0) REVERT: H 66 ASN cc_start: 0.5575 (OUTLIER) cc_final: 0.4746 (t0) REVERT: H 114 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5135 (tp30) REVERT: H 124 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.6020 (p) REVERT: H 127 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4690 (mp0) REVERT: H 129 GLU cc_start: 0.4825 (OUTLIER) cc_final: 0.3968 (mm-30) REVERT: I 3 LEU cc_start: 0.4295 (OUTLIER) cc_final: 0.4031 (mt) REVERT: I 38 MET cc_start: 0.4641 (ttm) cc_final: 0.4440 (ptp) REVERT: K 14 ASP cc_start: 0.8496 (m-30) cc_final: 0.7851 (t0) REVERT: K 23 LYS cc_start: 0.8552 (mttt) cc_final: 0.7758 (mmmt) REVERT: K 92 MET cc_start: 0.8338 (mmm) cc_final: 0.8102 (mmm) REVERT: K 118 MET cc_start: 0.8628 (mtt) cc_final: 0.8322 (mtt) REVERT: K 123 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7738 (mmpt) REVERT: K 131 ASN cc_start: 0.8324 (m110) cc_final: 0.7918 (m-40) REVERT: K 138 GLN cc_start: 0.8100 (mt0) cc_final: 0.7624 (mt0) REVERT: L 47 ILE cc_start: 0.8494 (pt) cc_final: 0.8136 (tp) REVERT: M 10 GLU cc_start: 0.8448 (tp30) cc_final: 0.8213 (tp30) REVERT: M 78 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7721 (mmt-90) REVERT: M 141 LYS cc_start: 0.6653 (tttt) cc_final: 0.6421 (ttmt) REVERT: N 60 GLN cc_start: 0.7802 (tp40) cc_final: 0.6768 (tt0) REVERT: N 104 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8223 (mt-10) REVERT: O 44 LEU cc_start: 0.9056 (tp) cc_final: 0.8843 (tt) REVERT: O 60 VAL cc_start: 0.8388 (t) cc_final: 0.8114 (p) REVERT: O 72 ASP cc_start: 0.8303 (t0) cc_final: 0.8035 (t0) REVERT: O 90 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7474 (ttm110) REVERT: O 114 GLU cc_start: 0.8845 (pt0) cc_final: 0.8550 (pt0) REVERT: O 118 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6801 (ttp80) REVERT: P 25 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6969 (ptt-90) REVERT: P 64 TYR cc_start: 0.6103 (t80) cc_final: 0.5397 (t80) REVERT: P 106 LEU cc_start: 0.8292 (tt) cc_final: 0.8060 (tt) REVERT: P 116 GLN cc_start: 0.7842 (tt0) cc_final: 0.6991 (tm-30) REVERT: Q 7 GLN cc_start: 0.7429 (tm-30) cc_final: 0.6937 (tp40) REVERT: Q 24 ASP cc_start: 0.8233 (m-30) cc_final: 0.7912 (m-30) REVERT: Q 57 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8536 (p) REVERT: R 81 ASN cc_start: 0.8152 (t0) cc_final: 0.7879 (t0) REVERT: S 23 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8095 (mm-30) REVERT: S 60 LYS cc_start: 0.7594 (mttt) cc_final: 0.7010 (ttmt) REVERT: S 73 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7792 (ttpp) REVERT: S 78 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8518 (tpp-160) REVERT: S 85 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8064 (ttmm) REVERT: T 1 MET cc_start: 0.7655 (ttt) cc_final: 0.7091 (ptp) REVERT: T 22 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: T 55 ILE cc_start: 0.8934 (mt) cc_final: 0.8689 (mt) REVERT: T 59 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8650 (mm-30) REVERT: U 1 MET cc_start: 0.6390 (ttm) cc_final: 0.6029 (ppp) REVERT: U 33 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7070 (tttm) REVERT: U 69 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7184 (mtm110) REVERT: U 77 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7803 (mtt-85) REVERT: V 27 ASN cc_start: 0.8286 (p0) cc_final: 0.8021 (p0) REVERT: V 37 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7881 (tm-30) REVERT: V 46 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7898 (mm-40) REVERT: V 73 PHE cc_start: 0.7713 (t80) cc_final: 0.7317 (t80) REVERT: W 1 MET cc_start: 0.6351 (tpt) cc_final: 0.5433 (mpp) REVERT: W 24 ASN cc_start: 0.7660 (t0) cc_final: 0.7391 (t0) REVERT: W 60 VAL cc_start: 0.8367 (t) cc_final: 0.8088 (t) REVERT: W 73 LYS cc_start: 0.7622 (mttt) cc_final: 0.7355 (mttm) REVERT: X 11 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6201 (mtp85) REVERT: X 35 SER cc_start: 0.9125 (m) cc_final: 0.8712 (m) REVERT: Y 11 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8281 (mpt180) REVERT: Z 29 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7186 (ptp-170) REVERT: Z 39 GLN cc_start: 0.7704 (mt0) cc_final: 0.7324 (mt0) REVERT: Z 58 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.7063 (t0) REVERT: 0 47 MET cc_start: 0.8555 (mtm) cc_final: 0.8244 (mtm) REVERT: 0 49 ASN cc_start: 0.8922 (t0) cc_final: 0.8628 (t0) REVERT: 1 8 LYS cc_start: 0.6702 (mmmt) cc_final: 0.5773 (tptt) REVERT: 1 22 MET cc_start: 0.5982 (ttm) cc_final: 0.5474 (mpp) REVERT: 2 31 ASP cc_start: 0.7732 (t70) cc_final: 0.7509 (t70) REVERT: 2 37 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8053 (mttp) REVERT: 3 28 ARG cc_start: 0.8206 (mpt-90) cc_final: 0.7412 (mmm-85) REVERT: 4 25 LYS cc_start: 0.8213 (tmmt) cc_final: 0.7462 (tttp) REVERT: 6 12 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8317 (ptm160) REVERT: 6 15 LYS cc_start: 0.8328 (mttt) cc_final: 0.8064 (mttt) REVERT: b 6 MET cc_start: 0.6659 (ttm) cc_final: 0.6304 (ptm) REVERT: b 23 TRP cc_start: 0.6450 (p-90) cc_final: 0.5863 (p-90) REVERT: b 27 MET cc_start: 0.7763 (mmm) cc_final: 0.7330 (mmm) REVERT: b 35 ARG cc_start: 0.6856 (mmt-90) cc_final: 0.6353 (mtm-85) REVERT: b 52 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: b 68 LEU cc_start: 0.6315 (tp) cc_final: 0.6061 (tp) REVERT: b 137 ARG cc_start: 0.4330 (OUTLIER) cc_final: 0.4025 (ttm110) REVERT: b 214 LEU cc_start: 0.6379 (mt) cc_final: 0.6024 (mt) REVERT: c 22 TRP cc_start: 0.6811 (p-90) cc_final: 0.5876 (p-90) REVERT: c 62 LYS cc_start: 0.5795 (mmtt) cc_final: 0.5297 (tmmt) REVERT: c 105 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.3782 (mp0) REVERT: c 121 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7462 (p) REVERT: c 135 LYS cc_start: 0.8508 (mttm) cc_final: 0.7854 (tptp) REVERT: c 179 ARG cc_start: 0.7041 (ptt-90) cc_final: 0.6775 (ptt-90) REVERT: d 60 LYS cc_start: 0.7477 (ttmt) cc_final: 0.7018 (tttt) REVERT: d 62 ARG cc_start: 0.7612 (mtp180) cc_final: 0.7385 (ptm160) REVERT: d 121 LYS cc_start: 0.7440 (mttt) cc_final: 0.7234 (mtmt) REVERT: d 185 LYS cc_start: 0.8079 (ptmt) cc_final: 0.7315 (mtpt) REVERT: d 187 GLU cc_start: 0.6779 (tt0) cc_final: 0.6376 (mp0) REVERT: e 15 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6645 (tt) REVERT: f 17 GLN cc_start: 0.7643 (mp10) cc_final: 0.7347 (mp10) REVERT: f 45 ARG cc_start: 0.6928 (mtp-110) cc_final: 0.6702 (mtp-110) REVERT: g 101 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7047 (ttm) REVERT: g 130 ASN cc_start: 0.6277 (m-40) cc_final: 0.6016 (m-40) REVERT: h 101 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7806 (tp) REVERT: k 34 ILE cc_start: 0.8752 (mm) cc_final: 0.8429 (mp) REVERT: k 57 LYS cc_start: 0.8196 (pttt) cc_final: 0.7771 (pttm) REVERT: k 80 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7709 (mmtm) REVERT: k 119 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7206 (m110) REVERT: l 6 GLN cc_start: 0.7549 (mt0) cc_final: 0.7183 (mt0) REVERT: l 58 THR cc_start: 0.8065 (m) cc_final: 0.7699 (m) REVERT: l 78 SER cc_start: 0.8042 (t) cc_final: 0.7600 (m) REVERT: l 79 VAL cc_start: 0.8257 (t) cc_final: 0.8014 (p) REVERT: l 108 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7913 (mtmm) REVERT: l 120 LYS cc_start: 0.7709 (mmmt) cc_final: 0.6945 (mppt) REVERT: m 31 LYS cc_start: 0.7648 (mttt) cc_final: 0.7424 (mmmm) REVERT: m 87 ARG cc_start: 0.6026 (mtm110) cc_final: 0.5618 (ttp-170) REVERT: m 93 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6930 (mpt-90) REVERT: m 101 ARG cc_start: 0.7328 (ptp-110) cc_final: 0.6829 (ptp-110) REVERT: n 16 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6465 (mt) REVERT: n 28 LYS cc_start: 0.6958 (mttt) cc_final: 0.6691 (mmtt) REVERT: o 10 LYS cc_start: 0.7558 (tppt) cc_final: 0.7341 (tppt) REVERT: o 24 SER cc_start: 0.7258 (t) cc_final: 0.6752 (p) REVERT: o 32 LEU cc_start: 0.8455 (mm) cc_final: 0.8231 (mm) REVERT: o 39 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7956 (tp) REVERT: o 74 ASP cc_start: 0.6955 (t0) cc_final: 0.5962 (m-30) REVERT: q 43 LYS cc_start: 0.7226 (mttt) cc_final: 0.7003 (mtpt) REVERT: q 50 ASN cc_start: 0.6546 (m110) cc_final: 0.6078 (t0) REVERT: r 52 GLN cc_start: 0.8041 (tp40) cc_final: 0.7517 (tp40) REVERT: s 21 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6776 (pptt) REVERT: t 15 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: t 48 GLN cc_start: 0.7427 (mm-40) cc_final: 0.6909 (tp-100) REVERT: t 52 ASN cc_start: 0.7785 (m110) cc_final: 0.7515 (m110) REVERT: v 142 GLN cc_start: 0.7936 (mt0) cc_final: 0.7369 (mm-40) REVERT: v 147 MET cc_start: 0.7607 (ttp) cc_final: 0.7197 (ptm) REVERT: v 193 ARG cc_start: 0.7077 (ptt-90) cc_final: 0.6586 (ptt180) REVERT: v 201 LEU cc_start: 0.8157 (tp) cc_final: 0.7654 (tp) REVERT: v 255 ASN cc_start: 0.6909 (m-40) cc_final: 0.6520 (m110) REVERT: v 257 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.7970 (p) REVERT: v 273 GLN cc_start: 0.8430 (mt0) cc_final: 0.7843 (tt0) REVERT: v 295 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7220 (mm) REVERT: v 300 MET cc_start: 0.7029 (mmm) cc_final: 0.6803 (mmm) REVERT: v 316 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6849 (m-30) REVERT: w 30 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7289 (mt-10) outliers start: 410 outliers final: 267 residues processed: 1545 average time/residue: 1.4096 time to fit residues: 3666.5369 Evaluate side-chains 1549 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1237 time to evaluate : 6.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 57 ASN Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 86 MET Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 0 residue 54 MET Chi-restraints excluded: chain 0 residue 58 GLU Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 5 residue 44 LEU Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 137 ARG Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 139 GLN Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 40 GLU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 64 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 38 TYR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 52 GLN Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain o residue 18 ASP Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 45 THR Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 78 GLU Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 257 THR Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 325 SER Chi-restraints excluded: chain v residue 357 ILE Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 871 optimal weight: 7.9990 chunk 593 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 778 optimal weight: 20.0000 chunk 431 optimal weight: 20.0000 chunk 892 optimal weight: 6.9990 chunk 722 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 534 optimal weight: 2.9990 chunk 938 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 156 ASN G 64 GLN G 111 HIS ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN V 69 ASN Z 15 ASN ** 3 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN c 41 GLN g 153 HIS ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN i 37 GLN l 5 ASN t 13 GLN v 5 ASN v 286 GLN v 290 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 163943 Z= 0.285 Angle : 0.655 14.776 244682 Z= 0.350 Chirality : 0.038 0.559 31096 Planarity : 0.006 0.131 13510 Dihedral : 23.503 178.647 80691 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 6.32 % Allowed : 23.15 % Favored : 70.53 % 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: -0.20 (0.10), residues: 6269 helix: 1.50 (0.11), residues: 2259 sheet: -0.91 (0.15), residues: 1168 loop : -1.11 (0.11), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP c 201 HIS 0.012 0.001 HIS K 80 PHE 0.025 0.002 PHE p 38 TYR 0.030 0.002 TYR b 213 ARG 0.009 0.001 ARG g 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1280 time to evaluate : 6.