Starting phenix.real_space_refine on Sun Feb 25 05:35:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mdz_3493/02_2024/5mdz_3493_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4638 5.49 5 Mg 437 5.21 5 S 160 5.16 5 C 73640 2.51 5 N 27239 2.21 5 O 40523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 55": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W GLU 85": "OE1" <-> "OE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 43": "OE1" <-> "OE2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 11": "OE1" <-> "OE2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b GLU 36": "OE1" <-> "OE2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 118": "OE1" <-> "OE2" Residue "g GLU 133": "OE1" <-> "OE2" Residue "g GLU 169": "OE1" <-> "OE2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h GLU 28": "OE1" <-> "OE2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h GLU 110": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h GLU 152": "OE1" <-> "OE2" Residue "h GLU 161": "OE1" <-> "OE2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h GLU 166": "OE1" <-> "OE2" Residue "h GLU 188": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 147": "OE1" <-> "OE2" Residue "i GLU 160": "OE1" <-> "OE2" Residue "i GLU 166": "OE1" <-> "OE2" Residue "i GLU 172": "OE1" <-> "OE2" Residue "i GLU 202": "OE1" <-> "OE2" Residue "j GLU 10": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 55": "OE1" <-> "OE2" Residue "j GLU 65": "OE1" <-> "OE2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j GLU 101": "OE1" <-> "OE2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "j GLU 151": "OE1" <-> "OE2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "j GLU 162": "OE1" <-> "OE2" Residue "k GLU 5": "OE1" <-> "OE2" Residue "k PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k GLU 65": "OE1" <-> "OE2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "k GLU 73": "OE1" <-> "OE2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l GLU 21": "OE1" <-> "OE2" Residue "l GLU 40": "OE1" <-> "OE2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l GLU 58": "OE1" <-> "OE2" Residue "l GLU 63": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l GLU 123": "OE1" <-> "OE2" Residue "l GLU 146": "OE1" <-> "OE2" Residue "m GLU 42": "OE1" <-> "OE2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m GLU 52": "OE1" <-> "OE2" Residue "m GLU 73": "OE1" <-> "OE2" Residue "m GLU 124": "OE1" <-> "OE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n GLU 36": "OE1" <-> "OE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o GLU 24": "OE1" <-> "OE2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o GLU 81": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p GLU 83": "OE1" <-> "OE2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q GLU 76": "OE1" <-> "OE2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s GLU 26": "OE1" <-> "OE2" Residue "s GLU 39": "OE1" <-> "OE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t GLU 6": "OE1" <-> "OE2" Residue "t GLU 26": "OE1" <-> "OE2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u GLU 34": "OE1" <-> "OE2" Residue "u GLU 45": "OE1" <-> "OE2" Residue "u GLU 47": "OE1" <-> "OE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "u GLU 77": "OE1" <-> "OE2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v GLU 26": "OE1" <-> "OE2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v GLU 52": "OE1" <-> "OE2" Residue "v GLU 63": "OE1" <-> "OE2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "v GLU 80": "OE1" <-> "OE2" Residue "w GLU 16": "OE1" <-> "OE2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x GLU 20": "OE1" <-> "OE2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "x GLU 65": "OE1" <-> "OE2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 8": "OE1" <-> "OE2" Residue "z GLU 24": "OE1" <-> "OE2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z GLU 39": "OE1" <-> "OE2" Residue "z GLU 44": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z GLU 63": "OE1" <-> "OE2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146639 Number of models: 1 Model: "" Number of chains: 66 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 459, 'rna3p': 2443} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 2, 'rna2p_pur': 117, 'rna2p_pyr': 89, 'rna3p': 9, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1326} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "5" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Unusual residues: {'8AN': 1} Classifications: {'RNA': 75, 'undetermined': 1} Modifications used: {'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 3, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'p': 1, 'rna2p': 13, 'rna3p': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 295 Unusual residues: {' MG': 295} Classifications: {'undetermined': 295} Link IDs: {None: 294} Chain: "2" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Unusual residues: {' MG': 128} Classifications: {'undetermined': 128} Link IDs: {None: 127} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "5" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0J2L SG CYS a 16 129.278 197.351 43.038 1.00145.46 S ATOM A0J7G SG CYS a 40 131.001 197.097 43.938 1.00143.14 S ATOM A0KSH SG CYS f 11 182.219 135.070 117.687 1.00 93.49 S ATOM A0KT6 SG CYS f 14 180.646 132.085 117.541 1.00 64.37 S ATOM A0KW1 SG CYS f 27 182.627 132.694 120.332 1.00 78.81 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13146 " occ=0.50 Time building chain proxies: 55.33, per 1000 atoms: 0.38 Number of scatterers: 146639 At special positions: 0 Unit cell: (245.44, 287.04, 273.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 160 16.00 P 4638 15.00 Mg 437 11.99 O 40523 8.00 N 27239 7.00 C 73640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=1.96 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 62.53 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 102 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 102 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 14 " Number of angles added : 3 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10976 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: 187 helices and 73 sheets defined 40.1% alpha, 19.3% beta 1541 base pairs and 2367 stacking pairs defined. Time for finding SS restraints: 73.40 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 7.490A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.533A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.818A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.679A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.753A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.341A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.809A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 97 through 103 removed outlier: 4.812A pdb=" N PHE C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.328A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 6.119A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.546A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.565A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 5.590A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.525A pdb=" N VAL E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 46 removed outlier: 4.786A pdb=" N ILE E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.598A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.875A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.532A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.695A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.854A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.812A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.528A pdb=" N ILE F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 50 removed outlier: 4.013A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 73 removed outlier: 4.164A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'H' and resid 3 through 22 removed outlier: 3.634A pdb=" N ASP H 7 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA H 22 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.509A pdb=" N ALA H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 Proline residue: H 68 - end of helix removed outlier: 4.181A pdb=" N CYS H 71 " --> pdb=" O THR H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 removed outlier: 4.261A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 73 through 79' Processing helix chain 'H' and resid 94 through 106 removed outlier: 4.105A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.990A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 48 removed outlier: 3.990A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 Processing helix chain 'I' and resid 101 through 117 removed outlier: 3.652A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.846A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.172A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.799A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.262A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.022A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.865A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.939A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.844A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.311A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 58 removed outlier: 4.180A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.148A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.430A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 3.605A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.237A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.787A pdb=" N LYS P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.553A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.826A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.737A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 73 removed outlier: 3.785A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.539A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.028A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.584A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.967A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.586A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.771A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.631A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.730A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 9 removed outlier: 4.104A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.506A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.690A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.289A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 64 Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.733A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.690A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.525A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 24 through 32 removed outlier: 4.058A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix removed outlier: 5.569A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 24 through 32' Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix removed outlier: 3.677A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.466A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 3.598A pdb=" N VAL g 107 " --> pdb=" O ASN g 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.808A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 Processing helix chain 'h' and resid 72 through 78 removed outlier: 3.887A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.453A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.508A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.075A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.521A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 4.963A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.549A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.562A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.775A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.667A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.589A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.409A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.522A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.576A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 17 removed outlier: 3.738A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 11 through 17' Processing helix chain 'k' and resid 18 through 33 removed outlier: 3.642A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 Processing helix chain 'l' and resid 20 through 31 Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.770A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.579A pdb=" N ALA l 61 " --> pdb=" O SER l 57 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.614A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.679A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 Proline residue: n 51 - end of helix removed outlier: 3.704A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 4.086A pdb=" N GLN n 75 " --> pdb=" O GLY n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.937A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.990A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.968A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.702A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 76 removed outlier: 3.527A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 3.917A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.675A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.656A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.145A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.560A pdb=" N ILE r 77 " --> pdb=" O ILE r 73 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.543A pdb=" N LYS s 7 " --> pdb=" O LYS s 3 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 52 Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 44 removed outlier: 3.894A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.593A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 Processing helix chain 'w' and resid 11 through 17 removed outlier: 3.967A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.895A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.690A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.278A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 41 removed outlier: 3.502A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 removed outlier: 5.296A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.633A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.886A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.725A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.278A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.160A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 7 removed outlier: 7.152A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.580A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.662A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.137A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 1 through 6 removed outlier: 3.826A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 42 through 46 removed outlier: 4.677A pdb=" N GLY D 42 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG D 44 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG D 88 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN D 46 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA D 86 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.549A pdb=" N VAL D 146 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 65 through 69 removed outlier: 5.868A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 13, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 14, first strand: chain 'F' and resid 94 through 98 removed outlier: 3.700A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.834A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LYS F 86 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 163 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 90 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 17 through 21 removed outlier: 4.920A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.499A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 23 through 27 removed outlier: 4.008A pdb=" N LEU H 23 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 25 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 27 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 55 through 58 removed outlier: 4.406A pdb=" N VAL I 69 " --> pdb=" O VAL I 57 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 15 through 18 Processing sheet with id= 21, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.141A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 5 through 9 removed outlier: 4.103A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.867A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.613A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 30 through 36 removed outlier: 8.126A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.082A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.593A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.687A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.510A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.594A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.256A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 33, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 34, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.141A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.527A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.996A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.365A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 40 through 45 removed outlier: 4.728A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 82 through 87 removed outlier: 7.191A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.770A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 51 through 54 removed outlier: 3.966A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 43, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.782A pdb=" N SER X 19 " --> pdb=" O ASN X 23 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 34 through 41 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.185A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'a' and resid 20 through 25 removed outlier: 3.891A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.264A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 19 through 25 removed outlier: 6.400A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.612A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'f' and resid 13 through 19 removed outlier: 8.604A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER f 28 " --> pdb=" O ASN f 13 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.191A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 90 through 93 Processing sheet with id= 53, first strand: chain 'h' and resid 54 through 59 Processing sheet with id= 54, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.709A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.646A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.808A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 83 through 88 removed outlier: 7.298A pdb=" N HIS j 83 " --> pdb=" O PRO j 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 33 through 41 removed outlier: 6.799A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.591A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL k 7 " --> pdb=" O MET k 88 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 43 through 47 removed outlier: 6.897A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 73 through 79 removed outlier: 6.281A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.159A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 74 through 77 removed outlier: 6.754A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.572A pdb=" N LYS n 68 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 37 through 42 removed outlier: 3.866A pdb=" N GLY o 38 " --> pdb=" O ASP o 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP o 75 " --> pdb=" O GLY o 38 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 67, first strand: chain 'p' and resid 42 through 45 Processing sheet with id= 68, first strand: chain 'q' and resid 29 through 34 removed outlier: 4.432A pdb=" N SER q 78 " --> pdb=" O CYS q 34 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 35 through 41 removed outlier: 5.045A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.086A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.910A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'x' and resid 30 through 34 removed outlier: 5.094A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 2034 hydrogen bonds defined for protein. 6009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3883 hydrogen bonds 6166 hydrogen bond angles 0 basepair planarities 1541 basepair parallelities 2367 stacking parallelities Total time for adding SS restraints: 271.96 Time building geometry restraints manager: 67.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.54: 147894 1.54 - 1.90: 10868 1.90 - 2.26: 0 2.26 - 2.62: 1 2.62 - 2.98: 4 Bond restraints: 158767 Sorted by residual: bond pdb=" O3' U 2 480 " pdb=" P G 2 481 " ideal model delta sigma weight residual 1.607 2.977 -1.370 1.50e-02 4.44e+03 8.34e+03 bond pdb=" O3' U 21390 " pdb=" P U 21391 " ideal model delta sigma weight residual 1.607 2.824 -1.217 1.50e-02 4.44e+03 6.58e+03 bond pdb=" O3' C 12196 " pdb=" P U 12197 " ideal model delta sigma weight residual 1.607 2.674 -1.067 1.50e-02 4.44e+03 5.06e+03 bond pdb=" O3' A 2 197 " pdb=" P G 2 198 " ideal model delta sigma weight residual 1.607 2.669 -1.062 1.50e-02 4.44e+03 5.01e+03 bond pdb=" O3' G 2 927 " pdb=" P G 2 928 " ideal model delta sigma weight residual 1.607 2.612 -1.005 1.50e-02 4.44e+03 4.49e+03 ... (remaining 158762 not shown) Histogram of bond angle deviations from ideal: 72.47 - 88.15: 8 88.15 - 103.83: 15894 103.83 - 119.52: 149252 119.52 - 135.20: 72144 135.20 - 150.88: 9 Bond angle restraints: 237307 Sorted by residual: angle pdb=" O3' A 2 197 " pdb=" P G 2 198 " pdb=" O5' G 2 198 " ideal model delta sigma weight residual 104.00 137.68 -33.68 1.50e+00 4.44e-01 5.04e+02 angle pdb=" O3' U 21390 " pdb=" P U 21391 " pdb=" O5' U 21391 " ideal model delta sigma weight residual 104.00 72.47 31.53 1.50e+00 4.44e-01 4.42e+02 angle pdb=" O3' C 12196 " pdb=" P U 12197 " pdb=" O5' U 12197 " ideal model delta sigma weight residual 104.00 73.59 30.41 1.50e+00 4.44e-01 4.11e+02 angle pdb=" C3' U 2 480 " pdb=" O3' U 2 480 " pdb=" P G 2 481 " ideal model delta sigma weight residual 120.20 95.77 24.43 1.50e+00 4.44e-01 2.65e+02 angle pdb=" C3' G 2 927 " pdb=" O3' G 2 927 " pdb=" P G 2 928 " ideal model delta sigma weight residual 120.20 97.43 22.77 1.50e+00 4.44e-01 2.30e+02 ... (remaining 237302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 89018 35.95 - 71.91: 11189 71.91 - 107.86: 1263 107.86 - 143.82: 28 143.82 - 179.77: 43 Dihedral angle restraints: 101541 sinusoidal: 84530 harmonic: 17011 Sorted by residual: dihedral pdb=" C5' A 21493 " pdb=" C4' A 21493 " pdb=" C3' A 21493 " pdb=" O3' A 21493 " ideal model delta sinusoidal sigma weight residual 147.00 75.02 71.98 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' A 1 404 " pdb=" C4' A 1 404 " pdb=" C3' A 1 404 " pdb=" O3' A 1 404 " ideal model delta sinusoidal sigma weight residual 147.00 77.03 69.97 1 8.00e+00 1.56e-02 9.86e+01 dihedral pdb=" C4' A 21493 " pdb=" C3' A 21493 " pdb=" C2' A 21493 " pdb=" C1' A 21493 " ideal model delta sinusoidal sigma weight residual -35.00 32.04 -67.04 1 8.00e+00 1.56e-02 9.15e+01 ... (remaining 101538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.320: 30111 0.320 - 0.640: 77 0.640 - 0.961: 8 0.961 - 1.281: 6 1.281 - 1.601: 9 Chirality restraints: 30211 Sorted by residual: chirality pdb=" C2* PSU 5 55 " pdb=" C3* PSU 5 55 " pdb=" O2* PSU 5 55 " pdb=" C1* PSU 5 55 " both_signs ideal model delta sigma weight residual False -2.75 -1.15 -1.60 2.00e-01 2.50e+01 6.41e+01 chirality pdb=" C3' 2MA 12503 " pdb=" C4' 2MA 12503 " pdb=" O3' 2MA 12503 " pdb=" C2' 2MA 12503 " both_signs ideal model delta sigma weight residual False -2.74 -1.19 -1.56 2.00e-01 2.50e+01 6.05e+01 chirality pdb=" C2' G7M 12069 " pdb=" C3' G7M 12069 " pdb=" O2' G7M 12069 " pdb=" C1' G7M 12069 " both_signs ideal model delta sigma weight residual False -2.75 -1.25 -1.50 2.00e-01 2.50e+01 5.66e+01 ... (remaining 30208 not shown) Planarity restraints: 12843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 2 966 " -0.197 2.00e-02 2.50e+03 6.49e-01 9.48e+03 pdb=" C4' 2MG 2 966 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG 2 966 " -0.290 2.00e-02 2.50e+03 pdb=" C3' 2MG 2 966 " 0.499 2.00e-02 2.50e+03 pdb=" O3' 2MG 2 966 " 0.889 2.00e-02 2.50e+03 pdb=" C2' 2MG 2 966 " 0.001 2.00e-02 2.50e+03 pdb=" O2' 2MG 2 966 " -1.239 2.00e-02 2.50e+03 pdb=" C1' 2MG 2 966 " -0.165 2.00e-02 2.50e+03 pdb=" N9 2MG 2 966 " 0.936 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " 0.025 2.00e-02 2.50e+03 6.29e-01 8.91e+03 pdb=" C4' 7MG 2 527 " 0.460 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.550 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.599 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.721 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.125 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 1.117 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.219 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " -0.028 2.00e-02 2.50e+03 6.23e-01 8.74e+03 pdb=" C4' 2MG 21207 " -0.479 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " -0.710 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " 0.625 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " 0.648 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " 0.216 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " -1.004 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " -0.194 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " 0.927 2.00e-02 2.50e+03 ... (remaining 12840 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 106 2.12 - 2.82: 35667 2.82 - 3.51: 203339 3.51 - 4.21: 492091 4.21 - 4.90: 636552 Nonbonded interactions: 1367755 Sorted by model distance: nonbonded pdb=" O4 U 11082 " pdb=" N1 A 11086 " model vdw 1.430 2.496 nonbonded pdb=" N1 A 12013 " pdb=" O4 U 12613 " model vdw 1.464 2.496 nonbonded pdb=" O4 U 2 827 " pdb=" N1 A 2 872 " model vdw 1.536 2.496 nonbonded pdb=" O4 U 2 37 " pdb=" N1 A 2 397 " model vdw 1.542 2.496 nonbonded pdb=" O4 U 11019 " pdb=" N1 A 11142 " model vdw 1.546 2.496 ... (remaining 1367750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 17.970 Check model and map are aligned: 1.550 Set scattering table: 0.980 Process input model: 592.290 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.410 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 623.