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8928 (t80) cc_final: 0.8688 (t80) REVERT: C 66 ASP cc_start: 0.8761 (t0) cc_final: 0.8295 (t0) REVERT: C 181 MET cc_start: 0.8225 (mmm) cc_final: 0.7842 (mmm) REVERT: C 242 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8208 (mmtm) REVERT: C 269 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7360 (ttt-90) REVERT: D 17 GLU cc_start: 0.8333 (tt0) cc_final: 0.7864 (mp0) REVERT: D 64 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7680 (mt-10) REVERT: D 94 GLN cc_start: 0.7044 (tt0) cc_final: 0.6324 (mt0) REVERT: D 106 LYS cc_start: 0.8594 (mttt) cc_final: 0.8142 (mttm) REVERT: D 114 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.7857 (mtmm) REVERT: D 150 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: E 3 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6513 (mp) REVERT: E 18 THR cc_start: 0.7372 (m) cc_final: 0.6991 (p) REVERT: E 22 ASP cc_start: 0.8344 (m-30) cc_final: 0.7271 (p0) REVERT: E 35 TYR cc_start: 0.8747 (t80) cc_final: 0.8485 (t80) REVERT: E 57 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5464 (pttt) REVERT: E 176 ASP cc_start: 0.8120 (p0) cc_final: 0.7406 (p0) REVERT: E 194 LYS cc_start: 0.7800 (tptp) cc_final: 0.7285 (mttp) REVERT: F 3 LYS cc_start: 0.7016 (tttt) cc_final: 0.6685 (tptt) REVERT: F 38 MET cc_start: 0.6617 (mtm) cc_final: 0.6377 (ptp) REVERT: F 105 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6612 (p) REVERT: F 130 MET cc_start: 0.6015 (ptp) cc_final: 0.5577 (tpt) REVERT: G 101 ASN cc_start: 0.6808 (p0) cc_final: 0.6195 (p0) REVERT: G 155 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: H 15 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6258 (tt) REVERT: H 27 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6711 (ptp90) REVERT: H 66 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5019 (t0) REVERT: H 114 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5195 (tp30) REVERT: H 121 VAL cc_start: 0.6102 (OUTLIER) cc_final: 0.5897 (p) REVERT: H 127 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.5126 (mp0) REVERT: H 129 GLU cc_start: 0.4876 (OUTLIER) cc_final: 0.3962 (mm-30) REVERT: I 3 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4273 (mt) REVERT: K 14 ASP cc_start: 0.8374 (m-30) cc_final: 0.7806 (t0) REVERT: K 23 LYS cc_start: 0.8616 (mttt) cc_final: 0.7790 (mmmt) REVERT: K 92 MET cc_start: 0.8326 (mmm) cc_final: 0.8119 (mmm) REVERT: K 118 MET cc_start: 0.8565 (mtt) cc_final: 0.8224 (mtt) REVERT: K 123 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7608 (mmpt) REVERT: K 131 ASN cc_start: 0.8235 (m110) cc_final: 0.7788 (m-40) REVERT: K 138 GLN cc_start: 0.8079 (mt0) cc_final: 0.7661 (mt0) REVERT: L 47 ILE cc_start: 0.8439 (pt) cc_final: 0.8091 (tp) REVERT: L 121 GLU cc_start: 0.7608 (tt0) cc_final: 0.7074 (tt0) REVERT: M 2 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7819 (mmt-90) REVERT: M 78 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7595 (mmt-90) REVERT: M 141 LYS cc_start: 0.6802 (tttt) cc_final: 0.6553 (ttmt) REVERT: N 60 GLN cc_start: 0.7812 (tp40) cc_final: 0.6729 (tt0) REVERT: N 104 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8213 (mt-10) REVERT: O 60 VAL cc_start: 0.8370 (t) cc_final: 0.8100 (p) REVERT: O 72 ASP cc_start: 0.8309 (t0) cc_final: 0.8066 (t0) REVERT: O 90 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7327 (ttm110) REVERT: O 114 GLU cc_start: 0.8731 (pt0) cc_final: 0.8420 (pt0) REVERT: O 118 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6863 (ttp80) REVERT: P 25 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6838 (ptt-90) REVERT: P 64 TYR cc_start: 0.6155 (t80) cc_final: 0.5254 (t80) REVERT: P 106 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8035 (tt) REVERT: P 116 GLN cc_start: 0.7910 (tt0) cc_final: 0.7028 (tm-30) REVERT: Q 7 GLN cc_start: 0.7463 (tm-30) cc_final: 0.6971 (tm-30) REVERT: Q 55 LEU cc_start: 0.9195 (tp) cc_final: 0.8767 (tp) REVERT: Q 89 ARG cc_start: 0.7198 (ptt90) cc_final: 0.6872 (ptt90) REVERT: S 23 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8013 (mm-30) REVERT: S 24 LYS cc_start: 0.8419 (ttpp) cc_final: 0.7995 (ttpp) REVERT: S 60 LYS cc_start: 0.7615 (mttt) cc_final: 0.7066 (ttmt) REVERT: S 73 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7928 (ttpp) REVERT: S 78 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8501 (tpp-160) REVERT: S 85 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8117 (ttmm) REVERT: T 1 MET cc_start: 0.7701 (ttt) cc_final: 0.7163 (ptp) REVERT: T 22 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: U 33 LYS cc_start: 0.7446 (ttmt) cc_final: 0.7142 (tttm) REVERT: U 69 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7190 (mtp-110) REVERT: U 77 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7931 (mtt-85) REVERT: V 27 ASN cc_start: 0.8203 (p0) cc_final: 0.7970 (p0) REVERT: V 37 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7696 (tm-30) REVERT: V 39 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8620 (mp) REVERT: V 46 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7993 (mm-40) REVERT: V 73 PHE cc_start: 0.7690 (t80) cc_final: 0.7334 (t80) REVERT: W 1 MET cc_start: 0.6443 (tpt) cc_final: 0.5516 (mpp) REVERT: W 24 ASN cc_start: 0.7687 (t0) cc_final: 0.7396 (t0) REVERT: W 25 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8175 (mtpt) REVERT: X 11 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6248 (mtp85) REVERT: X 35 SER cc_start: 0.9126 (m) cc_final: 0.8728 (m) REVERT: Y 11 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8280 (mpt180) REVERT: Z 19 LEU cc_start: 0.7306 (tp) cc_final: 0.7075 (tp) REVERT: Z 29 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7081 (ptp-170) REVERT: Z 39 GLN cc_start: 0.7710 (mt0) cc_final: 0.7294 (mt0) REVERT: 0 47 MET cc_start: 0.8475 (mtm) cc_final: 0.8122 (mtm) REVERT: 0 49 ASN cc_start: 0.8785 (t0) cc_final: 0.8439 (t0) REVERT: 1 8 LYS cc_start: 0.6708 (mmmt) cc_final: 0.5772 (tptt) REVERT: 1 22 MET cc_start: 0.5896 (ttm) cc_final: 0.5506 (mpp) REVERT: 2 10 ARG cc_start: 0.8947 (ptp90) cc_final: 0.8633 (ptp-170) REVERT: 2 31 ASP cc_start: 0.7573 (t70) cc_final: 0.7280 (t70) REVERT: 3 28 ARG cc_start: 0.8204 (mpt-90) cc_final: 0.7425 (mmm-85) REVERT: 4 25 LYS cc_start: 0.7967 (tmmt) cc_final: 0.7386 (tttp) REVERT: 5 15 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8206 (mmmm) REVERT: 5 30 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7307 (tpm170) REVERT: 5 61 CYS cc_start: 0.8783 (m) cc_final: 0.8304 (m) REVERT: 6 12 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8304 (ptm160) REVERT: 6 15 LYS cc_start: 0.8336 (mttt) cc_final: 0.8064 (mttt) REVERT: b 23 TRP cc_start: 0.6397 (p-90) cc_final: 0.5846 (p-90) REVERT: b 27 MET cc_start: 0.7588 (mmm) cc_final: 0.7261 (mmm) REVERT: b 35 ARG cc_start: 0.6775 (mmt-90) cc_final: 0.6318 (mtm-85) REVERT: b 117 LEU cc_start: 0.3187 (OUTLIER) cc_final: 0.2855 (mm) REVERT: b 137 ARG cc_start: 0.4283 (OUTLIER) cc_final: 0.4081 (ttm110) REVERT: b 154 MET cc_start: 0.5993 (mmm) cc_final: 0.5168 (mmm) REVERT: b 214 LEU cc_start: 0.6354 (mt) cc_final: 0.6017 (mt) REVERT: c 62 LYS cc_start: 0.5812 (mmtt) cc_final: 0.5373 (tmtt) REVERT: c 105 GLU cc_start: 0.5333 (OUTLIER) cc_final: 0.4008 (mp0) REVERT: c 121 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7468 (p) REVERT: c 135 LYS cc_start: 0.8494 (mttm) cc_final: 0.8019 (tttt) REVERT: d 54 GLN cc_start: 0.8861 (mt0) cc_final: 0.8515 (mt0) REVERT: d 58 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6789 (pttp) REVERT: d 60 LYS cc_start: 0.7430 (ttmt) cc_final: 0.6907 (tttt) REVERT: d 78 GLU cc_start: 0.7541 (tp30) cc_final: 0.7215 (pp20) REVERT: d 121 LYS cc_start: 0.7454 (mttt) cc_final: 0.7228 (mtmt) REVERT: d 185 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7335 (mtpp) REVERT: d 187 GLU cc_start: 0.6861 (tt0) cc_final: 0.6431 (mp0) REVERT: e 71 MET cc_start: 0.4116 (tpp) cc_final: 0.3822 (tpp) REVERT: e 105 ILE cc_start: 0.8494 (mp) cc_final: 0.8123 (mm) REVERT: e 123 VAL cc_start: 0.8408 (t) cc_final: 0.8186 (p) REVERT: g 78 ARG cc_start: 0.5267 (tpp80) cc_final: 0.5044 (tpt-90) REVERT: h 15 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7258 (ptp-110) REVERT: h 101 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7815 (tp) REVERT: k 34 ILE cc_start: 0.8796 (mm) cc_final: 0.8457 (mp) REVERT: k 57 LYS cc_start: 0.8031 (pttt) cc_final: 0.7602 (pttm) REVERT: k 69 ARG cc_start: 0.6842 (ttm-80) cc_final: 0.6577 (ttm-80) REVERT: k 80 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7629 (mmtm) REVERT: k 101 ASN cc_start: 0.6784 (t0) cc_final: 0.6538 (t0) REVERT: k 119 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7171 (m110) REVERT: l 6 GLN cc_start: 0.7490 (mt0) cc_final: 0.7093 (mt0) REVERT: l 58 THR cc_start: 0.7969 (m) cc_final: 0.7675 (m) REVERT: l 78 SER cc_start: 0.8034 (t) cc_final: 0.7567 (m) REVERT: l 79 VAL cc_start: 0.8301 (t) cc_final: 0.8065 (p) REVERT: l 108 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7923 (mtmm) REVERT: l 120 LYS cc_start: 0.7721 (mmmt) cc_final: 0.6950 (mppt) REVERT: m 31 LYS cc_start: 0.7825 (mttt) cc_final: 0.7192 (mtmt) REVERT: m 46 SER cc_start: 0.5883 (m) cc_final: 0.5562 (p) REVERT: m 93 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6921 (mpt-90) REVERT: m 101 ARG cc_start: 0.7156 (ptp-110) cc_final: 0.6520 (ptp-110) REVERT: n 28 LYS cc_start: 0.6815 (mttt) cc_final: 0.6610 (mtpp) REVERT: o 10 LYS cc_start: 0.7455 (tppt) cc_final: 0.7099 (tppt) REVERT: o 24 SER cc_start: 0.7573 (t) cc_final: 0.7128 (p) REVERT: o 39 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7995 (tp) REVERT: o 65 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7752 (mtpt) REVERT: o 70 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7797 (tt) REVERT: o 74 ASP cc_start: 0.6995 (t0) cc_final: 0.5861 (m-30) REVERT: p 51 ARG cc_start: 0.6064 (ptm160) cc_final: 0.5783 (ptp90) REVERT: q 5 ILE cc_start: 0.6553 (pt) cc_final: 0.6225 (mp) REVERT: q 50 ASN cc_start: 0.6561 (m110) cc_final: 0.6156 (t0) REVERT: r 52 GLN cc_start: 0.8051 (tp40) cc_final: 0.7552 (tp40) REVERT: s 21 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6757 (pptt) REVERT: s 44 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7809 (mpt) REVERT: s 66 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6324 (ptp) REVERT: t 15 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: t 40 GLU cc_start: 0.8594 (tp30) cc_final: 0.7971 (tm-30) REVERT: t 48 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7000 (tp-100) REVERT: v 142 GLN cc_start: 0.7864 (mt0) cc_final: 0.7662 (mm-40) REVERT: v 147 MET cc_start: 0.7582 (ttp) cc_final: 0.7196 (ptm) REVERT: v 193 ARG cc_start: 0.7111 (ptt-90) cc_final: 0.6666 (ptt180) REVERT: v 200 ARG cc_start: 0.7381 (ttt90) cc_final: 0.7080 (ttm-80) REVERT: v 201 LEU cc_start: 0.8066 (tp) cc_final: 0.7543 (tp) REVERT: v 255 ASN cc_start: 0.6990 (m-40) cc_final: 0.6605 (m110) REVERT: v 273 GLN cc_start: 0.8383 (mt0) cc_final: 0.7807 (tt0) REVERT: v 295 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7104 (mm) REVERT: v 300 MET cc_start: 0.7143 (mmm) cc_final: 0.6832 (mmm) REVERT: v 314 LYS cc_start: 0.6815 (mtpt) cc_final: 0.6420 (mmtt) REVERT: v 316 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: v 335 ASP cc_start: 0.7061 (t0) cc_final: 0.6679 (t70) REVERT: w 30 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7147 (mt-10) outliers start: 330 outliers final: 222 residues processed: 1479 average time/residue: 1.3789 time to fit residues: 3455.6109 Evaluate side-chains 1521 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1252 time to evaluate : 6.