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 : 0.010 1.370 158767 Z= 0.631 Angle : 1.266 42.884 237307 Z= 0.850 Chirality : 0.104 1.601 30211 Planarity : 0.021 0.649 12843 Dihedral : 23.728 179.774 90562 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.70 % Favored : 94.94 % Rotamer: Outliers : 6.88 % Allowed : 10.08 % Favored : 83.04 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 5867 helix: 0.06 (0.08), residues: 2035 sheet: -2.31 (0.13), residues: 1064 loop : -1.84 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 248 HIS 0.018 0.002 HIS X 34 PHE 0.063 0.003 PHE Q 106 TYR 0.036 0.003 TYR Q 47 ARG 0.027 0.002 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1351 time to evaluate : 6.245 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: B 28 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7611 (mttt) REVERT: B 82 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8487 (mt-10) REVERT: B 97 LYS cc_start: 0.8852 (mptt) cc_final: 0.8643 (mmtp) REVERT: B 183 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8274 (mtpt) REVERT: B 270 ARG cc_start: 0.8648 (mmm160) cc_final: 0.8029 (ttt-90) REVERT: C 1 MET cc_start: 0.6122 (ttt) cc_final: 0.5840 (ttt) REVERT: C 88 GLU cc_start: 0.8088 (mt-10) cc_final: 0.6875 (mp0) REVERT: C 128 ARG cc_start: 0.8962 (mtt90) cc_final: 0.8109 (mmp-170) REVERT: C 133 THR cc_start: 0.9158 (t) cc_final: 0.8949 (p) REVERT: D 57 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8745 (tttm) REVERT: D 69 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7556 (ptp-170) REVERT: D 123 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7526 (mmmt) REVERT: D 155 GLU cc_start: 0.8385 (tp30) cc_final: 0.8146 (tp30) REVERT: D 166 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7049 (mmtt) REVERT: D 176 ASP cc_start: 0.8294 (p0) cc_final: 0.7848 (p0) REVERT: E 9 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8523 (mtmm) REVERT: E 21 ASN cc_start: 0.7736 (t0) cc_final: 0.7353 (m-40) REVERT: E 33 LYS cc_start: 0.8553 (pttt) cc_final: 0.8146 (pttt) REVERT: E 95 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7555 (mmt180) REVERT: E 117 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7427 (mt) REVERT: E 134 GLU cc_start: 0.8491 (tt0) cc_final: 0.8243 (tt0) REVERT: E 149 VAL cc_start: 0.8027 (t) cc_final: 0.7818 (p) REVERT: E 161 LYS cc_start: 0.7762 (mttt) cc_final: 0.7475 (mmmm) REVERT: F 85 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7309 (mmmt) REVERT: F 86 LYS cc_start: 0.8140 (mttm) cc_final: 0.7588 (ttpp) REVERT: F 95 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7093 (ppt170) REVERT: F 99 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7419 (mttp) REVERT: F 157 TYR cc_start: 0.8179 (m-80) cc_final: 0.7705 (m-80) REVERT: G 7 ASP cc_start: 0.8242 (t70) cc_final: 0.7646 (t0) REVERT: I 10 LEU cc_start: 0.1917 (OUTLIER) cc_final: 0.1678 (tt) REVERT: I 48 ILE cc_start: 0.2183 (OUTLIER) cc_final: 0.1869 (tt) REVERT: J 67 ASN cc_start: 0.8569 (m-40) cc_final: 0.8251 (m-40) REVERT: J 71 ASP cc_start: 0.7871 (m-30) cc_final: 0.7614 (m-30) REVERT: J 108 MET cc_start: 0.8966 (mtt) cc_final: 0.8588 (mtt) REVERT: K 104 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8999 (m) REVERT: K 113 MET cc_start: 0.8498 (tpt) cc_final: 0.8284 (mmm) REVERT: L 78 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7484 (mtm180) REVERT: M 20 LEU cc_start: 0.9108 (mm) cc_final: 0.8905 (mt) REVERT: M 91 TYR cc_start: 0.9188 (p90) cc_final: 0.8970 (p90) REVERT: M 127 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7772 (tptt) REVERT: N 32 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8531 (mt-10) REVERT: O 13 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7649 (tpp80) REVERT: O 28 VAL cc_start: 0.9066 (p) cc_final: 0.8854 (t) REVERT: O 62 LEU cc_start: 0.8663 (mt) cc_final: 0.8410 (mt) REVERT: O 116 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: P 38 LYS cc_start: 0.8447 (mtmt) cc_final: 0.7930 (mttm) REVERT: P 82 ASP cc_start: 0.8820 (t70) cc_final: 0.8550 (t70) REVERT: P 102 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: P 103 ARG cc_start: 0.8331 (mtt90) cc_final: 0.8126 (mtt180) REVERT: P 111 LYS cc_start: 0.8585 (pttp) cc_final: 0.8329 (ptmm) REVERT: Q 104 VAL cc_start: 0.8639 (t) cc_final: 0.8385 (m) REVERT: R 13 ARG cc_start: 0.9019 (ttt180) cc_final: 0.8808 (ttt180) REVERT: R 16 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7691 (mt-10) REVERT: R 29 THR cc_start: 0.8243 (p) cc_final: 0.7726 (m) REVERT: R 31 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7813 (mm-30) REVERT: R 60 LYS cc_start: 0.8182 (mttt) cc_final: 0.7945 (mmtp) REVERT: S 22 ASP cc_start: 0.8297 (m-30) cc_final: 0.8018 (m-30) REVERT: S 84 ARG cc_start: 0.8821 (mmt-90) cc_final: 0.8567 (mmt180) REVERT: S 95 ARG cc_start: 0.8977 (ttp-170) cc_final: 0.8446 (ttm-80) REVERT: U 10 GLU cc_start: 0.8586 (tt0) cc_final: 0.8336 (tt0) REVERT: U 35 ILE cc_start: 0.8784 (mt) cc_final: 0.8504 (mp) REVERT: U 37 GLU cc_start: 0.8616 (tt0) cc_final: 0.8375 (tt0) REVERT: U 101 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: V 12 GLN cc_start: 0.8474 (mt0) cc_final: 0.8052 (pt0) REVERT: V 25 LYS cc_start: 0.8329 (mttt) cc_final: 0.8024 (mtpp) REVERT: V 46 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8816 (mmmt) REVERT: V 51 GLN cc_start: 0.8533 (pp30) cc_final: 0.8310 (pp30) REVERT: V 71 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7900 (mmmt) REVERT: W 78 LYS cc_start: 0.8870 (mptt) cc_final: 0.8068 (mmtt) REVERT: X 20 HIS cc_start: 0.8647 (t70) cc_final: 0.8375 (t-90) REVERT: Y 7 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8002 (ttm-80) REVERT: Y 16 THR cc_start: 0.8424 (m) cc_final: 0.8142 (p) REVERT: Y 40 SER cc_start: 0.9277 (m) cc_final: 0.8868 (p) REVERT: Z 3 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6843 (tptm) REVERT: Z 11 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8339 (mtm-85) REVERT: Z 54 MET cc_start: 0.9175 (ptm) cc_final: 0.8915 (ptm) REVERT: Z 58 GLU cc_start: 0.7522 (tt0) cc_final: 0.7253 (tt0) REVERT: a 24 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7888 (mm) REVERT: c 48 ILE cc_start: 0.8881 (mt) cc_final: 0.8496 (mt) REVERT: d 25 LYS cc_start: 0.8354 (tmmt) cc_final: 0.8125 (ttpp) REVERT: g 6 MET cc_start: 0.6245 (ttp) cc_final: 0.6007 (ttp) REVERT: g 7 ARG cc_start: 0.7920 (mpp-170) cc_final: 0.7370 (ttp80) REVERT: g 10 LEU cc_start: 0.6347 (tp) cc_final: 0.6110 (mp) REVERT: g 27 MET cc_start: 0.8298 (mmm) cc_final: 0.7901 (mmm) REVERT: g 28 LYS cc_start: 0.6784 (tttt) cc_final: 0.6507 (tptm) REVERT: g 64 LYS cc_start: 0.6453 (mtmm) cc_final: 0.6111 (mmmt) REVERT: g 105 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7664 (ptpp) REVERT: g 117 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4954 (mp) REVERT: g 137 ARG cc_start: 0.5160 (mmt-90) cc_final: 0.4766 (ttp80) REVERT: g 157 LEU cc_start: 0.8366 (mt) cc_final: 0.8158 (mt) REVERT: g 178 ASN cc_start: 0.6716 (m-40) cc_final: 0.6208 (t0) REVERT: g 181 ILE cc_start: 0.7744 (mt) cc_final: 0.7457 (mm) REVERT: g 205 ASP cc_start: 0.6217 (t0) cc_final: 0.5957 (m-30) REVERT: h 85 GLU cc_start: 0.8388 (tp30) cc_final: 0.7433 (tm-30) REVERT: h 89 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6893 (ptpp) REVERT: h 108 LYS cc_start: 0.8145 (mttt) cc_final: 0.7891 (mmtt) REVERT: h 128 VAL cc_start: 0.7674 (m) cc_final: 0.7454 (p) REVERT: h 132 ARG cc_start: 0.7507 (ttm170) cc_final: 0.7298 (ttm110) REVERT: h 135 LYS cc_start: 0.7964 (mptm) cc_final: 0.7683 (mmmt) REVERT: h 147 LYS cc_start: 0.7954 (mmpt) cc_final: 0.7672 (mmmm) REVERT: i 69 GLU cc_start: 0.8542 (tp30) cc_final: 0.8121 (tp30) REVERT: i 128 ARG cc_start: 0.6440 (mtp180) cc_final: 0.6227 (mtp-110) REVERT: i 130 VAL cc_start: 0.8148 (t) cc_final: 0.7667 (m) REVERT: i 172 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6692 (mm-30) REVERT: i 192 SER cc_start: 0.7252 (t) cc_final: 0.7014 (t) REVERT: j 10 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5390 (pm20) REVERT: j 45 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7864 (mtp85) REVERT: j 48 PHE cc_start: 0.9242 (p90) cc_final: 0.8925 (p90) REVERT: j 64 MET cc_start: 0.7666 (mmt) cc_final: 0.7440 (mmt) REVERT: j 77 ASN cc_start: 0.8697 (t0) cc_final: 0.8335 (t0) REVERT: j 78 ASN cc_start: 0.8681 (t0) cc_final: 0.8110 (m-40) REVERT: j 88 VAL cc_start: 0.9008 (m) cc_final: 0.8653 (t) REVERT: j 105 ILE cc_start: 0.9275 (mt) cc_final: 0.8989 (mt) REVERT: j 115 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8381 (mt) REVERT: j 130 SER cc_start: 0.9093 (t) cc_final: 0.8746 (t) REVERT: k 1 MET cc_start: 0.8115 (mpt) cc_final: 0.7770 (mpt) REVERT: k 2 ARG cc_start: 0.8282 (mtp85) cc_final: 0.8077 (mmm-85) REVERT: k 36 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7774 (mt) REVERT: k 81 ASN cc_start: 0.6895 (t0) cc_final: 0.6677 (t0) REVERT: k 86 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7938 (mtt-85) REVERT: k 91 ARG cc_start: 0.8468 (mmm160) cc_final: 0.8171 (mmm-85) REVERT: l 56 LYS cc_start: 0.6968 (mttt) cc_final: 0.6332 (mmtt) REVERT: l 58 GLU cc_start: 0.6841 (mp0) cc_final: 0.6387 (mt-10) REVERT: l 67 GLU cc_start: 0.7643 (tp30) cc_final: 0.7046 (tt0) REVERT: l 74 GLU cc_start: 0.7251 (pt0) cc_final: 0.6864 (tt0) REVERT: l 110 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8335 (mttp) REVERT: l 130 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7293 (t0) REVERT: l 148 ASN cc_start: 0.8227 (m-40) cc_final: 0.7877 (m-40) REVERT: m 42 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8013 (tp30) REVERT: n 46 MET cc_start: 0.7251 (ttp) cc_final: 0.6926 (ttp) REVERT: n 57 MET cc_start: 0.7154 (mtt) cc_final: 0.6716 (mmm) REVERT: o 100 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7348 (pp) REVERT: p 15 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6704 (mm-40) REVERT: p 34 ILE cc_start: 0.8643 (mm) cc_final: 0.8432 (mp) REVERT: p 56 ARG cc_start: 0.8304 (mpp80) cc_final: 0.7127 (mtp-110) REVERT: p 57 LYS cc_start: 0.8631 (pttt) cc_final: 0.8284 (pttt) REVERT: p 68 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7389 (mt-10) REVERT: p 77 TYR cc_start: 0.8998 (m-80) cc_final: 0.8523 (m-80) REVERT: p 85 MET cc_start: 0.7966 (mtt) cc_final: 0.7633 (mtp) REVERT: p 87 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7847 (ttmt) REVERT: q 10 LYS cc_start: 0.8505 (tttt) cc_final: 0.8136 (tmmt) REVERT: q 12 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7616 (mtt90) REVERT: q 56 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7706 (ttp80) REVERT: r 52 GLN cc_start: 0.7439 (mt0) cc_final: 0.7105 (mt0) REVERT: r 81 MET cc_start: 0.7716 (mmt) cc_final: 0.7306 (mtt) REVERT: r 116 ILE cc_start: 0.6733 (mt) cc_final: 0.6472 (mt) REVERT: r 117 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.6006 (mmtt) REVERT: s 6 MET cc_start: 0.8025 (mmm) cc_final: 0.7730 (mmp) REVERT: s 90 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.6957 (ttm110) REVERT: s 96 LEU cc_start: 0.9026 (tp) cc_final: 0.8716 (tp) REVERT: t 10 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7846 (tttt) REVERT: t 14 GLU cc_start: 0.7239 (tt0) cc_final: 0.6921 (mp0) REVERT: t 58 ARG cc_start: 0.8178 (ttt180) cc_final: 0.7778 (ttt-90) REVERT: t 71 LYS cc_start: 0.7958 (tttt) cc_final: 0.7748 (tptt) REVERT: t 79 THR cc_start: 0.7342 (m) cc_final: 0.7101 (p) REVERT: t 85 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8067 (mt) REVERT: u 24 SER cc_start: 0.9103 (t) cc_final: 0.8674 (p) REVERT: v 62 ARG cc_start: 0.8624 (ptt90) cc_final: 0.8422 (ttp-110) REVERT: v 81 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.6056 (ttmt) REVERT: w 29 LEU cc_start: 0.8468 (mp) cc_final: 0.8247 (mp) REVERT: w 48 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7559 (mmt-90) REVERT: x 44 MET cc_start: 0.8070 (mtp) cc_final: 0.7089 (ttp) REVERT: y 24 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7867 (mmp80) REVERT: y 52 ASN cc_start: 0.8135 (m-40) cc_final: 0.7855 (m110) REVERT: y 54 MET cc_start: 0.8349 (pp-130) cc_final: 0.8009 (pp-130) REVERT: z 17 ARG cc_start: 0.6735 (ttm110) cc_final: 0.6093 (mmm160) REVERT: z 21 ARG cc_start: 0.6678 (tpt170) cc_final: 0.6452 (mmm160) REVERT: z 33 ARG cc_start: 0.7628 (tmt170) cc_final: 0.6987 (mtt180) REVERT: z 55 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6832 (mtm180) outliers start: 335 outliers final: 85 residues processed: 1582 average time/residue: 1.4630 time to fit residues: 3862.9934 Evaluate side-chains 1188 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1068 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 122 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 99 ASN Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 11 ARG Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 105 LYS Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 128 LYS Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 97 ASN Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 100 ILE Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 48 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 873 optimal weight: 0.9990 chunk 784 optimal weight: 0.7980 chunk 435 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 529 optimal weight: 4.9990 chunk 419 optimal weight: 10.0000 chunk 811 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 493 optimal weight: 2.9990 chunk 603 optimal weight: 3.9990 chunk 939 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 143 ASN C 136 ASN C 150 GLN D 41 GLN E 63 GLN H 57 ASN L 4 ASN L 104 GLN O 98 GLN P 7 GLN P 66 ASN P 115 ASN Q 72 ASN S 61 ASN T 59 ASN a 41 HIS g 168 HIS g 177 ASN i 74 ASN i 136 GLN j 89 HIS j 132 ASN l 68 ASN l 97 ASN l 142 HIS o 64 GLN q 5 ASN r 105 ASN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 GLN w 31 ASN x 69 HIS y 48 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 158767 Z= 0.275 Angle : 0.718 16.242 237307 Z= 0.382 Chirality : 0.041 0.450 30211 Planarity : 0.007 0.133 12843 Dihedral : 23.549 179.496 79128 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 4.43 % Allowed : 14.97 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 5867 helix: 2.61 (0.12), residues: 2047 sheet: -1.59 (0.14), residues: 1073 loop : -1.35 (0.11), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 248 HIS 0.008 0.001 HIS C 67 PHE 0.019 0.002 PHE a 60 TYR 0.028 0.002 TYR h 42 ARG 0.007 0.001 ARG Q 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1138 time to evaluate : 6.207 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: B 28 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7713 (mttt) REVERT: B 183 LYS cc_start: 0.8383 (mttt) cc_final: 0.8144 (mtpt) REVERT: B 185 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8067 (tt0) REVERT: B 270 ARG cc_start: 0.8463 (mmm160) cc_final: 0.7856 (ttt-90) REVERT: C 18 ASP cc_start: 0.8700 (t0) cc_final: 0.8150 (m-30) REVERT: C 74 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7832 (tp30) REVERT: C 86 GLU cc_start: 0.8036 (pt0) cc_final: 0.7439 (mp0) REVERT: C 88 GLU cc_start: 0.7915 (mt-10) cc_final: 0.6769 (mp0) REVERT: C 106 LYS cc_start: 0.9034 (mttt) cc_final: 0.8774 (mttp) REVERT: D 69 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7487 (ptp-170) REVERT: D 123 LYS cc_start: 0.7850 (ptpp) cc_final: 0.7638 (mmmt) REVERT: D 198 GLU cc_start: 0.8233 (tt0) cc_final: 0.7954 (tp30) REVERT: E 11 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: E 21 ASN cc_start: 0.7732 (t0) cc_final: 0.7320 (m-40) REVERT: E 42 GLU cc_start: 0.6971 (pm20) cc_final: 0.6766 (mp0) REVERT: E 56 ASP cc_start: 0.8101 (m-30) cc_final: 0.7890 (m-30) REVERT: E 134 GLU cc_start: 0.8491 (tt0) cc_final: 0.8189 (tt0) REVERT: E 161 LYS cc_start: 0.7689 (mttt) cc_final: 0.7436 (mmtp) REVERT: E 164 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8261 (pm20) REVERT: F 86 LYS cc_start: 0.7978 (mttm) cc_final: 0.7480 (ttpp) REVERT: F 95 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6635 (ppt170) REVERT: F 99 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7525 (mttm) REVERT: F 157 TYR cc_start: 0.8143 (m-80) cc_final: 0.7862 (m-80) REVERT: G 7 ASP cc_start: 0.8008 (t70) cc_final: 0.7427 (t0) REVERT: G 28 ASN cc_start: 0.8373 (m-40) cc_final: 0.8110 (m-40) REVERT: I 11 GLN cc_start: 0.0591 (OUTLIER) cc_final: -0.1105 (tt0) REVERT: I 48 ILE cc_start: 0.1723 (OUTLIER) cc_final: 0.1375 (tt) REVERT: I 116 MET cc_start: -0.0074 (mmp) cc_final: -0.0524 (ptt) REVERT: J 31 GLU cc_start: 0.8693 (tp30) cc_final: 0.8420 (tp30) REVERT: J 44 TYR cc_start: 0.8919 (t80) cc_final: 0.8705 (t80) REVERT: J 67 ASN cc_start: 0.8736 (m-40) cc_final: 0.8443 (m-40) REVERT: J 98 GLU cc_start: 0.8890 (mp0) cc_final: 0.8680 (mp0) REVERT: J 106 LYS cc_start: 0.8789 (tttp) cc_final: 0.8423 (ttpt) REVERT: K 98 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7930 (ttp-170) REVERT: K 104 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9027 (m) REVERT: L 78 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7384 (mtm180) REVERT: M 73 ILE cc_start: 0.9502 (mm) cc_final: 0.9266 (mm) REVERT: M 91 TYR cc_start: 0.9280 (p90) cc_final: 0.9008 (p90) REVERT: M 127 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: N 18 GLN cc_start: 0.8615 (tt0) cc_final: 0.8361 (tt0) REVERT: N 40 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7935 (mttt) REVERT: O 13 ARG cc_start: 0.8446 (ttt-90) cc_final: 0.7903 (tpp80) REVERT: O 16 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7558 (mmt-90) REVERT: O 116 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: P 38 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8041 (mttt) REVERT: P 102 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: P 103 ARG cc_start: 0.8278 (mtt90) cc_final: 0.8035 (mtt180) REVERT: P 111 LYS cc_start: 0.8477 (pttp) cc_final: 0.8227 (ptmm) REVERT: Q 78 LYS cc_start: 0.8922 (mttm) cc_final: 0.8646 (mtmm) REVERT: R 13 ARG cc_start: 0.9081 (ttt180) cc_final: 0.8848 (ttt180) REVERT: R 16 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7855 (mt-10) REVERT: R 29 THR cc_start: 0.8328 (p) cc_final: 0.7765 (m) REVERT: R 31 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7822 (mm-30) REVERT: R 60 LYS cc_start: 0.8173 (mttt) cc_final: 0.7923 (mmtp) REVERT: S 81 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8707 (p) REVERT: S 95 ARG cc_start: 0.8831 (ttp-170) cc_final: 0.8287 (ttm-80) REVERT: T 56 GLU cc_start: 0.8241 (tt0) cc_final: 0.7848 (tp30) REVERT: U 37 GLU cc_start: 0.8547 (tt0) cc_final: 0.8203 (mt-10) REVERT: U 101 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: V 71 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7821 (mmmt) REVERT: W 38 VAL cc_start: 0.9133 (t) cc_final: 0.8931 (m) REVERT: W 78 LYS cc_start: 0.8828 (mptt) cc_final: 0.8624 (mttt) REVERT: X 43 GLU cc_start: 0.7222 (tt0) cc_final: 0.6915 (tt0) REVERT: Y 7 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7937 (ttm-80) REVERT: Z 3 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7010 (tptp) REVERT: Z 11 ARG cc_start: 0.8845 (mtt-85) cc_final: 0.8451 (mtt-85) REVERT: Z 25 LEU cc_start: 0.9073 (tm) cc_final: 0.8788 (tp) REVERT: Z 37 GLU cc_start: 0.8760 (tp30) cc_final: 0.8480 (tp30) REVERT: a 39 LYS cc_start: 0.7882 (mttt) cc_final: 0.7618 (mtpt) REVERT: b 40 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8525 (mmt180) REVERT: c 17 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7743 (p) REVERT: c 49 TYR cc_start: 0.9343 (m-80) cc_final: 0.8931 (m-80) REVERT: e 61 CYS cc_start: 0.8969 (m) cc_final: 0.8749 (m) REVERT: g 6 MET cc_start: 0.6097 (ttp) cc_final: 0.5645 (tmm) REVERT: g 7 ARG cc_start: 0.7901 (mpp-170) cc_final: 0.7685 (mtm110) REVERT: g 9 MET cc_start: 0.3793 (mtm) cc_final: 0.3504 (mtt) REVERT: g 10 LEU cc_start: 0.6422 (tp) cc_final: 0.6221 (mp) REVERT: g 27 MET cc_start: 0.8250 (mmm) cc_final: 0.7709 (mmm) REVERT: g 64 LYS cc_start: 0.6189 (mtmm) cc_final: 0.5786 (mmmt) REVERT: g 137 ARG cc_start: 0.5330 (mmt-90) cc_final: 0.4821 (ttp-170) REVERT: g 157 LEU cc_start: 0.8417 (mt) cc_final: 0.8206 (mt) REVERT: g 178 ASN cc_start: 0.6483 (m-40) cc_final: 0.6015 (t0) REVERT: g 192 ASP cc_start: 0.8366 (t70) cc_final: 0.7776 (t70) REVERT: g 194 ASP cc_start: 0.6465 (m-30) cc_final: 0.6073 (m-30) REVERT: g 205 ASP cc_start: 0.5823 (t0) cc_final: 0.5606 (m-30) REVERT: h 69 HIS cc_start: 0.7762 (m90) cc_final: 0.7536 (m90) REVERT: h 85 GLU cc_start: 0.8322 (tp30) cc_final: 0.7435 (tm-30) REVERT: h 89 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.7060 (ttmm) REVERT: h 132 ARG cc_start: 0.7681 (ttm170) cc_final: 0.7375 (ttt90) REVERT: h 135 LYS cc_start: 0.8147 (mptm) cc_final: 0.7799 (mmmt) REVERT: h 136 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7576 (ttm110) REVERT: h 147 LYS cc_start: 0.8058 (mmpt) cc_final: 0.7800 (mmmm) REVERT: i 69 GLU cc_start: 0.8512 (tp30) cc_final: 0.8093 (tp30) REVERT: i 73 ARG cc_start: 0.8182 (tpt-90) cc_final: 0.7507 (ttp-110) REVERT: j 26 LYS cc_start: 0.8934 (ttpm) cc_final: 0.8631 (ttmm) REVERT: j 52 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8576 (mtpt) REVERT: j 62 LYS cc_start: 0.8439 (mttt) cc_final: 0.8227 (mttt) REVERT: j 77 ASN cc_start: 0.8586 (t0) cc_final: 0.8331 (t0) REVERT: j 78 ASN cc_start: 0.8649 (t0) cc_final: 0.8021 (m-40) REVERT: j 130 SER cc_start: 0.8809 (t) cc_final: 0.8464 (t) REVERT: k 2 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7899 (mmm-85) REVERT: k 36 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7297 (mt) REVERT: k 90 MET cc_start: 0.7586 (ttp) cc_final: 0.7033 (ttt) REVERT: k 91 ARG cc_start: 0.8335 (mmm160) cc_final: 0.7953 (mmm-85) REVERT: l 4 ARG cc_start: 0.6146 (tpt170) cc_final: 0.5549 (tpm170) REVERT: l 58 GLU cc_start: 0.6848 (mp0) cc_final: 0.6422 (mt-10) REVERT: l 67 GLU cc_start: 0.7619 (tp30) cc_final: 0.7166 (tt0) REVERT: l 68 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.6134 (t0) REVERT: l 110 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8516 (mttm) REVERT: l 148 ASN cc_start: 0.8240 (m-40) cc_final: 0.7923 (m-40) REVERT: m 42 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8166 (tp30) REVERT: m 96 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8362 (ttm) REVERT: m 117 ARG cc_start: 0.8289 (ttp-170) cc_final: 0.7991 (mtm-85) REVERT: n 41 ARG cc_start: 0.6405 (mtp-110) cc_final: 0.5894 (mtp85) REVERT: n 119 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8012 (mtp85) REVERT: p 15 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6719 (mm-40) REVERT: p 34 ILE cc_start: 0.8340 (mm) cc_final: 0.8108 (mm) REVERT: p 68 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7563 (mt-10) REVERT: p 77 TYR cc_start: 0.9013 (m-80) cc_final: 0.8454 (m-80) REVERT: p 85 MET cc_start: 0.8011 (mtt) cc_final: 0.7609 (mtp) REVERT: p 98 ARG cc_start: 0.7062 (mtt-85) cc_final: 0.6765 (mtt90) REVERT: p 100 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7869 (mp) REVERT: p 101 ASN cc_start: 0.7552 (t0) cc_final: 0.7243 (t0) REVERT: q 10 LYS cc_start: 0.8371 (tttt) cc_final: 0.7966 (tmmt) REVERT: q 56 ARG cc_start: 0.8009 (ttt90) cc_final: 0.7677 (ttp80) REVERT: r 73 ILE cc_start: 0.8137 (mm) cc_final: 0.7895 (mt) REVERT: r 74 SER cc_start: 0.8756 (t) cc_final: 0.8433 (p) REVERT: r 92 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7619 (mtm180) REVERT: r 104 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8291 (p) REVERT: s 6 MET cc_start: 0.8272 (mmm) cc_final: 0.8046 (mmt) REVERT: s 90 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: s 92 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: s 96 LEU cc_start: 0.8912 (tp) cc_final: 0.8672 (tp) REVERT: t 10 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7746 (tttt) REVERT: t 14 GLU cc_start: 0.7346 (tt0) cc_final: 0.6887 (mp0) REVERT: t 58 ARG cc_start: 0.8523 (ttt180) cc_final: 0.8051 (ttt-90) REVERT: t 71 LYS cc_start: 0.8179 (tttt) cc_final: 0.7927 (tptt) REVERT: t 85 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7848 (mt) REVERT: u 24 SER cc_start: 0.8982 (t) cc_final: 0.8598 (p) REVERT: v 81 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5923 (mtpt) REVERT: x 44 MET cc_start: 0.7966 (mtp) cc_final: 0.7386 (ttm) REVERT: y 52 ASN cc_start: 0.8373 (m-40) cc_final: 0.8139 (m-40) REVERT: y 57 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7832 (mt) REVERT: z 17 ARG cc_start: 0.7172 (ttm110) cc_final: 0.6424 (mmm160) REVERT: z 21 ARG cc_start: 0.7067 (tpt170) cc_final: 0.6617 (mmm160) REVERT: z 25 LYS cc_start: 0.7452 (mmtt) cc_final: 0.7146 (mmtt) REVERT: z 33 ARG cc_start: 0.7645 (tmt170) cc_final: 0.7032 (mtt180) REVERT: z 34 ARG cc_start: 0.7164 (ttt-90) cc_final: 0.6661 (ttp-170) outliers start: 216 outliers final: 107 residues processed: 1274 average time/residue: 1.3573 time to fit residues: 2917.4332 Evaluate side-chains 1184 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1046 time to evaluate : 6.