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 57 ASN Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 82 MET Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 25 LYS Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 29 GLU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 54 MET Chi-restraints excluded: chain 0 residue 58 GLU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 2 residue 36 GLU Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 23 ILE Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 137 ARG Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 139 GLN Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 40 GLU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 111 MET Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 163 THR Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 325 SER Chi-restraints excluded: chain v residue 357 ILE Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 351 optimal weight: 8.9990 chunk 941 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 614 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 1046 optimal weight: 9.9990 chunk 869 optimal weight: 10.0000 chunk 484 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 346 optimal weight: 0.9990 chunk 549 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 32 ASN E 156 ASN T 61 ASN ** 3 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 GLN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN t 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 163943 Z= 0.240 Angle : 0.616 14.640 244682 Z= 0.331 Chirality : 0.036 0.558 31096 Planarity : 0.006 0.129 13510 Dihedral : 23.432 179.590 80686 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 6.61 % Allowed : 23.32 % Favored : 70.07 % 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: -0.06 (0.10), residues: 6269 helix: 1.61 (0.11), residues: 2251 sheet: -0.81 (0.15), residues: 1170 loop : -1.03 (0.11), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 201 HIS 0.007 0.001 HIS r 74 PHE 0.021 0.002 PHE V 95 TYR 0.033 0.002 TYR b 213 ARG 0.010 0.001 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1258 time to evaluate : 6.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8949 (t80) cc_final: 0.8709 (t80) REVERT: C 66 ASP cc_start: 0.8726 (t0) cc_final: 0.8236 (t0) REVERT: C 181 MET cc_start: 0.8189 (mmm) cc_final: 0.7886 (mmm) REVERT: C 242 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8159 (mmtm) REVERT: C 269 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7370 (ttt-90) REVERT: D 17 GLU cc_start: 0.8381 (tt0) cc_final: 0.7964 (mp0) REVERT: D 64 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 94 GLN cc_start: 0.7061 (tt0) cc_final: 0.6335 (mt0) REVERT: D 106 LYS cc_start: 0.8576 (mttt) cc_final: 0.8150 (mttm) REVERT: D 114 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.7593 (mtmm) REVERT: E 3 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6412 (mt) REVERT: E 18 THR cc_start: 0.7290 (m) cc_final: 0.6913 (p) REVERT: E 22 ASP cc_start: 0.8354 (m-30) cc_final: 0.7228 (p0) REVERT: E 35 TYR cc_start: 0.8798 (t80) cc_final: 0.8556 (t80) REVERT: E 57 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5657 (pttt) REVERT: E 162 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7208 (ttp80) REVERT: E 176 ASP cc_start: 0.8056 (p0) cc_final: 0.7340 (p0) REVERT: E 194 LYS cc_start: 0.7801 (tptp) cc_final: 0.7286 (mttp) REVERT: F 3 LYS cc_start: 0.7155 (tttt) cc_final: 0.6773 (tptt) REVERT: F 83 TYR cc_start: 0.8056 (m-80) cc_final: 0.7783 (m-80) REVERT: F 105 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6614 (p) REVERT: F 130 MET cc_start: 0.5993 (ptp) cc_final: 0.5461 (tpt) REVERT: G 86 LYS cc_start: 0.7884 (mttm) cc_final: 0.7082 (tttp) REVERT: G 95 ARG cc_start: 0.6961 (mtm110) cc_final: 0.6469 (ttp80) REVERT: G 101 ASN cc_start: 0.6850 (p0) cc_final: 0.6294 (p0) REVERT: G 155 GLU cc_start: 0.8593 (pm20) cc_final: 0.7934 (pm20) REVERT: H 15 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6341 (tt) REVERT: H 66 ASN cc_start: 0.5463 (OUTLIER) cc_final: 0.4654 (m-40) REVERT: H 121 VAL cc_start: 0.6221 (OUTLIER) cc_final: 0.5944 (p) REVERT: H 127 GLU cc_start: 0.5365 (OUTLIER) cc_final: 0.5108 (mp0) REVERT: H 129 GLU cc_start: 0.4840 (OUTLIER) cc_final: 0.3904 (mm-30) REVERT: I 52 MET cc_start: 0.1679 (mmm) cc_final: 0.0765 (mtt) REVERT: I 86 MET cc_start: 0.1795 (ttp) cc_final: 0.1356 (ttp) REVERT: K 14 ASP cc_start: 0.8346 (m-30) cc_final: 0.7790 (t0) REVERT: K 23 LYS cc_start: 0.8675 (mttt) cc_final: 0.7922 (mmmt) REVERT: K 92 MET cc_start: 0.8339 (mmm) cc_final: 0.8131 (mmm) REVERT: K 118 MET cc_start: 0.8592 (mtt) cc_final: 0.8236 (mtt) REVERT: K 123 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7495 (mmpt) REVERT: K 138 GLN cc_start: 0.8102 (mt0) cc_final: 0.7770 (mt0) REVERT: L 18 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7979 (mtp85) REVERT: L 121 GLU cc_start: 0.7597 (tt0) cc_final: 0.7092 (tt0) REVERT: M 78 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7587 (mmt-90) REVERT: M 141 LYS cc_start: 0.6856 (tttt) cc_final: 0.6614 (ttmt) REVERT: M 143 GLU cc_start: 0.6647 (pm20) cc_final: 0.6232 (pm20) REVERT: N 104 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8207 (mt-10) REVERT: O 60 VAL cc_start: 0.8348 (t) cc_final: 0.8069 (p) REVERT: O 72 ASP cc_start: 0.8338 (t0) cc_final: 0.8041 (t0) REVERT: O 90 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7370 (ttm110) REVERT: O 114 GLU cc_start: 0.8736 (pt0) cc_final: 0.8400 (pt0) REVERT: O 118 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6869 (ttp80) REVERT: P 25 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6837 (ptt-90) REVERT: P 116 GLN cc_start: 0.7818 (tt0) cc_final: 0.6973 (tm-30) REVERT: Q 7 GLN cc_start: 0.7376 (tm-30) cc_final: 0.7010 (tp40) REVERT: Q 55 LEU cc_start: 0.9164 (tp) cc_final: 0.8714 (tp) REVERT: S 23 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8009 (mm-30) REVERT: S 60 LYS cc_start: 0.7578 (mttt) cc_final: 0.7021 (ttmt) REVERT: S 73 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7896 (ttpp) REVERT: S 78 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8486 (tpp-160) REVERT: S 85 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8131 (ttmm) REVERT: T 1 MET cc_start: 0.7709 (ttt) cc_final: 0.7131 (ptp) REVERT: T 22 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7067 (m-30) REVERT: U 33 LYS cc_start: 0.7494 (ttmt) cc_final: 0.7198 (tttm) REVERT: U 69 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7201 (mtp-110) REVERT: U 77 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7852 (mtt-85) REVERT: V 27 ASN cc_start: 0.8216 (p0) cc_final: 0.8004 (p0) REVERT: V 37 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7950 (tm-30) REVERT: V 39 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8650 (mp) REVERT: V 46 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7948 (mm-40) REVERT: V 62 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7173 (mt-10) REVERT: V 73 PHE cc_start: 0.7706 (t80) cc_final: 0.7334 (t80) REVERT: V 88 GLU cc_start: 0.7690 (tp30) cc_final: 0.7061 (pp20) REVERT: W 1 MET cc_start: 0.6604 (tpt) cc_final: 0.5683 (mpp) REVERT: W 24 ASN cc_start: 0.7632 (t0) cc_final: 0.7319 (t0) REVERT: W 25 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8070 (mtpt) REVERT: X 11 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6034 (mtp85) REVERT: X 35 SER cc_start: 0.9123 (m) cc_final: 0.8714 (m) REVERT: Y 11 ARG cc_start: 0.8623 (mmm160) cc_final: 0.8274 (mpt180) REVERT: Y 16 ASN cc_start: 0.9149 (m-40) cc_final: 0.8869 (m110) REVERT: Y 45 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6511 (ptt-90) REVERT: Z 19 LEU cc_start: 0.7335 (tp) cc_final: 0.7021 (tp) REVERT: Z 29 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7185 (ptp-170) REVERT: Z 39 GLN cc_start: 0.7702 (mt0) cc_final: 0.7263 (mt0) REVERT: 0 47 MET cc_start: 0.8447 (mtm) cc_final: 0.8108 (mtm) REVERT: 0 49 ASN cc_start: 0.8742 (t0) cc_final: 0.8402 (t0) REVERT: 1 8 LYS cc_start: 0.6742 (mmmt) cc_final: 0.5763 (tptt) REVERT: 1 22 MET cc_start: 0.5791 (ttm) cc_final: 0.5560 (mpp) REVERT: 2 10 ARG cc_start: 0.8900 (ptp90) cc_final: 0.8609 (ptp-170) REVERT: 3 28 ARG cc_start: 0.8233 (mpt-90) cc_final: 0.7431 (mmm-85) REVERT: 4 25 LYS cc_start: 0.7963 (tmmt) cc_final: 0.7377 (tttp) REVERT: 5 15 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8230 (mmmm) REVERT: 5 30 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.7567 (tpm170) REVERT: 5 61 CYS cc_start: 0.8768 (m) cc_final: 0.8304 (m) REVERT: 6 12 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8269 (ptm160) REVERT: b 23 TRP cc_start: 0.6463 (p-90) cc_final: 0.5944 (p-90) REVERT: b 27 MET cc_start: 0.7545 (mmm) cc_final: 0.7230 (mmm) REVERT: b 35 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.6396 (mtm-85) REVERT: b 49 MET cc_start: 0.6130 (mtp) cc_final: 0.5513 (ttm) REVERT: b 68 LEU cc_start: 0.6338 (tp) cc_final: 0.6061 (tp) REVERT: b 137 ARG cc_start: 0.4206 (OUTLIER) cc_final: 0.4003 (ttm-80) REVERT: b 154 MET cc_start: 0.6004 (mmm) cc_final: 0.5234 (mmm) REVERT: b 214 LEU cc_start: 0.6364 (mt) cc_final: 0.6019 (mt) REVERT: c 62 LYS cc_start: 0.5892 (mmtt) cc_final: 0.5461 (tmtt) REVERT: c 105 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.4167 (mp0) REVERT: c 121 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7526 (p) REVERT: c 135 LYS cc_start: 0.8485 (mttm) cc_final: 0.7901 (tptp) REVERT: d 54 GLN cc_start: 0.8853 (mt0) cc_final: 0.8366 (mt0) REVERT: d 58 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6518 (pttp) REVERT: d 60 LYS cc_start: 0.7357 (ttmt) cc_final: 0.6940 (tttt) REVERT: d 78 GLU cc_start: 0.7534 (tp30) cc_final: 0.7209 (pp20) REVERT: d 172 GLU cc_start: 0.4802 (mp0) cc_final: 0.4225 (mp0) REVERT: d 183 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8077 (tppt) REVERT: d 185 LYS cc_start: 0.8067 (ptmt) cc_final: 0.7189 (mtpp) REVERT: d 187 GLU cc_start: 0.6909 (tt0) cc_final: 0.6452 (mp0) REVERT: e 71 MET cc_start: 0.4260 (tpp) cc_final: 0.4050 (tpp) REVERT: g 4 ARG cc_start: 0.6041 (ttt90) cc_final: 0.4920 (tpp-160) REVERT: g 78 ARG cc_start: 0.5272 (tpp80) cc_final: 0.5020 (tpt-90) REVERT: j 9 ARG cc_start: 0.5992 (mtp-110) cc_final: 0.5290 (mtp180) REVERT: k 34 ILE cc_start: 0.8799 (mm) cc_final: 0.8430 (mp) REVERT: k 57 LYS cc_start: 0.8060 (pttt) cc_final: 0.7681 (pttm) REVERT: k 69 ARG cc_start: 0.6810 (ttm-80) cc_final: 0.6561 (ttm-80) REVERT: k 80 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7674 (mmtm) REVERT: k 119 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7192 (m110) REVERT: l 6 GLN cc_start: 0.7511 (mt0) cc_final: 0.7160 (mt0) REVERT: l 58 THR cc_start: 0.7973 (m) cc_final: 0.7721 (m) REVERT: l 78 SER cc_start: 0.7864 (t) cc_final: 0.7420 (m) REVERT: l 79 VAL cc_start: 0.8356 (t) cc_final: 0.8099 (p) REVERT: l 108 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7945 (mtmm) REVERT: l 120 LYS cc_start: 0.7724 (mmmt) cc_final: 0.6957 (mppt) REVERT: m 31 LYS cc_start: 0.7824 (mttt) cc_final: 0.7098 (mttt) REVERT: m 46 SER cc_start: 0.6150 (m) cc_final: 0.5826 (p) REVERT: m 93 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7072 (mpt-90) REVERT: m 101 ARG cc_start: 0.7084 (ptp-110) cc_final: 0.6523 (ptp-110) REVERT: n 16 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6282 (mt) REVERT: n 28 LYS cc_start: 0.6928 (mttt) cc_final: 0.6682 (mtpp) REVERT: o 24 SER cc_start: 0.7255 (t) cc_final: 0.6825 (p) REVERT: o 70 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7725 (tt) REVERT: o 74 ASP cc_start: 0.6796 (t0) cc_final: 0.5602 (m-30) REVERT: o 80 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7769 (pt0) REVERT: q 5 ILE cc_start: 0.6496 (pt) cc_final: 0.6195 (mp) REVERT: q 33 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8029 (tt) REVERT: q 50 ASN cc_start: 0.6455 (m110) cc_final: 0.6063 (t0) REVERT: r 52 GLN cc_start: 0.8047 (tp40) cc_final: 0.7551 (tp40) REVERT: s 21 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6754 (pptt) REVERT: s 44 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7789 (mpt) REVERT: s 66 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6256 (ptp) REVERT: t 15 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: t 40 GLU cc_start: 0.8585 (tp30) cc_final: 0.7949 (tm-30) REVERT: t 48 GLN cc_start: 0.7473 (mm-40) cc_final: 0.6989 (tp-100) REVERT: v 60 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.4913 (ttp-170) REVERT: v 85 GLU cc_start: 0.3253 (mt-10) cc_final: 0.2855 (pt0) REVERT: v 142 GLN cc_start: 0.7740 (mt0) cc_final: 0.7318 (mm-40) REVERT: v 147 MET cc_start: 0.7561 (ttp) cc_final: 0.7205 (ptm) REVERT: v 193 ARG cc_start: 0.7096 (ptt-90) cc_final: 0.6681 (ptt180) REVERT: v 200 ARG cc_start: 0.7400 (ttt90) cc_final: 0.7086 (ttm-80) REVERT: v 201 LEU cc_start: 0.8013 (tp) cc_final: 0.7502 (tp) REVERT: v 245 ARG cc_start: 0.6969 (mpt-90) cc_final: 0.6525 (mtt180) REVERT: v 255 ASN cc_start: 0.7009 (m-40) cc_final: 0.6598 (m110) REVERT: v 273 GLN cc_start: 0.8277 (mt0) cc_final: 0.7711 (tt0) REVERT: v 286 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6160 (mt0) REVERT: v 295 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7068 (mm) REVERT: v 300 MET cc_start: 0.7256 (mmm) cc_final: 0.6921 (mmm) REVERT: v 314 LYS cc_start: 0.6835 (mtpt) cc_final: 0.6405 (mmtt) REVERT: v 316 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6809 (m-30) outliers start: 345 outliers final: 235 residues processed: 1475 average time/residue: 1.4211 time to fit residues: 3557.3861 Evaluate side-chains 1492 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1215 time to evaluate : 6.