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 151 LYS Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 146 ASN Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 68 ASN Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 522 optimal weight: 7.9990 chunk 291 optimal weight: 7.9990 chunk 782 optimal weight: 10.0000 chunk 640 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 941 optimal weight: 9.9990 chunk 1017 optimal weight: 10.0000 chunk 838 optimal weight: 5.9990 chunk 933 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 755 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN E 127 ASN F 73 ASN J 128 ASN L 4 ASN N 9 GLN O 98 GLN O 100 HIS O 116 GLN Q 72 ASN R 18 GLN R 43 ASN S 15 GLN S 60 HIS V 12 GLN b 42 HIS d 6 GLN e 26 HIS f 13 ASN h 190 HIS i 36 GLN i 89 ASN k 55 HIS l 142 HIS o 58 ASN o 64 GLN x 14 HIS x 52 HIS y 21 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 158767 Z= 0.491 Angle : 0.773 15.799 237307 Z= 0.403 Chirality : 0.045 0.399 30211 Planarity : 0.007 0.149 12843 Dihedral : 23.374 179.841 79006 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 5.73 % Allowed : 16.16 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: -0.13 (0.11), residues: 5867 helix: 2.01 (0.11), residues: 2050 sheet: -1.21 (0.15), residues: 1079 loop : -1.25 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP T 80 HIS 0.011 0.002 HIS t 46 PHE 0.024 0.002 PHE G 29 TYR 0.024 0.002 TYR h 42 ARG 0.010 0.001 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1073 time to evaluate : 6.134 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: B 5 LYS cc_start: 0.8321 (tppt) cc_final: 0.7931 (tptm) REVERT: B 28 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7725 (mttt) REVERT: B 174 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8972 (mt) REVERT: B 183 LYS cc_start: 0.8373 (mttt) cc_final: 0.8038 (mtpt) REVERT: B 185 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8094 (tt0) REVERT: B 270 ARG cc_start: 0.8484 (mmm160) cc_final: 0.7727 (ttt-90) REVERT: B 271 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7848 (ptt-90) REVERT: C 1 MET cc_start: 0.6464 (ttt) cc_final: 0.6174 (tpt) REVERT: C 86 GLU cc_start: 0.8208 (pt0) cc_final: 0.7644 (mp0) REVERT: C 88 GLU cc_start: 0.7836 (mt-10) cc_final: 0.6882 (mp0) REVERT: D 40 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8085 (ttm170) REVERT: D 51 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8500 (mt-10) REVERT: D 69 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7542 (ptp-170) REVERT: D 123 LYS cc_start: 0.7804 (ptpp) cc_final: 0.7560 (mmmt) REVERT: D 136 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: D 184 ASP cc_start: 0.8344 (m-30) cc_final: 0.7839 (m-30) REVERT: D 198 GLU cc_start: 0.8236 (tt0) cc_final: 0.7963 (mm-30) REVERT: E 21 ASN cc_start: 0.7481 (t0) cc_final: 0.7129 (m110) REVERT: E 42 GLU cc_start: 0.7047 (pm20) cc_final: 0.6837 (mp0) REVERT: E 134 GLU cc_start: 0.8450 (tt0) cc_final: 0.8065 (tt0) REVERT: E 161 LYS cc_start: 0.7789 (mttt) cc_final: 0.7503 (mmtp) REVERT: F 86 LYS cc_start: 0.7929 (mttm) cc_final: 0.7452 (ttpp) REVERT: F 94 TYR cc_start: 0.8800 (m-80) cc_final: 0.8595 (m-80) REVERT: F 95 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6715 (ppt170) REVERT: F 157 TYR cc_start: 0.8273 (m-80) cc_final: 0.7972 (m-80) REVERT: G 7 ASP cc_start: 0.7921 (t70) cc_final: 0.7398 (t0) REVERT: G 28 ASN cc_start: 0.8441 (m-40) cc_final: 0.8205 (m-40) REVERT: I 48 ILE cc_start: 0.1811 (OUTLIER) cc_final: 0.1498 (tt) REVERT: I 116 MET cc_start: 0.0513 (mmp) cc_final: 0.0149 (tpp) REVERT: I 124 MET cc_start: 0.1440 (OUTLIER) cc_final: 0.0458 (mmp) REVERT: J 106 LYS cc_start: 0.8862 (tttp) cc_final: 0.8558 (ttmt) REVERT: K 53 LYS cc_start: 0.7935 (tmmt) cc_final: 0.7420 (mttm) REVERT: K 73 ASP cc_start: 0.8933 (p0) cc_final: 0.8686 (p0) REVERT: K 104 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9144 (m) REVERT: K 106 GLU cc_start: 0.8246 (mp0) cc_final: 0.7668 (mp0) REVERT: K 121 GLU cc_start: 0.8241 (tt0) cc_final: 0.7846 (tt0) REVERT: M 16 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8077 (mmt90) REVERT: M 73 ILE cc_start: 0.9497 (mm) cc_final: 0.9272 (mm) REVERT: M 84 LYS cc_start: 0.8535 (mptp) cc_final: 0.7955 (mtmm) REVERT: M 127 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8058 (mtpp) REVERT: N 18 GLN cc_start: 0.8701 (tt0) cc_final: 0.8439 (tt0) REVERT: O 13 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8056 (tpp80) REVERT: O 16 ARG cc_start: 0.7876 (mmm160) cc_final: 0.7567 (mmt-90) REVERT: P 38 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8021 (mttt) REVERT: P 82 ASP cc_start: 0.8599 (t70) cc_final: 0.8212 (t0) REVERT: P 102 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: P 103 ARG cc_start: 0.8286 (mtt90) cc_final: 0.8035 (mtt-85) REVERT: P 111 LYS cc_start: 0.8392 (pttp) cc_final: 0.8127 (ptmm) REVERT: Q 78 LYS cc_start: 0.8985 (mttm) cc_final: 0.8660 (mtmm) REVERT: R 16 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7911 (mt-10) REVERT: R 29 THR cc_start: 0.8403 (p) cc_final: 0.7723 (m) REVERT: R 31 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8102 (mm-30) REVERT: R 43 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8094 (t0) REVERT: R 60 LYS cc_start: 0.8262 (mttt) cc_final: 0.7786 (mmtp) REVERT: S 81 SER cc_start: 0.9017 (m) cc_final: 0.8786 (p) REVERT: S 95 ARG cc_start: 0.8811 (ttp-170) cc_final: 0.8228 (ttm-80) REVERT: T 1 MET cc_start: 0.6179 (tpt) cc_final: 0.5444 (tpt) REVERT: T 56 GLU cc_start: 0.8479 (tt0) cc_final: 0.8117 (tp30) REVERT: T 91 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6981 (mm-40) REVERT: U 26 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7607 (mmtt) REVERT: U 27 ASN cc_start: 0.8529 (p0) cc_final: 0.8257 (p0) REVERT: U 101 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: V 71 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7793 (mmmt) REVERT: W 66 LYS cc_start: 0.8318 (mttt) cc_final: 0.7974 (mtmt) REVERT: W 68 LYS cc_start: 0.8463 (tptt) cc_final: 0.7870 (tttt) REVERT: Z 3 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7620 (mmtt) REVERT: Z 11 ARG cc_start: 0.8921 (mtt-85) cc_final: 0.8514 (mtt-85) REVERT: Z 25 LEU cc_start: 0.9126 (tm) cc_final: 0.8846 (tp) REVERT: Z 37 GLU cc_start: 0.8712 (tp30) cc_final: 0.8462 (tp30) REVERT: a 39 LYS cc_start: 0.8057 (mttt) cc_final: 0.7833 (mtpt) REVERT: c 49 TYR cc_start: 0.9302 (m-80) cc_final: 0.8825 (m-80) REVERT: e 61 CYS cc_start: 0.8996 (m) cc_final: 0.8771 (m) REVERT: f 15 LYS cc_start: 0.8367 (mttt) cc_final: 0.8019 (mtpp) REVERT: g 9 MET cc_start: 0.3709 (mtm) cc_final: 0.3450 (mtt) REVERT: g 27 MET cc_start: 0.8224 (mmm) cc_final: 0.7630 (mmm) REVERT: g 64 LYS cc_start: 0.6164 (mtmm) cc_final: 0.5862 (mmmt) REVERT: g 137 ARG cc_start: 0.5369 (mmt-90) cc_final: 0.4958 (ttp-170) REVERT: g 183 VAL cc_start: 0.8033 (t) cc_final: 0.7770 (p) REVERT: g 192 ASP cc_start: 0.8120 (t70) cc_final: 0.7469 (t70) REVERT: g 194 ASP cc_start: 0.6490 (m-30) cc_final: 0.6088 (m-30) REVERT: g 205 ASP cc_start: 0.5549 (t0) cc_final: 0.5257 (m-30) REVERT: h 79 LYS cc_start: 0.5706 (mptt) cc_final: 0.5498 (mttm) REVERT: h 89 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6753 (ptpp) REVERT: h 132 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7502 (ttt90) REVERT: h 135 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7826 (mmmt) REVERT: i 69 GLU cc_start: 0.8631 (tp30) cc_final: 0.8048 (tp30) REVERT: i 73 ARG cc_start: 0.8150 (tpt-90) cc_final: 0.7399 (ttp-110) REVERT: i 185 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7935 (mtpp) REVERT: j 10 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5438 (pm20) REVERT: j 15 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8786 (tp) REVERT: j 26 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8743 (ttmm) REVERT: j 52 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8282 (mtpp) REVERT: j 62 LYS cc_start: 0.8469 (mttt) cc_final: 0.8228 (mtmt) REVERT: j 68 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7466 (mtt180) REVERT: j 78 ASN cc_start: 0.8701 (t0) cc_final: 0.8005 (m-40) REVERT: j 152 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7832 (mmp) REVERT: k 1 MET cc_start: 0.8053 (mpt) cc_final: 0.7638 (mpt) REVERT: k 2 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8199 (mtt180) REVERT: k 14 GLN cc_start: 0.8229 (mp10) cc_final: 0.7905 (mp10) REVERT: k 86 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8235 (mtt-85) REVERT: k 90 MET cc_start: 0.7672 (ttp) cc_final: 0.7125 (mtp) REVERT: k 91 ARG cc_start: 0.8339 (mmm160) cc_final: 0.8086 (mmm-85) REVERT: l 4 ARG cc_start: 0.5907 (tpt170) cc_final: 0.5391 (tpt170) REVERT: l 56 LYS cc_start: 0.7089 (mttt) cc_final: 0.6557 (mmtt) REVERT: l 67 GLU cc_start: 0.7861 (tp30) cc_final: 0.7609 (mt-10) REVERT: l 68 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.6466 (t0) REVERT: l 106 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7539 (pt0) REVERT: l 110 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8441 (mttm) REVERT: l 148 ASN cc_start: 0.8148 (m-40) cc_final: 0.7842 (m-40) REVERT: m 2 SER cc_start: 0.8478 (m) cc_final: 0.8243 (t) REVERT: m 52 GLU cc_start: 0.6587 (tt0) cc_final: 0.6382 (mt-10) REVERT: m 66 PHE cc_start: 0.8838 (t80) cc_final: 0.8449 (t80) REVERT: m 96 MET cc_start: 0.8943 (mtt) cc_final: 0.8579 (ttm) REVERT: m 117 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8051 (mtm-85) REVERT: n 87 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6682 (mp) REVERT: n 119 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8169 (mtp85) REVERT: o 9 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7324 (mtp85) REVERT: o 64 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: o 99 GLN cc_start: 0.6668 (tt0) cc_final: 0.6461 (mp10) REVERT: p 15 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6622 (mm-40) REVERT: p 34 ILE cc_start: 0.8540 (mm) cc_final: 0.8315 (mm) REVERT: p 77 TYR cc_start: 0.9018 (m-80) cc_final: 0.8560 (m-80) REVERT: p 85 MET cc_start: 0.8090 (mtt) cc_final: 0.7721 (mtp) REVERT: p 100 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7879 (mp) REVERT: p 106 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7586 (ttp-170) REVERT: q 10 LYS cc_start: 0.8250 (tttt) cc_final: 0.7950 (tmmt) REVERT: q 12 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.6494 (mtt90) REVERT: q 56 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7712 (ttp80) REVERT: r 74 SER cc_start: 0.8609 (t) cc_final: 0.8208 (p) REVERT: s 6 MET cc_start: 0.8357 (mmm) cc_final: 0.8017 (mmt) REVERT: s 92 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: s 96 LEU cc_start: 0.8867 (tp) cc_final: 0.8631 (tp) REVERT: t 10 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7776 (tttt) REVERT: t 14 GLU cc_start: 0.7271 (tt0) cc_final: 0.6731 (mp0) REVERT: t 17 ARG cc_start: 0.7100 (ptt-90) cc_final: 0.6716 (ptt180) REVERT: t 37 ASN cc_start: 0.8679 (m-40) cc_final: 0.8298 (m-40) REVERT: t 58 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8174 (ttt-90) REVERT: t 71 LYS cc_start: 0.8263 (tttt) cc_final: 0.7921 (tptt) REVERT: t 85 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8053 (mt) REVERT: u 24 SER cc_start: 0.8890 (t) cc_final: 0.8512 (p) REVERT: w 43 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7582 (ptp-170) REVERT: x 63 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7621 (p) REVERT: x 70 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7781 (mtpt) REVERT: y 57 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8089 (mt) REVERT: y 74 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8250 (ttp-110) REVERT: z 17 ARG cc_start: 0.7510 (ttm110) cc_final: 0.6569 (mmm160) REVERT: z 21 ARG cc_start: 0.7057 (tpt170) cc_final: 0.6617 (mmm160) REVERT: z 25 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7376 (mmtt) REVERT: z 33 ARG cc_start: 0.7774 (tmt170) cc_final: 0.7171 (mtt180) REVERT: z 34 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.7131 (ttt180) outliers start: 279 outliers final: 173 residues processed: 1253 average time/residue: 1.3820 time to fit residues: 2933.8469 Evaluate side-chains 1241 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1032 time to evaluate : 6.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 15 SER Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 12 SER Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 151 LYS Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 111 MET Chi-restraints excluded: chain j residue 146 ASN Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain j residue 152 MET Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 68 GLN Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 86 ARG Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 68 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 64 GLN Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain t residue 10 LYS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 12 ILE Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 930 optimal weight: 8.9990 chunk 707 optimal weight: 0.0030 chunk 488 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 632 optimal weight: 0.7980 chunk 944 optimal weight: 10.0000 chunk 1000 optimal weight: 3.9990 chunk 493 optimal weight: 0.9990 chunk 895 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN D 115 GLN D 165 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN L 38 GLN O 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 43 ASN V 12 GLN V 75 GLN X 17 ASN X 34 HIS h 185 ASN h 190 HIS i 136 GLN k 55 HIS l 142 HIS ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 158767 Z= 0.154 Angle : 0.609 15.272 237307 Z= 0.328 Chirality : 0.034 0.401 30211 Planarity : 0.006 0.124 12843 Dihedral : 23.342 179.975 78984 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 3.78 % Allowed : 18.81 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.21 (0.11), residues: 5867 helix: 2.25 (0.11), residues: 2058 sheet: -0.95 (0.15), residues: 1101 loop : -1.07 (0.11), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP h 201 HIS 0.005 0.001 HIS C 67 PHE 0.021 0.001 PHE k 8 TYR 0.021 0.001 TYR R 2 ARG 0.009 0.000 ARG j 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1098 time to evaluate : 6.280 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: B 5 LYS cc_start: 0.8213 (tppt) cc_final: 0.7893 (tptm) REVERT: B 28 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7675 (mttt) REVERT: B 70 ASN cc_start: 0.8408 (m-40) cc_final: 0.8206 (p0) REVERT: B 82 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 183 LYS cc_start: 0.8197 (mttt) cc_final: 0.7878 (mtpt) REVERT: B 185 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8121 (tt0) REVERT: B 270 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7629 (ttt-90) REVERT: C 1 MET cc_start: 0.6420 (ttt) cc_final: 0.6095 (tpt) REVERT: C 88 GLU cc_start: 0.7862 (mt-10) cc_final: 0.6784 (mp0) REVERT: C 106 LYS cc_start: 0.8971 (mttt) cc_final: 0.8660 (mttp) REVERT: D 35 TYR cc_start: 0.8900 (t80) cc_final: 0.8576 (t80) REVERT: D 51 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8552 (mt-10) REVERT: D 69 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8251 (ptp-170) REVERT: D 163 ASN cc_start: 0.9206 (t0) cc_final: 0.8548 (t0) REVERT: D 184 ASP cc_start: 0.8289 (m-30) cc_final: 0.7796 (m-30) REVERT: D 198 GLU cc_start: 0.8274 (tt0) cc_final: 0.7960 (mm-30) REVERT: E 133 ARG cc_start: 0.8034 (mpt90) cc_final: 0.7595 (mtm-85) REVERT: E 134 GLU cc_start: 0.8369 (tt0) cc_final: 0.8008 (tt0) REVERT: E 161 LYS cc_start: 0.7774 (mttt) cc_final: 0.7512 (mmtp) REVERT: F 86 LYS cc_start: 0.7915 (mttm) cc_final: 0.7436 (ttpp) REVERT: F 95 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6745 (ppt170) REVERT: F 157 TYR cc_start: 0.8065 (m-80) cc_final: 0.7843 (m-80) REVERT: F 176 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5263 (mmtt) REVERT: G 6 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7165 (tp) REVERT: G 7 ASP cc_start: 0.7843 (t70) cc_final: 0.7408 (t0) REVERT: G 28 ASN cc_start: 0.8361 (m-40) cc_final: 0.8063 (m-40) REVERT: I 48 ILE cc_start: 0.1570 (OUTLIER) cc_final: 0.1289 (tt) REVERT: I 116 MET cc_start: 0.0581 (mmp) cc_final: 0.0008 (ttp) REVERT: J 106 LYS cc_start: 0.8750 (tttp) cc_final: 0.8470 (ttmt) REVERT: K 53 LYS cc_start: 0.7930 (tmmt) cc_final: 0.7423 (mttm) REVERT: K 73 ASP cc_start: 0.8818 (p0) cc_final: 0.8570 (p0) REVERT: K 89 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8576 (t0) REVERT: K 98 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7950 (ttp-170) REVERT: K 104 THR cc_start: 0.9241 (p) cc_final: 0.9041 (m) REVERT: K 106 GLU cc_start: 0.8212 (mp0) cc_final: 0.7642 (mp0) REVERT: K 121 GLU cc_start: 0.8223 (tt0) cc_final: 0.7894 (tt0) REVERT: M 73 ILE cc_start: 0.9477 (mm) cc_final: 0.9237 (mm) REVERT: M 84 LYS cc_start: 0.8592 (mptp) cc_final: 0.7975 (mppt) REVERT: M 127 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8070 (mtpp) REVERT: N 18 GLN cc_start: 0.8544 (tt0) cc_final: 0.8270 (tt0) REVERT: N 32 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8475 (mp0) REVERT: O 13 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8046 (tpp80) REVERT: O 16 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7620 (mmt-90) REVERT: P 29 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8199 (mmmt) REVERT: P 38 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8066 (mttt) REVERT: P 97 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9141 (mt) REVERT: P 103 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8012 (mtt180) REVERT: P 111 LYS cc_start: 0.8397 (pttp) cc_final: 0.8151 (ptmm) REVERT: Q 78 LYS cc_start: 0.8926 (mttm) cc_final: 0.8629 (mtmm) REVERT: R 16 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7743 (mm-30) REVERT: R 31 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8083 (mm-30) REVERT: R 33 VAL cc_start: 0.8807 (m) cc_final: 0.8442 (p) REVERT: R 60 LYS cc_start: 0.8335 (mttt) cc_final: 0.7825 (mmtp) REVERT: S 95 ARG cc_start: 0.8745 (ttp-170) cc_final: 0.8212 (ttm-80) REVERT: T 1 MET cc_start: 0.6289 (tpt) cc_final: 0.5556 (tpt) REVERT: T 56 GLU cc_start: 0.8347 (tt0) cc_final: 0.8011 (tp30) REVERT: U 26 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7599 (mmtt) REVERT: U 101 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: V 71 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7799 (mmmt) REVERT: V 75 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8241 (tp40) REVERT: W 14 ARG cc_start: 0.9105 (mtm-85) cc_final: 0.8798 (mtm-85) REVERT: W 44 LYS cc_start: 0.8603 (mttt) cc_final: 0.8367 (mtpt) REVERT: W 78 LYS cc_start: 0.8766 (mttt) cc_final: 0.8550 (mttt) REVERT: X 43 GLU cc_start: 0.7127 (tt0) cc_final: 0.6692 (tt0) REVERT: Z 11 ARG cc_start: 0.8915 (mtt-85) cc_final: 0.8554 (mtt-85) REVERT: Z 37 GLU cc_start: 0.8629 (tp30) cc_final: 0.8034 (mt-10) REVERT: a 1 MET cc_start: 0.8168 (mtp) cc_final: 0.7914 (mtp) REVERT: a 39 LYS cc_start: 0.8108 (mttt) cc_final: 0.7847 (mtpt) REVERT: b 40 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8469 (mmt180) REVERT: c 9 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8449 (pt) REVERT: c 17 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7717 (p) REVERT: g 9 MET cc_start: 0.3577 (mtm) cc_final: 0.3308 (mtm) REVERT: g 27 MET cc_start: 0.8239 (mmm) cc_final: 0.7993 (mmm) REVERT: g 64 LYS cc_start: 0.6211 (mtmm) cc_final: 0.5852 (mmmt) REVERT: g 100 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: g 137 ARG cc_start: 0.5347 (mmt-90) cc_final: 0.4933 (ttp-170) REVERT: g 192 ASP cc_start: 0.8132 (t70) cc_final: 0.7559 (t70) REVERT: g 194 ASP cc_start: 0.6384 (m-30) cc_final: 0.6044 (m-30) REVERT: h 69 HIS cc_start: 0.7617 (m-70) cc_final: 0.7139 (m90) REVERT: h 79 LYS cc_start: 0.5730 (mptt) cc_final: 0.5504 (mttm) REVERT: h 89 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6705 (ptpp) REVERT: h 132 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7382 (ttt90) REVERT: h 135 LYS cc_start: 0.8326 (mptm) cc_final: 0.7887 (mmmt) REVERT: h 136 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7665 (ttm110) REVERT: i 69 GLU cc_start: 0.8542 (tp30) cc_final: 0.8008 (tp30) REVERT: i 73 ARG cc_start: 0.8133 (tpt-90) cc_final: 0.7432 (ttp-110) REVERT: i 185 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7963 (mtpp) REVERT: j 10 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5434 (pm20) REVERT: j 26 LYS cc_start: 0.8964 (ttpm) cc_final: 0.8670 (ttmm) REVERT: j 52 LYS cc_start: 0.8765 (ttpp) cc_final: 0.8557 (mtpt) REVERT: j 62 LYS cc_start: 0.8457 (mttt) cc_final: 0.8151 (mttp) REVERT: j 68 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7596 (mtt180) REVERT: k 1 MET cc_start: 0.7970 (mpt) cc_final: 0.7469 (mpt) REVERT: k 2 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8185 (mtt180) REVERT: k 14 GLN cc_start: 0.8184 (mp10) cc_final: 0.7837 (mp10) REVERT: k 36 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7096 (mt) REVERT: k 79 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6328 (ptp-110) REVERT: k 90 MET cc_start: 0.7316 (ttp) cc_final: 0.6702 (ttt) REVERT: k 91 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7817 (mmm-85) REVERT: l 4 ARG cc_start: 0.5908 (tpt170) cc_final: 0.5330 (tpt170) REVERT: l 56 LYS cc_start: 0.6963 (mttt) cc_final: 0.6414 (mmtt) REVERT: l 67 GLU cc_start: 0.7664 (tp30) cc_final: 0.7352 (mt-10) REVERT: l 68 ASN cc_start: 0.7549 (t0) cc_final: 0.6475 (t0) REVERT: l 74 GLU cc_start: 0.6898 (pt0) cc_final: 0.6454 (tt0) REVERT: l 106 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7482 (pt0) REVERT: l 110 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8264 (mttm) REVERT: l 148 ASN cc_start: 0.8071 (m-40) cc_final: 0.7761 (m-40) REVERT: m 66 PHE cc_start: 0.8853 (t80) cc_final: 0.8568 (t80) REVERT: m 69 LYS cc_start: 0.8104 (ptpp) cc_final: 0.7757 (mtpp) REVERT: m 96 MET cc_start: 0.8811 (mtt) cc_final: 0.8445 (ttm) REVERT: n 119 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8144 (mtp85) REVERT: o 9 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7149 (mtp85) REVERT: o 64 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7952 (mm-40) REVERT: p 15 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6482 (mm-40) REVERT: p 34 ILE cc_start: 0.8475 (mm) cc_final: 0.8227 (mm) REVERT: p 56 ARG cc_start: 0.7963 (mpt-90) cc_final: 0.6893 (mtp-110) REVERT: p 77 TYR cc_start: 0.8946 (m-80) cc_final: 0.8463 (m-80) REVERT: p 85 MET cc_start: 0.8000 (mtt) cc_final: 0.7657 (mtp) REVERT: p 100 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (mp) REVERT: p 106 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7510 (ttp-170) REVERT: q 10 LYS cc_start: 0.8265 (tttt) cc_final: 0.7980 (tmmt) REVERT: q 56 ARG cc_start: 0.8066 (ttt90) cc_final: 0.7797 (ttm110) REVERT: q 75 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7610 (pt0) REVERT: r 74 SER cc_start: 0.8641 (t) cc_final: 0.8252 (p) REVERT: r 75 MET cc_start: 0.7836 (mtp) cc_final: 0.7605 (mtp) REVERT: r 92 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7309 (mtm180) REVERT: t 17 ARG cc_start: 0.7017 (ptt-90) cc_final: 0.6553 (ptt180) REVERT: t 37 ASN cc_start: 0.8575 (m-40) cc_final: 0.8176 (m-40) REVERT: t 58 ARG cc_start: 0.8443 (ttt180) cc_final: 0.7925 (ttt-90) REVERT: t 71 LYS cc_start: 0.8221 (tttt) cc_final: 0.7860 (tptt) REVERT: t 85 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7963 (mt) REVERT: u 1 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.5738 (pp-130) REVERT: u 19 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8060 (t) REVERT: u 24 SER cc_start: 0.8826 (t) cc_final: 0.8508 (p) REVERT: u 34 GLU cc_start: 0.8785 (tt0) cc_final: 0.8584 (tt0) REVERT: x 63 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7497 (p) REVERT: x 70 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7775 (mtpt) REVERT: z 17 ARG cc_start: 0.7486 (ttm110) cc_final: 0.6603 (mmm160) REVERT: z 21 ARG cc_start: 0.6956 (tpt170) cc_final: 0.6473 (mmm160) REVERT: z 25 LYS cc_start: 0.7288 (mmtt) cc_final: 0.7002 (mmtm) REVERT: z 33 ARG cc_start: 0.7773 (tmt170) cc_final: 0.7179 (mtt180) REVERT: z 34 ARG cc_start: 0.7213 (ttt-90) cc_final: 0.6934 (ttt180) outliers start: 184 outliers final: 118 residues processed: 1216 average time/residue: 1.4019 time to fit residues: 2877.2847 Evaluate side-chains 1191 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1045 time to evaluate : 6.