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 57 ASN Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 82 MET Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 25 LYS Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 29 GLU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 30 LEU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 54 MET Chi-restraints excluded: chain 0 residue 58 GLU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 2 residue 36 GLU Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 23 ILE Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 137 ARG Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain r residue 45 THR Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 60 ARG Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 256 ARG Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 1009 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 596 optimal weight: 0.9980 chunk 764 optimal weight: 30.0000 chunk 592 optimal weight: 8.9990 chunk 881 optimal weight: 0.7980 chunk 584 optimal weight: 8.9990 chunk 1042 optimal weight: 6.9990 chunk 652 optimal weight: 20.0000 chunk 635 optimal weight: 4.9990 chunk 481 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN E 156 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 GLN ** 3 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 GLN c 41 GLN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN t 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 163943 Z= 0.211 Angle : 0.594 15.187 244682 Z= 0.320 Chirality : 0.034 0.554 31096 Planarity : 0.006 0.128 13510 Dihedral : 23.397 179.897 80677 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 5.81 % Allowed : 24.28 % Favored : 69.91 % 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: 6269 helix: 1.67 (0.11), residues: 2252 sheet: -0.77 (0.15), residues: 1172 loop : -0.94 (0.11), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 201 HIS 0.007 0.001 HIS r 74 PHE 0.019 0.002 PHE b 90 TYR 0.036 0.001 TYR b 213 ARG 0.008 0.000 ARG n 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1540 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1237 time to evaluate : 6.069 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: C 62 TYR cc_start: 0.8953 (t80) cc_final: 0.8737 (t80) REVERT: C 66 ASP cc_start: 0.8712 (t0) cc_final: 0.8214 (t0) REVERT: C 181 MET cc_start: 0.8127 (mmm) cc_final: 0.7829 (mmm) REVERT: C 242 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8155 (mmtm) REVERT: C 269 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7373 (ttt-90) REVERT: D 17 GLU cc_start: 0.8371 (tt0) cc_final: 0.7968 (mp0) REVERT: D 64 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7664 (mt-10) REVERT: D 94 GLN cc_start: 0.6881 (tt0) cc_final: 0.6162 (mt0) REVERT: D 106 LYS cc_start: 0.8486 (mttt) cc_final: 0.8077 (mttm) REVERT: D 114 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7629 (mtmm) REVERT: E 3 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6544 (mt) REVERT: E 18 THR cc_start: 0.7281 (m) cc_final: 0.6896 (p) REVERT: E 22 ASP cc_start: 0.8394 (m-30) cc_final: 0.7288 (p0) REVERT: E 57 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5661 (pttt) REVERT: E 194 LYS cc_start: 0.7821 (tptp) cc_final: 0.7281 (mttp) REVERT: F 3 LYS cc_start: 0.7085 (tttt) cc_final: 0.6687 (tptt) REVERT: F 69 LYS cc_start: 0.8725 (mtpt) cc_final: 0.7787 (ttpt) REVERT: F 83 TYR cc_start: 0.8035 (m-80) cc_final: 0.7766 (m-80) REVERT: F 105 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.6671 (p) REVERT: F 123 ASP cc_start: 0.4575 (OUTLIER) cc_final: 0.4361 (p0) REVERT: F 130 MET cc_start: 0.5920 (ptp) cc_final: 0.5387 (tpt) REVERT: G 86 LYS cc_start: 0.7898 (mttm) cc_final: 0.7071 (tttp) REVERT: G 101 ASN cc_start: 0.6758 (p0) cc_final: 0.6239 (p0) REVERT: G 155 GLU cc_start: 0.8568 (pm20) cc_final: 0.7944 (pm20) REVERT: H 28 ASN cc_start: 0.8506 (m-40) cc_final: 0.8063 (m-40) REVERT: H 66 ASN cc_start: 0.5647 (OUTLIER) cc_final: 0.4903 (m-40) REVERT: H 121 VAL cc_start: 0.6252 (OUTLIER) cc_final: 0.6025 (p) REVERT: H 127 GLU cc_start: 0.5372 (OUTLIER) cc_final: 0.5097 (mp0) REVERT: H 129 GLU cc_start: 0.4824 (OUTLIER) cc_final: 0.3931 (mm-30) REVERT: I 38 MET cc_start: 0.4691 (ttm) cc_final: 0.4394 (ptp) REVERT: I 52 MET cc_start: 0.1402 (mmm) cc_final: 0.0528 (mtt) REVERT: I 86 MET cc_start: 0.1405 (ttp) cc_final: 0.1075 (ttp) REVERT: K 14 ASP cc_start: 0.8273 (m-30) cc_final: 0.7757 (t0) REVERT: K 23 LYS cc_start: 0.8702 (mttt) cc_final: 0.7948 (mmmt) REVERT: K 92 MET cc_start: 0.8302 (mmm) cc_final: 0.8095 (mmm) REVERT: K 123 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7494 (mmpt) REVERT: K 138 GLN cc_start: 0.8077 (mt0) cc_final: 0.7758 (mt0) REVERT: K 141 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6354 (t70) REVERT: L 23 LYS cc_start: 0.8748 (tppt) cc_final: 0.8431 (tppt) REVERT: M 78 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7589 (mmt-90) REVERT: M 123 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6627 (ttm110) REVERT: M 141 LYS cc_start: 0.6862 (tttt) cc_final: 0.6621 (ttmt) REVERT: M 143 GLU cc_start: 0.6518 (pm20) cc_final: 0.6115 (pm20) REVERT: N 58 LYS cc_start: 0.7818 (mmmm) cc_final: 0.7464 (ptmt) REVERT: N 104 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8205 (mt-10) REVERT: O 60 VAL cc_start: 0.8421 (t) cc_final: 0.8123 (p) REVERT: O 72 ASP cc_start: 0.8376 (t0) cc_final: 0.8082 (t0) REVERT: O 114 GLU cc_start: 0.8771 (pt0) cc_final: 0.8365 (pt0) REVERT: O 118 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6726 (ttp-170) REVERT: P 25 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6835 (ptt-90) REVERT: P 116 GLN cc_start: 0.7682 (tt0) cc_final: 0.6838 (tm-30) REVERT: Q 7 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7097 (tp40) REVERT: Q 55 LEU cc_start: 0.9159 (tp) cc_final: 0.8733 (tp) REVERT: Q 89 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6797 (ptt90) REVERT: S 23 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7939 (mm-30) REVERT: S 60 LYS cc_start: 0.7538 (mttt) cc_final: 0.6977 (ttmt) REVERT: S 73 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7909 (ttpp) REVERT: S 78 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8430 (tpp-160) REVERT: S 85 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8104 (ttmm) REVERT: T 1 MET cc_start: 0.7700 (ttt) cc_final: 0.7128 (ptp) REVERT: T 82 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8503 (ptt) REVERT: U 33 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7210 (tttm) REVERT: U 69 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7255 (mtp-110) REVERT: U 77 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7822 (mtt-85) REVERT: V 26 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6767 (mmmt) REVERT: V 37 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7883 (tm-30) REVERT: V 39 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8672 (mp) REVERT: V 46 GLN cc_start: 0.8234 (mm-40) cc_final: 0.8007 (mm-40) REVERT: V 62 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7101 (mt-10) REVERT: V 73 PHE cc_start: 0.7702 (t80) cc_final: 0.7389 (t80) REVERT: W 1 MET cc_start: 0.6595 (tpt) cc_final: 0.5676 (mpp) REVERT: W 24 ASN cc_start: 0.7713 (t0) cc_final: 0.7327 (t0) REVERT: W 25 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8080 (mtpt) REVERT: X 11 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.5935 (mtp85) REVERT: X 35 SER cc_start: 0.9112 (m) cc_final: 0.8800 (m) REVERT: Y 11 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8255 (mpt180) REVERT: Y 16 ASN cc_start: 0.9210 (m-40) cc_final: 0.8882 (m110) REVERT: Y 45 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6553 (ptt-90) REVERT: Z 19 LEU cc_start: 0.7294 (tp) cc_final: 0.6978 (tp) REVERT: Z 29 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7181 (ptp-170) REVERT: Z 39 GLN cc_start: 0.7709 (mt0) cc_final: 0.7254 (mt0) REVERT: 0 47 MET cc_start: 0.8416 (mtm) cc_final: 0.8084 (mtm) REVERT: 0 49 ASN cc_start: 0.8720 (t0) cc_final: 0.8382 (t0) REVERT: 2 10 ARG cc_start: 0.8851 (ptp90) cc_final: 0.8538 (ptp-170) REVERT: 3 28 ARG cc_start: 0.8219 (mpt-90) cc_final: 0.7451 (mmm-85) REVERT: 4 25 LYS cc_start: 0.8114 (tmmt) cc_final: 0.7349 (tttp) REVERT: 5 15 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8226 (mmmm) REVERT: 5 30 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7420 (tpm170) REVERT: 5 61 CYS cc_start: 0.8783 (m) cc_final: 0.8312 (m) REVERT: 6 12 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8270 (ptm160) REVERT: b 23 TRP cc_start: 0.6419 (p-90) cc_final: 0.5934 (p-90) REVERT: b 27 MET cc_start: 0.7523 (mmm) cc_final: 0.7212 (mmm) REVERT: b 35 ARG cc_start: 0.6826 (mmt-90) cc_final: 0.6396 (mtm-85) REVERT: b 49 MET cc_start: 0.5936 (mtp) cc_final: 0.5342 (ttm) REVERT: b 154 MET cc_start: 0.5728 (mmm) cc_final: 0.5275 (mmm) REVERT: b 214 LEU cc_start: 0.6471 (mt) cc_final: 0.6102 (mt) REVERT: c 62 LYS cc_start: 0.5905 (mmtt) cc_final: 0.5500 (tmtt) REVERT: c 105 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.4166 (mp0) REVERT: c 135 LYS cc_start: 0.8474 (mttm) cc_final: 0.7816 (tptp) REVERT: c 156 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5557 (mmm-85) REVERT: d 54 GLN cc_start: 0.8804 (mt0) cc_final: 0.8338 (mt0) REVERT: d 60 LYS cc_start: 0.7270 (ttmt) cc_final: 0.6808 (tttt) REVERT: d 62 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7411 (ptp-110) REVERT: d 78 GLU cc_start: 0.7496 (tp30) cc_final: 0.7196 (pp20) REVERT: d 183 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8091 (tppt) REVERT: d 185 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7195 (mtpp) REVERT: d 187 GLU cc_start: 0.6944 (tt0) cc_final: 0.6369 (mp0) REVERT: e 71 MET cc_start: 0.4152 (tpp) cc_final: 0.3919 (tpp) REVERT: e 105 ILE cc_start: 0.8315 (mp) cc_final: 0.8019 (mm) REVERT: g 4 ARG cc_start: 0.6052 (ttt90) cc_final: 0.4901 (tpp-160) REVERT: g 35 LYS cc_start: 0.7468 (ttmt) cc_final: 0.7260 (mtpt) REVERT: g 78 ARG cc_start: 0.5265 (tpp80) cc_final: 0.5003 (tpt-90) REVERT: k 34 ILE cc_start: 0.8726 (mm) cc_final: 0.8323 (mp) REVERT: k 57 LYS cc_start: 0.8028 (pttt) cc_final: 0.7641 (pttm) REVERT: k 119 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7160 (m110) REVERT: l 6 GLN cc_start: 0.7510 (mt0) cc_final: 0.7151 (mt0) REVERT: l 78 SER cc_start: 0.7793 (t) cc_final: 0.7339 (m) REVERT: l 79 VAL cc_start: 0.8398 (t) cc_final: 0.8136 (p) REVERT: l 108 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8060 (mtmm) REVERT: l 120 LYS cc_start: 0.7726 (mmmt) cc_final: 0.6957 (mppt) REVERT: m 31 LYS cc_start: 0.7772 (mttt) cc_final: 0.7098 (mtmt) REVERT: m 46 SER cc_start: 0.5969 (m) cc_final: 0.5613 (p) REVERT: m 93 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7091 (mpt-90) REVERT: m 101 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6412 (ptp-110) REVERT: n 16 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6545 (mt) REVERT: o 10 LYS cc_start: 0.7575 (tppt) cc_final: 0.7291 (mttt) REVERT: o 11 ILE cc_start: 0.5989 (mm) cc_final: 0.5664 (mp) REVERT: o 24 SER cc_start: 0.7399 (t) cc_final: 0.6959 (p) REVERT: o 74 ASP cc_start: 0.6922 (t0) cc_final: 0.6034 (m-30) REVERT: o 89 ARG cc_start: 0.6626 (ptm160) cc_final: 0.6382 (ttt180) REVERT: q 5 ILE cc_start: 0.6499 (pt) cc_final: 0.6189 (mp) REVERT: q 59 VAL cc_start: 0.5986 (p) cc_final: 0.5781 (t) REVERT: r 52 GLN cc_start: 0.8031 (tp40) cc_final: 0.7527 (tp40) REVERT: s 21 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6747 (pptt) REVERT: s 44 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7790 (mpt) REVERT: s 66 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6250 (ptp) REVERT: t 15 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: t 40 GLU cc_start: 0.8457 (tp30) cc_final: 0.7919 (tm-30) REVERT: t 48 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7087 (tp-100) REVERT: v 60 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4776 (ttp-170) REVERT: v 85 GLU cc_start: 0.3215 (mt-10) cc_final: 0.2789 (pt0) REVERT: v 142 GLN cc_start: 0.7727 (mt0) cc_final: 0.7194 (mm-40) REVERT: v 147 MET cc_start: 0.7563 (ttp) cc_final: 0.7193 (ptm) REVERT: v 193 ARG cc_start: 0.7147 (ptt-90) cc_final: 0.6756 (ptt180) REVERT: v 200 ARG cc_start: 0.7340 (ttt90) cc_final: 0.7052 (ttm-80) REVERT: v 201 LEU cc_start: 0.8066 (tp) cc_final: 0.7627 (tp) REVERT: v 245 ARG cc_start: 0.7126 (mpt-90) cc_final: 0.6710 (mpt-90) REVERT: v 255 ASN cc_start: 0.6977 (m-40) cc_final: 0.6599 (m110) REVERT: v 273 GLN cc_start: 0.8261 (mt0) cc_final: 0.7714 (tt0) REVERT: v 278 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7669 (mtt-85) REVERT: v 286 GLN cc_start: 0.7214 (tp-100) cc_final: 0.6238 (mt0) REVERT: v 295 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7055 (mm) REVERT: v 300 MET cc_start: 0.7202 (mmm) cc_final: 0.6848 (mmm) REVERT: v 314 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6349 (mmtt) REVERT: v 316 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6800 (m-30) outliers start: 303 outliers final: 226 residues processed: 1423 average time/residue: 1.5132 time to fit residues: 3672.8323 Evaluate side-chains 1483 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1218 time to evaluate : 6.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 89 ARG Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain T residue 61 ASN Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 82 MET Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 25 LYS Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 29 GLU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 30 LEU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 54 MET Chi-restraints excluded: chain 0 residue 58 GLU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 36 GLU Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 23 ILE Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 139 GLN Chi-restraints excluded: chain c residue 156 ARG Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain o residue 18 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 45 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 60 ARG Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 256 ARG Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 645 optimal weight: 10.0000 chunk 416 optimal weight: 8.9990 chunk 622 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 663 optimal weight: 40.0000 chunk 710 optimal weight: 10.0000 chunk 515 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 819 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS O 9 GLN P 98 GLN R 44 GLN V 53 ASN ** 1 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 GLN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN h 76 GLN k 101 ASN t 13 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 163943 Z= 0.515 Angle : 0.800 15.012 244682 Z= 0.411 Chirality : 0.045 0.553 31096 Planarity : 0.007 0.140 13510 Dihedral : 23.457 178.170 80671 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 6.82 % Allowed : 23.71 % Favored : 69.47 % 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: -0.54 (0.10), residues: 6269 helix: 1.06 (0.11), residues: 2270 sheet: -0.98 (0.15), residues: 1170 loop : -1.22 (0.11), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP U 80 HIS 0.009 0.002 HIS r 74 PHE 0.026 0.003 PHE E 183 TYR 0.032 0.003 TYR v 189 ARG 0.011 0.001 ARG G 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1579 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 1223 time to evaluate : 6.833 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: C 66 ASP cc_start: 0.8689 (t0) cc_final: 0.8199 (t0) REVERT: C 163 GLN cc_start: 0.8253 (mt0) cc_final: 0.8042 (mt0) REVERT: C 181 MET cc_start: 0.8214 (mmm) cc_final: 0.7958 (mmm) REVERT: C 192 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8435 (mt) REVERT: C 242 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8258 (mmtm) REVERT: C 269 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7271 (ttt-90) REVERT: D 17 GLU cc_start: 0.8435 (tt0) cc_final: 0.7982 (mp0) REVERT: D 18 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7119 (t70) REVERT: D 64 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 94 GLN cc_start: 0.7098 (tt0) cc_final: 0.6361 (mt0) REVERT: D 106 LYS cc_start: 0.8578 (mttt) cc_final: 0.8164 (mttm) REVERT: D 114 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8524 (mtmm) REVERT: E 18 THR cc_start: 0.7221 (m) cc_final: 0.6846 (p) REVERT: E 22 ASP cc_start: 0.8425 (m-30) cc_final: 0.7280 (p0) REVERT: E 57 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5663 (pttt) REVERT: E 176 ASP cc_start: 0.8011 (p0) cc_final: 0.7493 (p0) REVERT: E 194 LYS cc_start: 0.7821 (tptp) cc_final: 0.7287 (mttp) REVERT: F 83 TYR cc_start: 0.7913 (m-80) cc_final: 0.7589 (m-80) REVERT: F 105 THR cc_start: 0.7238 (OUTLIER) cc_final: 0.6780 (p) REVERT: F 123 ASP cc_start: 0.4899 (OUTLIER) cc_final: 0.4449 (p0) REVERT: F 130 MET cc_start: 0.6053 (ptp) cc_final: 0.5502 (tpt) REVERT: G 101 ASN cc_start: 0.6709 (p0) cc_final: 0.6183 (p0) REVERT: H 33 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: H 66 ASN cc_start: 0.5520 (OUTLIER) cc_final: 0.4560 (m-40) REVERT: H 121 VAL cc_start: 0.6212 (OUTLIER) cc_final: 0.5992 (p) REVERT: H 127 GLU cc_start: 0.5436 (OUTLIER) cc_final: 0.5203 (mp0) REVERT: H 129 GLU cc_start: 0.4672 (OUTLIER) cc_final: 0.3694 (mm-30) REVERT: H 138 VAL cc_start: 0.6196 (t) cc_final: 0.5850 (m) REVERT: K 14 ASP cc_start: 0.8398 (m-30) cc_final: 0.7724 (t0) REVERT: K 23 LYS cc_start: 0.8655 (mttt) cc_final: 0.7805 (mmmt) REVERT: K 92 MET cc_start: 0.8280 (mmm) cc_final: 0.8034 (mmm) REVERT: K 118 MET cc_start: 0.8660 (mtt) cc_final: 0.8327 (mtt) REVERT: K 123 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7796 (mmpt) REVERT: K 131 ASN cc_start: 0.8337 (m110) cc_final: 0.7915 (m110) REVERT: K 138 GLN cc_start: 0.8202 (mt0) cc_final: 0.7714 (mt0) REVERT: K 141 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6186 (t70) REVERT: L 18 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8129 (mtp85) REVERT: L 121 GLU cc_start: 0.7584 (tt0) cc_final: 0.7012 (tt0) REVERT: M 78 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7806 (mmt-90) REVERT: M 123 ARG cc_start: 0.6933 (ttm-80) cc_final: 0.6616 (ttm110) REVERT: M 141 LYS cc_start: 0.6836 (tttt) cc_final: 0.6568 (ttmt) REVERT: M 143 GLU cc_start: 0.6618 (pm20) cc_final: 0.5971 (pm20) REVERT: N 18 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8367 (ptm-80) REVERT: N 60 GLN cc_start: 0.7642 (tp40) cc_final: 0.6764 (tt0) REVERT: N 104 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8268 (mt-10) REVERT: O 60 VAL cc_start: 0.8426 (t) cc_final: 0.8141 (p) REVERT: O 72 ASP cc_start: 0.8400 (t0) cc_final: 0.8109 (t0) REVERT: O 90 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7400 (ttm110) REVERT: O 100 CYS cc_start: 0.8503 (p) cc_final: 0.8298 (p) REVERT: O 114 GLU cc_start: 0.8849 (pt0) cc_final: 0.8644 (pt0) REVERT: O 118 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6549 (ttp80) REVERT: P 25 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6972 (ptt-90) REVERT: P 116 GLN cc_start: 0.7579 (tt0) cc_final: 0.6827 (tm-30) REVERT: Q 7 GLN cc_start: 0.7626 (tm-30) cc_final: 0.6997 (tm-30) REVERT: Q 24 ASP cc_start: 0.8135 (m-30) cc_final: 0.7857 (m-30) REVERT: Q 55 LEU cc_start: 0.9150 (tp) cc_final: 0.8799 (tp) REVERT: Q 57 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8518 (p) REVERT: Q 89 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6825 (ptt90) REVERT: R 81 ASN cc_start: 0.8062 (t0) cc_final: 0.7791 (t0) REVERT: S 23 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8081 (mm-30) REVERT: S 60 LYS cc_start: 0.7607 (mttt) cc_final: 0.7041 (ttmt) REVERT: S 73 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7808 (ttpp) REVERT: S 78 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8422 (tpp-160) REVERT: S 98 ILE cc_start: 0.8730 (mm) cc_final: 0.8516 (mp) REVERT: T 1 MET cc_start: 0.7780 (ttt) cc_final: 0.7107 (ptp) REVERT: T 55 ILE cc_start: 0.8900 (mt) cc_final: 0.8688 (mt) REVERT: U 1 MET cc_start: 0.6482 (ptm) cc_final: 0.6078 (ptt) REVERT: U 33 LYS cc_start: 0.7388 (ttmt) cc_final: 0.7082 (tttm) REVERT: U 69 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7233 (mtm110) REVERT: U 77 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7825 (mtt-85) REVERT: V 37 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8012 (tm-30) REVERT: V 39 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8698 (mp) REVERT: V 46 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7908 (mm-40) REVERT: V 62 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: V 73 PHE cc_start: 0.7780 (t80) cc_final: 0.7482 (t80) REVERT: W 1 MET cc_start: 0.6201 (tpt) cc_final: 0.5580 (mpp) REVERT: W 24 ASN cc_start: 0.7654 (t0) cc_final: 0.7322 (t0) REVERT: W 25 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: W 60 VAL cc_start: 0.8447 (t) cc_final: 0.8234 (t) REVERT: X 35 SER cc_start: 0.9123 (m) cc_final: 0.8714 (m) REVERT: Y 11 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8335 (mpt180) REVERT: Y 37 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7912 (mtm110) REVERT: Y 45 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6469 (ptt-90) REVERT: Z 19 LEU cc_start: 0.7378 (tp) cc_final: 0.7143 (tp) REVERT: Z 29 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.6959 (ptp-170) REVERT: Z 39 GLN cc_start: 0.7653 (mt0) cc_final: 0.7211 (mt0) REVERT: 0 47 MET cc_start: 0.8524 (mtm) cc_final: 0.8186 (mtm) REVERT: 0 49 ASN cc_start: 0.8922 (t0) cc_final: 0.8609 (t0) REVERT: 1 8 LYS cc_start: 0.6774 (mmmt) cc_final: 0.5807 (tptt) REVERT: 2 10 ARG cc_start: 0.8887 (ptp90) cc_final: 0.8579 (ptp-170) REVERT: 2 31 ASP cc_start: 0.7721 (t70) cc_final: 0.7475 (t70) REVERT: 3 28 ARG cc_start: 0.8244 (mpt-90) cc_final: 0.7423 (mmm-85) REVERT: 4 25 LYS cc_start: 0.8102 (tmmt) cc_final: 0.7519 (tttp) REVERT: 5 15 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8182 (mmmm) REVERT: 5 61 CYS cc_start: 0.8890 (m) cc_final: 0.8335 (m) REVERT: 6 12 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8274 (ptm160) REVERT: b 23 TRP cc_start: 0.6243 (p-90) cc_final: 0.5733 (p-90) REVERT: b 35 ARG cc_start: 0.6806 (mmt-90) cc_final: 0.6309 (mtm-85) REVERT: b 154 MET cc_start: 0.5852 (mmm) cc_final: 0.5269 (mmm) REVERT: b 214 LEU cc_start: 0.6383 (mt) cc_final: 0.6056 (mt) REVERT: c 62 LYS cc_start: 0.6027 (mmtt) cc_final: 0.5759 (tmtt) REVERT: c 105 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4237 (mp0) REVERT: c 135 LYS cc_start: 0.8580 (mttm) cc_final: 0.8076 (tttt) REVERT: c 156 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5072 (mtt180) REVERT: d 54 GLN cc_start: 0.8812 (mt0) cc_final: 0.8391 (mt0) REVERT: d 58 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6806 (pttp) REVERT: d 60 LYS cc_start: 0.7293 (ttmt) cc_final: 0.6972 (tttt) REVERT: d 62 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: d 167 LYS cc_start: 0.5181 (mttt) cc_final: 0.4720 (pptt) REVERT: d 172 GLU cc_start: 0.4988 (mp0) cc_final: 0.4451 (mp0) REVERT: d 183 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8092 (tptt) REVERT: d 185 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7305 (mtpt) REVERT: d 187 GLU cc_start: 0.6765 (tt0) cc_final: 0.6192 (mp0) REVERT: e 29 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6885 (mtt90) REVERT: e 73 ASN cc_start: 0.6570 (m110) cc_final: 0.6005 (t0) REVERT: g 4 ARG cc_start: 0.6023 (ttt90) cc_final: 0.4869 (tpp-160) REVERT: i 46 MET cc_start: 0.7106 (mtm) cc_final: 0.6872 (mtm) REVERT: i 57 MET cc_start: 0.5936 (mmm) cc_final: 0.5729 (mtm) REVERT: k 34 ILE cc_start: 0.8823 (mm) cc_final: 0.8470 (mp) REVERT: k 57 LYS cc_start: 0.8211 (pttt) cc_final: 0.7786 (pttm) REVERT: k 85 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7184 (mmt) REVERT: k 119 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7070 (m110) REVERT: l 6 GLN cc_start: 0.7611 (mt0) cc_final: 0.7229 (mt0) REVERT: l 78 SER cc_start: 0.7757 (t) cc_final: 0.7319 (m) REVERT: l 79 VAL cc_start: 0.8378 (t) cc_final: 0.8113 (p) REVERT: l 108 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8121 (mtmm) REVERT: l 120 LYS cc_start: 0.7723 (mmmt) cc_final: 0.6939 (mppt) REVERT: m 31 LYS cc_start: 0.7637 (mttt) cc_final: 0.7395 (mmmm) REVERT: m 93 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7102 (mpt-90) REVERT: m 101 ARG cc_start: 0.6920 (ptp-110) cc_final: 0.6511 (ptp-110) REVERT: n 16 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6304 (mt) REVERT: n 23 LYS cc_start: 0.6895 (tttt) cc_final: 0.6562 (tppt) REVERT: o 74 ASP cc_start: 0.7155 (t0) cc_final: 0.6093 (m-30) REVERT: o 80 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7777 (pt0) REVERT: o 89 ARG cc_start: 0.6607 (ptm160) cc_final: 0.5605 (ptp-170) REVERT: p 53 ASP cc_start: 0.7019 (t0) cc_final: 0.6761 (p0) REVERT: q 5 ILE cc_start: 0.6576 (pt) cc_final: 0.6256 (mp) REVERT: q 50 ASN cc_start: 0.6627 (m110) cc_final: 0.6131 (t0) REVERT: q 68 SER cc_start: 0.8186 (t) cc_final: 0.7839 (t) REVERT: r 52 GLN cc_start: 0.8000 (tp40) cc_final: 0.7491 (tp40) REVERT: s 21 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6782 (pptt) REVERT: s 66 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6613 (ptp) REVERT: s 71 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7721 (mp) REVERT: t 15 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: t 40 GLU cc_start: 0.8634 (tp30) cc_final: 0.7966 (tm-30) REVERT: t 48 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6876 (tp-100) REVERT: v 60 ARG cc_start: 0.5293 (OUTLIER) cc_final: 0.4739 (ttp-170) REVERT: v 85 GLU cc_start: 0.3238 (mt-10) cc_final: 0.2793 (pt0) REVERT: v 142 GLN cc_start: 0.7860 (mt0) cc_final: 0.7442 (mm-40) REVERT: v 193 ARG cc_start: 0.6944 (ptt-90) cc_final: 0.6458 (ptt180) REVERT: v 201 LEU cc_start: 0.8171 (tp) cc_final: 0.7914 (tp) REVERT: v 245 ARG cc_start: 0.7160 (mpt-90) cc_final: 0.6727 (mpt-90) REVERT: v 255 ASN cc_start: 0.6794 (m-40) cc_final: 0.6438 (m110) REVERT: v 257 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8017 (p) REVERT: v 273 GLN cc_start: 0.8283 (mt0) cc_final: 0.7719 (tt0) REVERT: v 295 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7111 (mm) REVERT: v 314 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6628 (mmtt) REVERT: v 316 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6824 (m-30) outliers start: 356 outliers final: 265 residues processed: 1435 average time/residue: 1.3771 time to fit residues: 3347.8470 Evaluate side-chains 1522 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1209 time to evaluate : 5.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 89 ARG Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 61 ASN Chi-restraints excluded: chain T residue 70 LYS Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 86 MET Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 62 GLU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 25 LYS Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 29 GLU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 30 LEU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 54 MET Chi-restraints excluded: chain 0 residue 58 GLU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 36 GLU Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 23 ILE Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 139 GLN Chi-restraints excluded: chain c residue 156 ARG Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 57 GLU Chi-restraints excluded: chain d residue 58 LYS Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 29 ARG Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 85 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 106 THR Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 85 MET Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain o residue 18 ASP Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain r residue 45 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 60 ARG Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 257 THR Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 325 SER Chi-restraints excluded: chain v residue 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 948 optimal weight: 0.9990 chunk 999 optimal weight: 10.0000 chunk 911 optimal weight: 20.0000 chunk 971 optimal weight: 9.9990 chunk 998 optimal weight: 7.9990 chunk 584 optimal weight: 1.9990 chunk 423 optimal weight: 0.6980 chunk 763 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 chunk 878 optimal weight: 9.9990 chunk 919 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN R 44 GLN W 49 ASN W 78 GLN ** 1 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 GLN c 41 GLN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN k 101 ASN t 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 163943 Z= 0.244 Angle : 0.633 14.784 244682 Z= 0.338 Chirality : 0.036 0.565 31096 Planarity : 0.006 0.130 13510 Dihedral : 23.470 179.500 80666 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 5.69 % Allowed : 25.35 % Favored : 68.95 % 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: -0.27 (0.10), residues: 6269 helix: 1.33 (0.11), residues: 2259 sheet: -0.87 (0.15), residues: 1168 loop : -1.09 (0.11), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 201 HIS 0.009 0.001 HIS r 74 PHE 0.017 0.002 PHE H 91 TYR 0.040 0.002 TYR b 213 ARG 0.009 0.000 ARG n 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1230 time to evaluate : 6.827 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: C 66 ASP cc_start: 0.8637 (t0) cc_final: 0.8149 (t0) REVERT: C 95 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7795 (tp) REVERT: C 181 MET cc_start: 0.8185 (mmm) cc_final: 0.7916 (mmm) REVERT: C 242 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8174 (mmtm) REVERT: C 269 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7324 (ttt-90) REVERT: D 17 GLU cc_start: 0.8430 (tt0) cc_final: 0.8015 (mp0) REVERT: D 64 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7796 (mt-10) REVERT: D 94 GLN cc_start: 0.7049 (tt0) cc_final: 0.6330 (mt0) REVERT: D 106 LYS cc_start: 0.8544 (mttt) cc_final: 0.8135 (mttm) REVERT: E 18 THR cc_start: 0.7209 (m) cc_final: 0.6817 (p) REVERT: E 22 ASP cc_start: 0.8508 (m-30) cc_final: 0.7341 (p0) REVERT: E 57 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5737 (pttt) REVERT: E 194 LYS cc_start: 0.7828 (tptp) cc_final: 0.7284 (mttp) REVERT: F 3 LYS cc_start: 0.7088 (tttt) cc_final: 0.6754 (tptt) REVERT: F 63 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7019 (mt0) REVERT: F 69 LYS cc_start: 0.8723 (mtpt) cc_final: 0.7743 (ttpt) REVERT: F 83 TYR cc_start: 0.7947 (m-80) cc_final: 0.7656 (m-80) REVERT: F 105 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6638 (p) REVERT: F 130 MET cc_start: 0.6031 (ptp) cc_final: 0.5507 (tpt) REVERT: G 64 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7500 (mm-40) REVERT: G 86 LYS cc_start: 0.7904 (mttm) cc_final: 0.7050 (tmtp) REVERT: G 95 ARG cc_start: 0.6837 (mtm110) cc_final: 0.6531 (ttp80) REVERT: G 101 ASN cc_start: 0.6705 (p0) cc_final: 0.6176 (p0) REVERT: G 155 GLU cc_start: 0.8636 (pm20) cc_final: 0.8036 (pm20) REVERT: H 66 ASN cc_start: 0.5611 (OUTLIER) cc_final: 0.4738 (m-40) REVERT: H 121 VAL cc_start: 0.6241 (OUTLIER) cc_final: 0.6015 (p) REVERT: H 127 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.5202 (mp0) REVERT: H 129 GLU cc_start: 0.4699 (OUTLIER) cc_final: 0.3772 (mm-30) REVERT: H 138 VAL cc_start: 0.6405 (t) cc_final: 0.6073 (m) REVERT: I 52 MET cc_start: 0.2015 (mmm) cc_final: 0.1384 (mtt) REVERT: I 86 MET cc_start: 0.2001 (tmm) cc_final: 0.1266 (tmm) REVERT: K 14 ASP cc_start: 0.8382 (m-30) cc_final: 0.7825 (t0) REVERT: K 23 LYS cc_start: 0.8490 (mttt) cc_final: 0.7881 (mmmt) REVERT: K 123 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7565 (mmpt) REVERT: K 131 ASN cc_start: 0.8232 (m110) cc_final: 0.7784 (m-40) REVERT: K 138 GLN cc_start: 0.8176 (mt0) cc_final: 0.7789 (mt0) REVERT: K 141 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6333 (t70) REVERT: L 18 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8069 (mtp85) REVERT: L 121 GLU cc_start: 0.7551 (tt0) cc_final: 0.6993 (tt0) REVERT: M 78 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7630 (mmt-90) REVERT: M 141 LYS cc_start: 0.6826 (tttt) cc_final: 0.6589 (ttmt) REVERT: N 18 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8382 (ptm-80) REVERT: N 104 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8179 (mt-10) REVERT: O 60 VAL cc_start: 0.8367 (t) cc_final: 0.8088 (p) REVERT: O 72 ASP cc_start: 0.8415 (t0) cc_final: 0.8152 (t0) REVERT: O 90 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7289 (ttm110) REVERT: O 114 GLU cc_start: 0.8803 (pt0) cc_final: 0.8486 (pt0) REVERT: O 118 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6907 (ttp80) REVERT: P 25 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6753 (ptt-90) REVERT: P 116 GLN cc_start: 0.7583 (tt0) cc_final: 0.6835 (tm-30) REVERT: Q 7 GLN cc_start: 0.7537 (tm-30) cc_final: 0.6951 (tm-30) REVERT: Q 24 ASP cc_start: 0.8053 (m-30) cc_final: 0.7747 (m-30) REVERT: Q 34 GLU cc_start: 0.5312 (pm20) cc_final: 0.4722 (pm20) REVERT: Q 55 LEU cc_start: 0.9197 (tp) cc_final: 0.8775 (tp) REVERT: Q 89 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6754 (ptt90) REVERT: R 117 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7155 (mp) REVERT: S 23 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8027 (mm-30) REVERT: S 60 LYS cc_start: 0.7588 (mttt) cc_final: 0.7027 (ttmt) REVERT: S 73 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7888 (ttpp) REVERT: S 78 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8400 (tpp-160) REVERT: S 85 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8090 (ttmm) REVERT: S 98 ILE cc_start: 