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 124 MET Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 151 LYS Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 146 ASN Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 79 ARG Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 64 GLN Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 37 ARG Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 39 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 833 optimal weight: 7.9990 chunk 567 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 744 optimal weight: 9.9990 chunk 412 optimal weight: 10.0000 chunk 853 optimal weight: 10.0000 chunk 691 optimal weight: 0.0980 chunk 1 optimal weight: 6.9990 chunk 510 optimal weight: 0.8980 chunk 897 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN D 115 GLN E 127 ASN F 73 ASN L 38 GLN O 43 ASN O 98 GLN O 100 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN S 9 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN W 57 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS h 190 HIS i 74 ASN i 89 ASN i 136 GLN ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 ASN o 64 GLN p 101 ASN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 158767 Z= 0.412 Angle : 0.705 15.662 237307 Z= 0.369 Chirality : 0.041 0.401 30211 Planarity : 0.007 0.144 12843 Dihedral : 23.247 179.304 78957 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 5.07 % Allowed : 19.09 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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 (0.11), residues: 5867 helix: 1.98 (0.11), residues: 2049 sheet: -0.92 (0.15), residues: 1099 loop : -1.05 (0.11), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP h 201 HIS 0.008 0.001 HIS e 24 PHE 0.020 0.002 PHE G 29 TYR 0.023 0.002 TYR R 2 ARG 0.008 0.001 ARG j 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1059 time to evaluate : 6.215 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: B 5 LYS cc_start: 0.8291 (tppt) cc_final: 0.7896 (tptm) REVERT: B 28 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7774 (mttt) REVERT: B 82 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8379 (mt-10) REVERT: B 183 LYS cc_start: 0.8297 (mttt) cc_final: 0.7939 (mtpt) REVERT: B 185 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8132 (tt0) REVERT: B 270 ARG cc_start: 0.8538 (mmm160) cc_final: 0.7807 (ttt-90) REVERT: B 271 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7831 (ptt-90) REVERT: C 1 MET cc_start: 0.6551 (ttt) cc_final: 0.6210 (ttm) REVERT: C 88 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6769 (mp0) REVERT: C 106 LYS cc_start: 0.9025 (mttt) cc_final: 0.8698 (mttp) REVERT: D 40 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8140 (ttt180) REVERT: D 51 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8516 (mt-10) REVERT: D 69 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7450 (ptp-170) REVERT: D 111 GLU cc_start: 0.8639 (tp30) cc_final: 0.8377 (tp30) REVERT: D 163 ASN cc_start: 0.9296 (t0) cc_final: 0.8639 (t0) REVERT: D 184 ASP cc_start: 0.8273 (m-30) cc_final: 0.7732 (m-30) REVERT: D 198 GLU cc_start: 0.8281 (tt0) cc_final: 0.7979 (mm-30) REVERT: E 21 ASN cc_start: 0.7444 (t0) cc_final: 0.7145 (m110) REVERT: E 95 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8135 (mmt180) REVERT: E 133 ARG cc_start: 0.8202 (mpt90) cc_final: 0.7843 (mpt90) REVERT: E 134 GLU cc_start: 0.8373 (tt0) cc_final: 0.8017 (tt0) REVERT: E 161 LYS cc_start: 0.7780 (mttt) cc_final: 0.7486 (mmtp) REVERT: E 164 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8174 (pm20) REVERT: F 86 LYS cc_start: 0.7909 (mttm) cc_final: 0.7425 (ttpp) REVERT: F 95 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6754 (ppt170) REVERT: F 176 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.5537 (mmtt) REVERT: G 7 ASP cc_start: 0.7891 (t70) cc_final: 0.7373 (t0) REVERT: G 28 ASN cc_start: 0.8362 (m-40) cc_final: 0.8104 (m-40) REVERT: I 48 ILE cc_start: 0.1472 (OUTLIER) cc_final: 0.1177 (tt) REVERT: I 116 MET cc_start: 0.0456 (mmp) cc_final: -0.0256 (ptm) REVERT: J 106 LYS cc_start: 0.8858 (tttp) cc_final: 0.8560 (ttmt) REVERT: K 53 LYS cc_start: 0.7942 (tmmt) cc_final: 0.7447 (mttm) REVERT: K 73 ASP cc_start: 0.8910 (p0) cc_final: 0.8659 (p0) REVERT: K 106 GLU cc_start: 0.8232 (mp0) cc_final: 0.7524 (mp0) REVERT: K 121 GLU cc_start: 0.8291 (tt0) cc_final: 0.7937 (tt0) REVERT: L 78 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7414 (mtm180) REVERT: M 16 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8170 (mmt90) REVERT: M 51 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7358 (mtp180) REVERT: M 73 ILE cc_start: 0.9485 (mm) cc_final: 0.9259 (mm) REVERT: M 84 LYS cc_start: 0.8595 (mptp) cc_final: 0.7996 (mtmm) REVERT: M 127 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8057 (mtpp) REVERT: M 136 MET cc_start: 0.6710 (ttm) cc_final: 0.6298 (ttm) REVERT: N 18 GLN cc_start: 0.8659 (tt0) cc_final: 0.8426 (tt0) REVERT: O 13 ARG cc_start: 0.8556 (ttt-90) cc_final: 0.8089 (tpp80) REVERT: O 16 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7585 (mmt-90) REVERT: P 38 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8071 (mttt) REVERT: P 82 ASP cc_start: 0.8550 (t70) cc_final: 0.8110 (t0) REVERT: P 97 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9200 (mt) REVERT: P 102 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: P 103 ARG cc_start: 0.8257 (mtt90) cc_final: 0.7971 (mtt-85) REVERT: P 111 LYS cc_start: 0.8405 (pttp) cc_final: 0.8145 (ptmm) REVERT: R 16 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7872 (mm-30) REVERT: R 31 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8118 (mm-30) REVERT: R 60 LYS cc_start: 0.8350 (mttt) cc_final: 0.7684 (mmtp) REVERT: S 95 ARG cc_start: 0.8765 (ttp-170) cc_final: 0.8192 (ttm-80) REVERT: T 1 MET cc_start: 0.6644 (tpt) cc_final: 0.5610 (tpt) REVERT: T 56 GLU cc_start: 0.8453 (tt0) cc_final: 0.8100 (tp30) REVERT: U 26 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7393 (mmtt) REVERT: U 101 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: V 71 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7805 (mmmt) REVERT: W 44 LYS cc_start: 0.8709 (mttt) cc_final: 0.8432 (mtpt) REVERT: W 66 LYS cc_start: 0.8311 (mttt) cc_final: 0.7935 (mtpt) REVERT: W 68 LYS cc_start: 0.8398 (tptt) cc_final: 0.7874 (tttt) REVERT: Z 11 ARG cc_start: 0.8939 (mtt-85) cc_final: 0.8569 (mtt-85) REVERT: Z 37 GLU cc_start: 0.8601 (tp30) cc_final: 0.8348 (tp30) REVERT: a 1 MET cc_start: 0.8318 (mtp) cc_final: 0.8104 (mtp) REVERT: a 39 LYS cc_start: 0.8084 (mttt) cc_final: 0.7816 (mtpt) REVERT: f 15 LYS cc_start: 0.8342 (mttt) cc_final: 0.7997 (mtpp) REVERT: g 9 MET cc_start: 0.3355 (mtm) cc_final: 0.3111 (mtm) REVERT: g 27 MET cc_start: 0.8242 (mmm) cc_final: 0.7989 (mmm) REVERT: g 64 LYS cc_start: 0.6275 (mtmm) cc_final: 0.5895 (mmmt) REVERT: g 100 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7466 (mtp) REVERT: g 117 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4793 (mp) REVERT: g 137 ARG cc_start: 0.5390 (mmt-90) cc_final: 0.4859 (ttp-170) REVERT: g 169 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7531 (mp0) REVERT: g 178 ASN cc_start: 0.6270 (m-40) cc_final: 0.5770 (t0) REVERT: g 183 VAL cc_start: 0.7882 (t) cc_final: 0.7586 (p) REVERT: g 192 ASP cc_start: 0.8108 (t70) cc_final: 0.7524 (t70) REVERT: g 194 ASP cc_start: 0.6371 (m-30) cc_final: 0.6019 (m-30) REVERT: h 89 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6768 (ptpp) REVERT: h 132 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7505 (ttt90) REVERT: h 135 LYS cc_start: 0.8371 (mptm) cc_final: 0.7825 (mmtp) REVERT: h 172 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6465 (ptt90) REVERT: i 73 ARG cc_start: 0.8092 (tpt-90) cc_final: 0.7410 (ttp-110) REVERT: i 185 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8043 (mtpp) REVERT: j 10 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5631 (pm20) REVERT: j 13 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7060 (mt-10) REVERT: j 26 LYS cc_start: 0.8987 (ttpm) cc_final: 0.8699 (ttmm) REVERT: j 52 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8554 (mtpp) REVERT: j 62 LYS cc_start: 0.8473 (mttt) cc_final: 0.8148 (mttp) REVERT: j 68 ARG cc_start: 0.7926 (mtt90) cc_final: 0.7432 (mtt180) REVERT: j 71 MET cc_start: 0.7829 (mmt) cc_final: 0.7423 (mmt) REVERT: k 1 MET cc_start: 0.7935 (mpt) cc_final: 0.7397 (mpt) REVERT: k 2 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8236 (mtt180) REVERT: k 14 GLN cc_start: 0.8212 (mp10) cc_final: 0.7897 (mp10) REVERT: k 90 MET cc_start: 0.7479 (ttp) cc_final: 0.6983 (mtp) REVERT: k 91 ARG cc_start: 0.8243 (mmm160) cc_final: 0.8024 (mmm-85) REVERT: l 4 ARG cc_start: 0.5700 (tpt170) cc_final: 0.5104 (tpt170) REVERT: l 56 LYS cc_start: 0.7015 (mttt) cc_final: 0.6492 (mmtt) REVERT: l 67 GLU cc_start: 0.7863 (tp30) cc_final: 0.7534 (mt-10) REVERT: l 68 ASN cc_start: 0.7697 (t0) cc_final: 0.6445 (t0) REVERT: l 106 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7555 (pt0) REVERT: l 110 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8502 (mttm) REVERT: l 148 ASN cc_start: 0.8133 (m-40) cc_final: 0.7822 (m-40) REVERT: m 66 PHE cc_start: 0.8865 (t80) cc_final: 0.8566 (t80) REVERT: m 69 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7833 (mtpp) REVERT: m 88 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7421 (mtm-85) REVERT: m 94 LYS cc_start: 0.8428 (mttm) cc_final: 0.8060 (mtmm) REVERT: m 96 MET cc_start: 0.8869 (mtt) cc_final: 0.8498 (ttm) REVERT: n 119 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8171 (mtp85) REVERT: o 9 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7304 (mtp85) REVERT: p 15 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6566 (mm-40) REVERT: p 34 ILE cc_start: 0.8491 (mm) cc_final: 0.8261 (mm) REVERT: p 77 TYR cc_start: 0.8989 (m-80) cc_final: 0.8529 (m-80) REVERT: p 85 MET cc_start: 0.8076 (mtt) cc_final: 0.7747 (mtp) REVERT: p 100 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7826 (mp) REVERT: p 106 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7498 (ttp-170) REVERT: q 10 LYS cc_start: 0.8265 (tttt) cc_final: 0.7989 (tmmt) REVERT: q 56 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7785 (ttp80) REVERT: q 94 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7840 (mtt-85) REVERT: r 74 SER cc_start: 0.8598 (t) cc_final: 0.8189 (p) REVERT: r 75 MET cc_start: 0.7749 (mtp) cc_final: 0.7509 (mtp) REVERT: s 90 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7543 (ttm110) REVERT: t 17 ARG cc_start: 0.7011 (ptt-90) cc_final: 0.6617 (ptm-80) REVERT: t 37 ASN cc_start: 0.8594 (m-40) cc_final: 0.8162 (m-40) REVERT: t 58 ARG cc_start: 0.8596 (ttt180) cc_final: 0.8078 (ttt-90) REVERT: t 71 LYS cc_start: 0.8276 (tttt) cc_final: 0.7889 (tptt) REVERT: u 24 SER cc_start: 0.8919 (t) cc_final: 0.8568 (p) REVERT: x 63 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7656 (p) REVERT: x 70 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7738 (mtpt) REVERT: y 57 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8108 (mt) REVERT: z 17 ARG cc_start: 0.7525 (ttm110) cc_final: 0.6649 (mmm160) REVERT: z 21 ARG cc_start: 0.6978 (tpt170) cc_final: 0.6506 (mmm160) REVERT: z 25 LYS cc_start: 0.7467 (mmtt) cc_final: 0.7204 (mmtt) REVERT: z 33 ARG cc_start: 0.7803 (tmt170) cc_final: 0.7158 (mtt180) REVERT: z 34 ARG cc_start: 0.7354 (ttt-90) cc_final: 0.7096 (ttt180) REVERT: z 55 ARG cc_start: 0.6777 (mtm180) cc_final: 0.6570 (mtm180) outliers start: 247 outliers final: 173 residues processed: 1220 average time/residue: 1.3945 time to fit residues: 2869.4320 Evaluate side-chains 1243 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1044 time to evaluate : 5.