0.8684 (mm) cc_final: 0.8443 (mp) REVERT: T 1 MET cc_start: 0.7808 (ttt) cc_final: 0.7146 (ptp) REVERT: U 1 MET cc_start: 0.6072 (ptm) cc_final: 0.5757 (ptt) REVERT: U 33 LYS cc_start: 0.7500 (ttmt) cc_final: 0.7198 (tttm) REVERT: U 69 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7327 (mtp-110) REVERT: U 77 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7822 (mtt-85) REVERT: V 26 LYS cc_start: 0.7282 (mmtt) cc_final: 0.6893 (mmmt) REVERT: V 37 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7727 (tm-30) REVERT: V 39 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8697 (mp) REVERT: V 46 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7982 (mm-40) REVERT: V 62 GLU cc_start: 0.7887 (mt-10) cc_final: 0.6953 (mt-10) REVERT: V 73 PHE cc_start: 0.7754 (t80) cc_final: 0.7500 (t80) REVERT: V 88 GLU cc_start: 0.7683 (tp30) cc_final: 0.7195 (pp20) REVERT: W 1 MET cc_start: 0.6260 (tpt) cc_final: 0.5692 (mpp) REVERT: W 24 ASN cc_start: 0.7672 (t0) cc_final: 0.7353 (t0) REVERT: W 25 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8104 (mtpt) REVERT: X 11 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6014 (mtp85) REVERT: X 35 SER cc_start: 0.9120 (m) cc_final: 0.8720 (m) REVERT: Y 11 ARG cc_start: 0.8627 (mmm160) cc_final: 0.8284 (mpt180) REVERT: Y 16 ASN cc_start: 0.9160 (m-40) cc_final: 0.8941 (m110) REVERT: Y 37 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7826 (mtm110) REVERT: Y 45 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6555 (ptt-90) REVERT: Z 19 LEU cc_start: 0.7308 (tp) cc_final: 0.7072 (tp) REVERT: Z 39 GLN cc_start: 0.7683 (mt0) cc_final: 0.7232 (mt0) REVERT: 0 47 MET cc_start: 0.8456 (mtm) cc_final: 0.8112 (mtm) REVERT: 0 49 ASN cc_start: 0.8809 (t0) cc_final: 0.8477 (t0) REVERT: 1 8 LYS cc_start: 0.6760 (mmmt) cc_final: 0.5772 (tptt) REVERT: 2 10 ARG cc_start: 0.8847 (ptp90) cc_final: 0.8532 (ptp-170) REVERT: 2 31 ASP cc_start: 0.7449 (t70) cc_final: 0.7139 (t70) REVERT: 3 28 ARG cc_start: 0.8230 (mpt-90) cc_final: 0.7456 (mmm-85) REVERT: 4 25 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7375 (tttp) REVERT: 5 15 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8214 (mmmm) REVERT: 5 30 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7610 (tpm170) REVERT: 5 61 CYS cc_start: 0.8816 (m) cc_final: 0.8329 (m) REVERT: 6 12 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8327 (ptm160) REVERT: b 23 TRP cc_start: 0.6353 (p-90) cc_final: 0.5794 (p-90) REVERT: b 35 ARG cc_start: 0.6858 (mmt-90) cc_final: 0.6417 (mtm-85) REVERT: b 49 MET cc_start: 0.6038 (mtp) cc_final: 0.5351 (ttm) REVERT: b 145 GLU cc_start: 0.7064 (tp30) cc_final: 0.6400 (mt-10) REVERT: b 154 MET cc_start: 0.5814 (mmm) cc_final: 0.5421 (mmm) REVERT: b 214 LEU cc_start: 0.6334 (mt) cc_final: 0.6032 (mt) REVERT: c 62 LYS cc_start: 0.6072 (mmtt) cc_final: 0.5808 (tmtt) REVERT: c 105 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4098 (mp0) REVERT: c 135 LYS cc_start: 0.8526 (mttm) cc_final: 0.8016 (tttt) REVERT: c 156 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5499 (mmm-85) REVERT: d 54 GLN cc_start: 0.8769 (mt0) cc_final: 0.8283 (mt0) REVERT: d 60 LYS cc_start: 0.7279 (ttmt) cc_final: 0.6840 (tttt) REVERT: d 62 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7381 (ptp-170) REVERT: d 78 GLU cc_start: 0.7581 (tp30) cc_final: 0.7198 (pp20) REVERT: d 167 LYS cc_start: 0.5164 (mttt) cc_final: 0.4711 (pptt) REVERT: d 183 LYS cc_start: 0.8555 (ttmt) cc_final: 0.7979 (tptt) REVERT: d 185 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7386 (mtpp) REVERT: d 187 GLU cc_start: 0.6849 (tt0) cc_final: 0.6252 (mp0) REVERT: e 105 ILE cc_start: 0.8353 (mp) cc_final: 0.8095 (mm) REVERT: f 17 GLN cc_start: 0.7773 (mp10) cc_final: 0.7454 (mp10) REVERT: h 69 LYS cc_start: 0.7445 (mptt) cc_final: 0.7186 (pttp) REVERT: h 101 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7822 (tp) REVERT: k 34 ILE cc_start: 0.8785 (mm) cc_final: 0.8389 (mp) REVERT: k 57 LYS cc_start: 0.8185 (pttt) cc_final: 0.7788 (pttm) REVERT: k 119 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7133 (m110) REVERT: l 6 GLN cc_start: 0.7599 (mt0) cc_final: 0.7229 (mt0) REVERT: l 78 SER cc_start: 0.7768 (t) cc_final: 0.7331 (m) REVERT: l 79 VAL cc_start: 0.8389 (t) cc_final: 0.8127 (p) REVERT: l 108 LYS cc_start: 0.8347 (mmmt) cc_final: 0.8075 (mtmm) REVERT: l 120 LYS cc_start: 0.7732 (mmmt) cc_final: 0.6944 (mppt) REVERT: m 31 LYS cc_start: 0.7644 (mttt) cc_final: 0.7396 (mmmm) REVERT: m 46 SER cc_start: 0.5964 (OUTLIER) cc_final: 0.5602 (p) REVERT: m 93 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7154 (mpt-90) REVERT: m 101 ARG cc_start: 0.6935 (ptp-110) cc_final: 0.6473 (ptp-110) REVERT: n 16 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6449 (mt) REVERT: n 23 LYS cc_start: 0.6897 (tttt) cc_final: 0.6574 (tppt) REVERT: o 74 ASP cc_start: 0.7004 (t0) cc_final: 0.6044 (m-30) REVERT: o 80 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7775 (pt0) REVERT: p 51 ARG cc_start: 0.5943 (ptm160) cc_final: 0.5575 (ptp-170) REVERT: p 53 ASP cc_start: 0.7024 (t0) cc_final: 0.6741 (p0) REVERT: q 5 ILE cc_start: 0.6509 (pt) cc_final: 0.6195 (mp) REVERT: q 50 ASN cc_start: 0.6550 (m110) cc_final: 0.6104 (t0) REVERT: r 52 GLN cc_start: 0.8022 (tp40) cc_final: 0.7548 (tp40) REVERT: s 21 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6767 (pptt) REVERT: s 44 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8028 (mpt) REVERT: s 66 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6519 (ptp) REVERT: t 15 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: t 40 GLU cc_start: 0.8541 (tp30) cc_final: 0.7932 (tm-30) REVERT: t 48 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7115 (tp-100) REVERT: v 60 ARG cc_start: 0.5126 (OUTLIER) cc_final: 0.4625 (ttp-170) REVERT: v 85 GLU cc_start: 0.3299 (mt-10) cc_final: 0.2873 (pt0) REVERT: v 147 MET cc_start: 0.7597 (ttp) cc_final: 0.7097 (ptp) REVERT: v 193 ARG cc_start: 0.7040 (ptt-90) cc_final: 0.6623 (ptt180) REVERT: v 201 LEU cc_start: 0.8055 (tp) cc_final: 0.7747 (tp) REVERT: v 245 ARG cc_start: 0.7108 (mpt-90) cc_final: 0.6710 (mtt90) REVERT: v 255 ASN cc_start: 0.6704 (m-40) cc_final: 0.6417 (m110) REVERT: v 257 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8079 (p) REVERT: v 273 GLN cc_start: 0.8295 (mt0) cc_final: 0.7761 (tt0) REVERT: v 278 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7659 (mtt-85) REVERT: v 295 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7096 (mm) REVERT: v 300 MET cc_start: 0.7251 (mmm) cc_final: 0.6913 (mmm) REVERT: v 314 LYS cc_start: 0.7219 (mtpt) cc_final: 0.6600 (mmtt) REVERT: v 316 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6807 (m-30) outliers start: 297 outliers final: 228 residues processed: 1409 average time/residue: 1.4083 time to fit residues: 3378.4700 Evaluate side-chains 1496 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1223 time to evaluate : 6.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 89 ARG Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 25 LYS Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 29 GLU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 30 LEU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 54 MET Chi-restraints excluded: chain 0 residue 58 GLU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 2 residue 36 GLU Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 23 ILE Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 139 GLN Chi-restraints excluded: chain c residue 156 ARG Chi-restraints excluded: chain d residue 57 GLU Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 85 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 101 ASN Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain o residue 18 ASP Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain r residue 45 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 60 ARG Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 257 THR Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 325 SER Chi-restraints excluded: chain v residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 968 optimal weight: 7.9990 chunk 638 optimal weight: 1.9990 chunk 1027 optimal weight: 20.0000 chunk 627 optimal weight: 0.9990 chunk 487 optimal weight: 0.8980 chunk 714 optimal weight: 10.0000 chunk 1077 optimal weight: 40.0000 chunk 992 optimal weight: 0.0980 chunk 858 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 663 optimal weight: 40.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 36 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 ASN ** 1 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 GLN ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN k 101 ASN r 52 GLN t 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 163943 Z= 0.182 Angle : 0.589 14.403 244682 Z= 0.317 Chirality : 0.034 0.568 31096 Planarity : 0.005 0.126 13510 Dihedral : 23.412 179.791 80663 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 4.93 % Allowed : 26.12 % Favored : 68.95 % 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: -0.07 (0.10), residues: 6269 helix: 1.50 (0.11), residues: 2252 sheet: -0.77 (0.15), residues: 1171 loop : -0.96 (0.11), residues: 2846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP c 201 HIS 0.008 0.001 HIS r 74 PHE 0.030 0.002 PHE b 90 TYR 0.043 0.002 TYR b 213 ARG 0.010 0.000 ARG n 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1233 time to evaluate : 6.676 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: C 66 ASP cc_start: 0.8620 (t0) cc_final: 0.8126 (t0) REVERT: C 95 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7995 (tp) REVERT: C 181 MET cc_start: 0.8112 (mmm) cc_final: 0.7828 (mmm) REVERT: C 242 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8148 (mmtm) REVERT: C 269 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7331 (ttt-90) REVERT: D 17 GLU cc_start: 0.8360 (tt0) cc_final: 0.7960 (mp0) REVERT: D 64 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7689 (mt-10) REVERT: D 94 GLN cc_start: 0.6861 (tt0) cc_final: 0.6166 (mt0) REVERT: D 106 LYS cc_start: 0.8472 (mttt) cc_final: 0.8130 (mttm) REVERT: E 18 THR cc_start: 0.7209 (m) cc_final: 0.6843 (p) REVERT: E 22 ASP cc_start: 0.8507 (m-30) cc_final: 0.7327 (p0) REVERT: E 57 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.5769 (pttt) REVERT: E 194 LYS cc_start: 0.7837 (tptp) cc_final: 0.7306 (mttp) REVERT: F 3 LYS cc_start: 0.7036 (tttt) cc_final: 0.6700 (tptt) REVERT: F 69 LYS cc_start: 0.8690 (mtpt) cc_final: 0.7714 (ttpt) REVERT: F 83 TYR cc_start: 0.7934 (m-80) cc_final: 0.7650 (m-80) REVERT: F 130 MET cc_start: 0.5882 (ptp) cc_final: 0.5419 (tpt) REVERT: G 95 ARG cc_start: 0.6815 (mtm110) cc_final: 0.6577 (ttp80) REVERT: G 101 ASN cc_start: 0.6828 (p0) cc_final: 0.6333 (p0) REVERT: G 155 GLU cc_start: 0.8559 (pm20) cc_final: 0.7932 (pm20) REVERT: H 66 ASN cc_start: 0.5651 (OUTLIER) cc_final: 0.4925 (m-40) REVERT: H 121 VAL cc_start: 0.6277 (OUTLIER) cc_final: 0.6067 (p) REVERT: H 127 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.5119 (mp0) REVERT: H 129 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.3904 (mm-30) REVERT: I 52 MET cc_start: 0.2088 (mmm) cc_final: 0.1361 (mtt) REVERT: I 86 MET cc_start: 0.2261 (tmm) cc_final: 0.1520 (tmm) REVERT: K 14 ASP cc_start: 0.8268 (m-30) cc_final: 0.7715 (t0) REVERT: K 23 LYS cc_start: 0.8553 (mttt) cc_final: 0.8036 (mmmt) REVERT: K 108 MET cc_start: 0.8284 (mtt) cc_final: 0.7969 (mtt) REVERT: K 123 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7390 (mmpt) REVERT: K 138 GLN cc_start: 0.8109 (mt0) cc_final: 0.7569 (mt0) REVERT: L 18 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8031 (mtp85) REVERT: L 23 LYS cc_start: 0.8689 (tppt) cc_final: 0.8392 (tppt) REVERT: L 121 GLU cc_start: 0.7550 (tt0) cc_final: 0.7036 (tt0) REVERT: M 78 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7703 (mmt-90) REVERT: M 143 GLU cc_start: 0.6604 (pm20) cc_final: 0.6161 (pm20) REVERT: N 60 GLN cc_start: 0.7657 (tp40) cc_final: 0.6654 (tt0) REVERT: N 104 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8120 (mt-10) REVERT: O 44 LEU cc_start: 0.8517 (tt) cc_final: 0.8310 (tp) REVERT: O 60 VAL cc_start: 0.8368 (t) cc_final: 0.8076 (p) REVERT: O 90 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7281 (ttm110) REVERT: O 114 GLU cc_start: 0.8741 (pt0) cc_final: 0.8285 (pt0) REVERT: O 118 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6893 (ttp-170) REVERT: P 25 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6804 (ptt-90) REVERT: P 116 GLN cc_start: 0.7557 (tt0) cc_final: 0.6799 (tm-30) REVERT: Q 55 LEU cc_start: 0.9150 (tp) cc_final: 0.8710 (tp) REVERT: Q 89 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6643 (ptp90) REVERT: R 117 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7129 (mp) REVERT: S 23 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7952 (mm-30) REVERT: S 60 LYS cc_start: 0.7564 (mttt) cc_final: 0.7001 (ttmt) REVERT: S 73 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7929 (ttpp) REVERT: S 78 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8367 (tpp-160) REVERT: S 85 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8072 (ttmm) REVERT: T 1 MET cc_start: 0.7935 (ttt) cc_final: 0.7360 (ptp) REVERT: U 1 MET cc_start: 0.6307 (ptm) cc_final: 0.5931 (ptt) REVERT: U 33 LYS cc_start: 0.7514 (ttmt) cc_final: 0.7218 (tttm) REVERT: U 69 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7289 (mtm110) REVERT: U 77 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7753 (mtt-85) REVERT: V 26 LYS cc_start: 0.7355 (mmtt) cc_final: 0.6979 (mmmt) REVERT: V 37 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7674 (tm-30) REVERT: V 39 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8683 (mp) REVERT: V 46 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8002 (mm-40) REVERT: V 62 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7006 (mt-10) REVERT: V 73 PHE cc_start: 0.7782 (t80) cc_final: 0.7524 (t80) REVERT: V 88 GLU cc_start: 0.7670 (tp30) cc_final: 0.7177 (pp20) REVERT: W 1 MET cc_start: 0.6196 (tpt) cc_final: 0.5585 (mpp) REVERT: W 24 ASN cc_start: 0.7682 (t0) cc_final: 0.7300 (t0) REVERT: W 25 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8058 (mtpt) REVERT: W 71 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6699 (mttm) REVERT: X 11 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.5824 (mtt-85) REVERT: X 35 SER cc_start: 0.9114 (m) cc_final: 0.8800 (m) REVERT: Y 11 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8269 (mpt180) REVERT: Y 16 ASN cc_start: 0.9168 (m-40) cc_final: 0.8825 (m110) REVERT: Y 28 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8397 (mtp180) REVERT: Y 45 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6531 (ptt-90) REVERT: Z 19 LEU cc_start: 0.7308 (tp) cc_final: 0.7007 (tp) REVERT: Z 29 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.7198 (ptp-170) REVERT: Z 39 GLN cc_start: 0.7701 (mt0) cc_final: 0.7238 (mt0) REVERT: 0 47 MET cc_start: 0.8384 (mtm) cc_final: 0.8049 (mtm) REVERT: 0 49 ASN cc_start: 0.8670 (t0) cc_final: 0.8393 (t0) REVERT: 2 10 ARG cc_start: 0.8845 (ptp90) cc_final: 0.8530 (ptp-170) REVERT: 3 28 ARG cc_start: 0.8223 (mpt-90) cc_final: 0.7454 (mmm-85) REVERT: 4 25 LYS cc_start: 0.8075 (tmmt) cc_final: 0.7323 (tttp) REVERT: 5 30 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7380 (tpm170) REVERT: 5 61 CYS cc_start: 0.8786 (m) cc_final: 0.8330 (m) REVERT: 6 12 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8341 (ptm160) REVERT: b 23 TRP cc_start: 0.6465 (p-90) cc_final: 0.5929 (p-90) REVERT: b 35 ARG cc_start: 0.6941 (mmt-90) cc_final: 0.6489 (mtm-85) REVERT: b 49 MET cc_start: 0.5807 (mtp) cc_final: 0.5198 (ttm) REVERT: b 68 LEU cc_start: 0.6258 (tp) cc_final: 0.5965 (tp) REVERT: b 145 GLU cc_start: 0.6956 (tp30) cc_final: 0.6208 (mt-10) REVERT: b 154 MET cc_start: 0.5805 (mmm) cc_final: 0.5417 (mmm) REVERT: b 214 LEU cc_start: 0.6477 (mt) cc_final: 0.6120 (mt) REVERT: c 22 TRP cc_start: 0.6587 (p-90) cc_final: 0.5849 (p-90) REVERT: c 62 LYS cc_start: 0.6143 (mmtt) cc_final: 0.5883 (tmtt) REVERT: c 105 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.4168 (mp0) REVERT: c 135 LYS cc_start: 0.8516 (mttm) cc_final: 0.8025 (tttt) REVERT: c 156 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.5461 (mmm-85) REVERT: d 54 GLN cc_start: 0.8747 (mt0) cc_final: 0.8213 (mt0) REVERT: d 60 LYS cc_start: 0.7213 (ttmt) cc_final: 0.6738 (tttt) REVERT: d 62 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7322 (ptp-170) REVERT: d 78 GLU cc_start: 0.7559 (tp30) cc_final: 0.7180 (pp20) REVERT: d 167 LYS cc_start: 0.5151 (mttt) cc_final: 0.4757 (pptt) REVERT: d 183 LYS cc_start: 0.8509 (ttmt) cc_final: 0.7984 (tptt) REVERT: d 185 LYS cc_start: 0.8160 (ptmt) cc_final: 0.7394 (mtpp) REVERT: d 187 GLU cc_start: 0.6822 (tt0) cc_final: 0.6223 (mp0) REVERT: d 197 GLU cc_start: 0.6998 (pm20) cc_final: 0.6603 (mp0) REVERT: e 105 ILE cc_start: 0.8465 (mp) cc_final: 0.8217 (mm) REVERT: f 17 GLN cc_start: 0.7756 (mp10) cc_final: 0.7435 (mp10) REVERT: g 4 ARG cc_start: 0.5971 (ttt90) cc_final: 0.4984 (tpp-160) REVERT: g 48 GLU cc_start: 0.7007 (tp30) cc_final: 0.6697 (pt0) REVERT: g 78 ARG cc_start: 0.5057 (tpp80) cc_final: 0.4758 (tpt-90) REVERT: h 69 LYS cc_start: 0.7400 (mptt) cc_final: 0.7153 (pttm) REVERT: h 101 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7798 (tp) REVERT: k 34 ILE cc_start: 0.8761 (mm) cc_final: 0.8365 (mp) REVERT: k 57 LYS cc_start: 0.8179 (pttt) cc_final: 0.7919 (pttm) REVERT: k 119 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7122 (m110) REVERT: l 6 GLN cc_start: 0.7544 (mt0) cc_final: 0.7200 (mt0) REVERT: l 78 SER cc_start: 0.7799 (t) cc_final: 0.7281 (m) REVERT: l 79 VAL cc_start: 0.8425 (t) cc_final: 0.8154 (p) REVERT: l 108 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8073 (mtmm) REVERT: l 120 LYS cc_start: 0.7738 (mmmt) cc_final: 0.6960 (mppt) REVERT: m 31 LYS cc_start: 0.7631 (mttt) cc_final: 0.7385 (mmmm) REVERT: m 46 SER cc_start: 0.5960 (OUTLIER) cc_final: 0.5592 (p) REVERT: m 93 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7222 (mpt-90) REVERT: m 101 ARG cc_start: 0.6934 (ptp-110) cc_final: 0.6472 (ptp-110) REVERT: n 16 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6230 (mt) REVERT: n 23 LYS cc_start: 0.6604 (tttt) cc_final: 0.6333 (tppt) REVERT: o 11 ILE cc_start: 0.5953 (mm) cc_final: 0.5595 (mp) REVERT: o 24 SER cc_start: 0.8254 (m) cc_final: 0.7259 (p) REVERT: o 74 ASP cc_start: 0.6925 (t0) cc_final: 0.5929 (m-30) REVERT: o 80 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7818 (pt0) REVERT: p 51 ARG cc_start: 0.6182 (ptm160) cc_final: 0.5784 (ptp-170) REVERT: q 5 ILE cc_start: 0.6475 (pt) cc_final: 0.6154 (mp) REVERT: r 52 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7575 (tp-100) REVERT: s 21 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6773 (pptt) REVERT: s 44 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7802 (mpt) REVERT: s 66 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6458 (ptp) REVERT: s 71 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7650 (mp) REVERT: t 15 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: t 40 GLU cc_start: 0.8497 (tp30) cc_final: 0.7925 (tm-30) REVERT: t 48 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7257 (tp-100) REVERT: t 52 ASN cc_start: 0.7905 (m110) cc_final: 0.7501 (m-40) REVERT: v 85 GLU cc_start: 0.3340 (mt-10) cc_final: 0.2939 (pt0) REVERT: v 147 MET cc_start: 0.7584 (ttp) cc_final: 0.7102 (ptp) REVERT: v 193 ARG cc_start: 0.6886 (ptt-90) cc_final: 0.6559 (ptt180) REVERT: v 200 ARG cc_start: 0.7314 (ttt90) cc_final: 0.6968 (ttm-80) REVERT: v 201 LEU cc_start: 0.8016 (tp) cc_final: 0.7681 (tp) REVERT: v 245 ARG cc_start: 0.7054 (mpt-90) cc_final: 0.6310 (mtt180) REVERT: v 255 ASN cc_start: 0.6884 (m-40) cc_final: 0.6574 (m110) REVERT: v 273 GLN cc_start: 0.8235 (mt0) cc_final: 0.7721 (tt0) REVERT: v 278 ARG cc_start: 0.8011 (mtt-85) cc_final: 0.7623 (mtt-85) REVERT: v 286 GLN cc_start: 0.7214 (tp-100) cc_final: 0.6242 (mt0) REVERT: v 295 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7115 (mm) REVERT: v 300 MET cc_start: 0.7333 (mmm) cc_final: 0.7008 (mmm) REVERT: v 314 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6568 (mmtt) REVERT: v 316 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6790 (m-30) outliers start: 257 outliers final: 203 residues processed: 1392 average time/residue: 1.3934 time to fit residues: 3286.5462 Evaluate side-chains 1446 residues out of total 5218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1203 time to evaluate : 6.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 90 ARG Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 89 ARG Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 61 ASN Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 25 LYS Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 2 residue 36 GLU Chi-restraints excluded: chain 3 residue 13 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 5 residue 30 ARG Chi-restraints excluded: chain 6 residue 3 VAL Chi-restraints excluded: chain 6 residue 12 ARG Chi-restraints excluded: chain 6 residue 23 ILE Chi-restraints excluded: chain 6 residue 30 GLU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 175 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 105 GLU Chi-restraints excluded: chain c residue 156 ARG Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 137 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain h residue 2 SER Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 85 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain o residue 18 ASP Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 28 VAL Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain v residue 30 LYS Chi-restraints excluded: chain v residue 60 ARG Chi-restraints excluded: chain v residue 113 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 183 ILE Chi-restraints excluded: chain v residue 195 GLU Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 295 LEU Chi-restraints excluded: chain v residue 306 GLU Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1082 random chunks: chunk 526 optimal weight: 10.0000 chunk 681 optimal weight: 20.0000 chunk 914 optimal weight: 0.9990 chunk 262 optimal weight: 10.0000 chunk 791 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 859 optimal weight: 20.0000 chunk 359 optimal weight: 0.8980 chunk 882 optimal weight: 0.7980 chunk 108 optimal weight: 40.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 ASN ** 1 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN k 101 ASN r 52 GLN v 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.187056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.145382 restraints weight = 193027.051| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 0.96 r_work: 0.3228 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 163943 Z= 0.246 Angle : 0.617 59.196 244682 Z= 0.335 Chirality : 0.035 0.573 31096 Planarity : 0.005 0.126 13510 Dihedral : 23.409 179.823 80661 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 5.16 % Allowed : 26.12 % Favored : 68.72 % Cbeta Deviations : 0.02 % 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: -0.07 (0.10), residues: 6269 helix: 1.49 (0.11), residues: 2252 sheet: -0.76 (0.15), residues: 1166 loop : -0.95 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 201 HIS 0.008 0.001 HIS r 74 PHE 0.021 0.002 PHE b 90 TYR 0.039 0.002 TYR b 213 ARG 0.019 0.000 ARG M 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49100.41 seconds wall clock time: 853 minutes 14.91 seconds (51194.91 seconds total)