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 39 HIS Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 151 LYS Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 146 ASN Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 88 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 37 ARG Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 94 ARG Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 13 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 336 optimal weight: 20.0000 chunk 900 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 587 optimal weight: 50.0000 chunk 246 optimal weight: 6.9990 chunk 1001 optimal weight: 10.0000 chunk 831 optimal weight: 7.9990 chunk 463 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 331 optimal weight: 10.0000 chunk 525 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN E 127 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN O 98 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN V 12 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN k 17 GLN k 55 HIS k 63 ASN ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 ASN p 38 GLN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 158767 Z= 0.453 Angle : 0.735 15.829 237307 Z= 0.383 Chirality : 0.043 0.407 30211 Planarity : 0.007 0.144 12843 Dihedral : 23.286 179.561 78954 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 5.81 % Allowed : 19.34 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: -0.13 (0.11), residues: 5867 helix: 1.65 (0.11), residues: 2051 sheet: -0.83 (0.15), residues: 1098 loop : -1.10 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 62 HIS 0.008 0.001 HIS V 88 PHE 0.020 0.002 PHE G 29 TYR 0.024 0.002 TYR R 2 ARG 0.010 0.001 ARG h 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1051 time to evaluate : 6.265 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: B 5 LYS cc_start: 0.8291 (tppt) cc_final: 0.7904 (tptm) REVERT: B 28 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7768 (mttt) REVERT: B 82 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8388 (mt-10) REVERT: B 183 LYS cc_start: 0.8311 (mttt) cc_final: 0.7914 (mtpt) REVERT: B 185 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8058 (tt0) REVERT: B 270 ARG cc_start: 0.8572 (mmm160) cc_final: 0.7865 (ttt-90) REVERT: B 271 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7783 (ptt-90) REVERT: C 1 MET cc_start: 0.6522 (ttt) cc_final: 0.6215 (ttm) REVERT: C 88 GLU cc_start: 0.7772 (mt-10) cc_final: 0.6746 (mp0) REVERT: D 40 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8346 (ttm170) REVERT: D 51 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8504 (mt-10) REVERT: D 111 GLU cc_start: 0.8646 (tp30) cc_final: 0.8382 (tp30) REVERT: D 115 GLN cc_start: 0.8433 (mt0) cc_final: 0.8229 (mt0) REVERT: D 152 GLU cc_start: 0.8441 (tp30) cc_final: 0.8027 (pp20) REVERT: D 184 ASP cc_start: 0.8290 (m-30) cc_final: 0.7741 (m-30) REVERT: D 198 GLU cc_start: 0.8302 (tt0) cc_final: 0.8000 (mm-30) REVERT: E 21 ASN cc_start: 0.7377 (t0) cc_final: 0.7092 (m110) REVERT: E 95 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7975 (mmt-90) REVERT: E 133 ARG cc_start: 0.8339 (mpt90) cc_final: 0.7974 (mpt90) REVERT: E 134 GLU cc_start: 0.8399 (tt0) cc_final: 0.8005 (tt0) REVERT: E 153 ASP cc_start: 0.8701 (p0) cc_final: 0.8499 (p0) REVERT: E 161 LYS cc_start: 0.7807 (mttt) cc_final: 0.7448 (mmtp) REVERT: E 164 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8125 (pm20) REVERT: F 10 VAL cc_start: 0.6649 (OUTLIER) cc_final: 0.6299 (t) REVERT: F 86 LYS cc_start: 0.7865 (mttm) cc_final: 0.7352 (ttpp) REVERT: F 95 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6752 (ppt170) REVERT: F 176 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.5605 (mmtt) REVERT: G 7 ASP cc_start: 0.7867 (t70) cc_final: 0.7360 (t0) REVERT: G 28 ASN cc_start: 0.8361 (m-40) cc_final: 0.8117 (m-40) REVERT: I 48 ILE cc_start: 0.1471 (OUTLIER) cc_final: 0.1131 (tt) REVERT: I 116 MET cc_start: 0.1045 (mmp) cc_final: 0.0094 (ttp) REVERT: J 106 LYS cc_start: 0.8852 (tttp) cc_final: 0.8549 (ttmt) REVERT: K 53 LYS cc_start: 0.7992 (tmmt) cc_final: 0.7611 (mttm) REVERT: K 106 GLU cc_start: 0.8050 (mp0) cc_final: 0.7681 (mp0) REVERT: K 110 GLU cc_start: 0.7853 (pt0) cc_final: 0.7457 (tp30) REVERT: K 121 GLU cc_start: 0.8355 (tt0) cc_final: 0.7997 (tt0) REVERT: L 78 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7458 (mtm180) REVERT: M 16 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8123 (mmt90) REVERT: M 51 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7352 (mtp180) REVERT: M 73 ILE cc_start: 0.9489 (mm) cc_final: 0.9269 (mm) REVERT: M 84 LYS cc_start: 0.8581 (mptp) cc_final: 0.7977 (mtmm) REVERT: M 127 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8039 (mtpp) REVERT: N 18 GLN cc_start: 0.8666 (tt0) cc_final: 0.8454 (tt0) REVERT: O 13 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8133 (tpp80) REVERT: O 16 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7543 (mmt-90) REVERT: P 38 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8107 (mttt) REVERT: P 82 ASP cc_start: 0.8592 (t70) cc_final: 0.8158 (t0) REVERT: P 97 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9187 (mt) REVERT: P 102 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: P 103 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7953 (mtt-85) REVERT: P 111 LYS cc_start: 0.8393 (pttp) cc_final: 0.8120 (ptmm) REVERT: Q 51 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8318 (mtt-85) REVERT: R 11 GLN cc_start: 0.8746 (mt0) cc_final: 0.8498 (mt0) REVERT: R 16 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7975 (mt-10) REVERT: R 31 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8152 (mm-30) REVERT: R 60 LYS cc_start: 0.8436 (mttt) cc_final: 0.7721 (mmtp) REVERT: S 95 ARG cc_start: 0.8710 (ttp-170) cc_final: 0.8116 (ttm-80) REVERT: T 1 MET cc_start: 0.6869 (tpt) cc_final: 0.5930 (tpt) REVERT: T 56 GLU cc_start: 0.8455 (tt0) cc_final: 0.8157 (tp30) REVERT: U 26 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7611 (mmtt) REVERT: U 46 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: V 71 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7801 (mmmt) REVERT: W 44 LYS cc_start: 0.8753 (mttt) cc_final: 0.8465 (mtpt) REVERT: W 66 LYS cc_start: 0.8337 (mttt) cc_final: 0.7955 (mtpt) REVERT: W 68 LYS cc_start: 0.8413 (tptt) cc_final: 0.7873 (tttt) REVERT: X 45 ARG cc_start: 0.7738 (ptt90) cc_final: 0.7446 (ptt90) REVERT: Y 40 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.8876 (p) REVERT: Z 11 ARG cc_start: 0.8942 (mtt-85) cc_final: 0.8580 (mtt-85) REVERT: Z 37 GLU cc_start: 0.8525 (tp30) cc_final: 0.8279 (tp30) REVERT: a 39 LYS cc_start: 0.8075 (mttt) cc_final: 0.7809 (mtpt) REVERT: c 9 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8594 (pt) REVERT: e 19 LYS cc_start: 0.8881 (mttp) cc_final: 0.8613 (mttm) REVERT: f 15 LYS cc_start: 0.8379 (mttt) cc_final: 0.8001 (mtpp) REVERT: g 9 MET cc_start: 0.3596 (mtm) cc_final: 0.3252 (mtt) REVERT: g 27 MET cc_start: 0.8266 (mmm) cc_final: 0.7991 (mmm) REVERT: g 64 LYS cc_start: 0.6308 (mtmm) cc_final: 0.6041 (mmmt) REVERT: g 117 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4749 (mp) REVERT: g 137 ARG cc_start: 0.5434 (mmt-90) cc_final: 0.4883 (ttp-170) REVERT: g 178 ASN cc_start: 0.6336 (m-40) cc_final: 0.5753 (t0) REVERT: g 183 VAL cc_start: 0.7794 (t) cc_final: 0.7566 (p) REVERT: g 192 ASP cc_start: 0.8000 (t70) cc_final: 0.7386 (t70) REVERT: g 194 ASP cc_start: 0.6391 (m-30) cc_final: 0.6046 (m-30) REVERT: h 89 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6751 (ptpp) REVERT: h 132 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7430 (ttt90) REVERT: h 136 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7824 (ttm110) REVERT: h 172 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6353 (ptt90) REVERT: i 73 ARG cc_start: 0.7961 (tpt-90) cc_final: 0.7348 (ttp-110) REVERT: i 185 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7988 (mtpp) REVERT: j 10 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5201 (pm20) REVERT: j 26 LYS cc_start: 0.8984 (ttpm) cc_final: 0.8701 (ttmm) REVERT: j 52 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8600 (mtpp) REVERT: j 68 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7335 (mtt180) REVERT: k 1 MET cc_start: 0.7835 (mpt) cc_final: 0.7277 (mpt) REVERT: k 2 ARG cc_start: 0.8532 (mtp85) cc_final: 0.8253 (mtt180) REVERT: k 14 GLN cc_start: 0.8133 (mp10) cc_final: 0.7806 (mp10) REVERT: k 90 MET cc_start: 0.7658 (ttp) cc_final: 0.7034 (ttt) REVERT: k 91 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7839 (mmm-85) REVERT: l 4 ARG cc_start: 0.5366 (tpt170) cc_final: 0.4717 (tpt170) REVERT: l 56 LYS cc_start: 0.7047 (mttt) cc_final: 0.6518 (mmtm) REVERT: l 67 GLU cc_start: 0.7915 (tp30) cc_final: 0.7589 (mt-10) REVERT: l 68 ASN cc_start: 0.7721 (t0) cc_final: 0.6383 (t0) REVERT: l 76 LYS cc_start: 0.6249 (ptmt) cc_final: 0.6016 (pttt) REVERT: l 106 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7555 (pt0) REVERT: l 110 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8377 (mttm) REVERT: l 148 ASN cc_start: 0.8167 (m-40) cc_final: 0.7898 (m-40) REVERT: m 2 SER cc_start: 0.8559 (m) cc_final: 0.8129 (p) REVERT: m 49 PHE cc_start: 0.9025 (p90) cc_final: 0.8715 (p90) REVERT: m 66 PHE cc_start: 0.8812 (t80) cc_final: 0.8491 (t80) REVERT: m 69 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7878 (mtpp) REVERT: m 88 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7487 (mtm-85) REVERT: m 94 LYS cc_start: 0.8494 (mttm) cc_final: 0.8123 (mtmm) REVERT: m 96 MET cc_start: 0.8917 (mtt) cc_final: 0.8631 (ttm) REVERT: n 119 ARG cc_start: 0.8491 (mtp85) cc_final: 0.8022 (mtp85) REVERT: o 64 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8180 (mt0) REVERT: p 15 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6406 (mm-40) REVERT: p 34 ILE cc_start: 0.8502 (mm) cc_final: 0.8215 (mm) REVERT: p 77 TYR cc_start: 0.9000 (m-80) cc_final: 0.8572 (m-80) REVERT: p 85 MET cc_start: 0.8061 (mtt) cc_final: 0.7728 (mtp) REVERT: p 100 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7808 (mp) REVERT: p 106 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7440 (ttp-170) REVERT: q 10 LYS cc_start: 0.8200 (tttt) cc_final: 0.7963 (tmmt) REVERT: q 12 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.6506 (mtt90) REVERT: q 56 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7789 (ttp80) REVERT: q 94 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7895 (mtt-85) REVERT: r 74 SER cc_start: 0.8629 (t) cc_final: 0.8263 (p) REVERT: r 75 MET cc_start: 0.7801 (mtp) cc_final: 0.7568 (mtp) REVERT: r 92 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7563 (mtm180) REVERT: s 90 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7511 (ttm110) REVERT: t 37 ASN cc_start: 0.8666 (m-40) cc_final: 0.8236 (m-40) REVERT: t 58 ARG cc_start: 0.8616 (ttt180) cc_final: 0.8083 (ttt-90) REVERT: u 1 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.5698 (pp-130) REVERT: u 6 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8542 (mp) REVERT: u 24 SER cc_start: 0.8981 (t) cc_final: 0.8589 (p) REVERT: v 9 GLN cc_start: 0.8713 (mt0) cc_final: 0.8468 (mt0) REVERT: x 63 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7935 (p) REVERT: y 57 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8208 (mp) REVERT: z 17 ARG cc_start: 0.7399 (ttm110) cc_final: 0.6556 (mmm160) REVERT: z 21 ARG cc_start: 0.6909 (tpt170) cc_final: 0.6433 (mmm160) REVERT: z 25 LYS cc_start: 0.7466 (mmtt) cc_final: 0.7187 (mmtt) REVERT: z 33 ARG cc_start: 0.7854 (tmt170) cc_final: 0.7195 (mtt180) REVERT: z 34 ARG cc_start: 0.7366 (ttt-90) cc_final: 0.7092 (ttt180) outliers start: 283 outliers final: 201 residues processed: 1230 average time/residue: 1.4769 time to fit residues: 3075.1903 Evaluate side-chains 1259 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1024 time to evaluate : 6.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 39 HIS Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 189 THR Chi-restraints excluded: chain g residue 220 THR Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 138 SER Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 151 LYS Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 146 ASN Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 88 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 64 GLN Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 37 ARG Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 94 ARG Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain z residue 13 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 965 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 570 optimal weight: 30.0000 chunk 731 optimal weight: 0.9990 chunk 566 optimal weight: 0.7980 chunk 842 optimal weight: 5.9990 chunk 559 optimal weight: 6.9990 chunk 997 optimal weight: 5.9990 chunk 624 optimal weight: 0.9980 chunk 608 optimal weight: 1.9990 chunk 460 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN R 18 GLN R 43 ASN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN U 46 GLN V 12 GLN V 75 GLN g 39 HIS ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 190 HIS i 116 GLN k 55 HIS l 142 HIS ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 158767 Z= 0.155 Angle : 0.598 15.393 237307 Z= 0.322 Chirality : 0.033 0.398 30211 Planarity : 0.006 0.125 12843 Dihedral : 23.262 179.863 78948 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 3.94 % Allowed : 21.45 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.18 (0.11), residues: 5867 helix: 1.93 (0.11), residues: 2060 sheet: -0.64 (0.15), residues: 1116 loop : -0.97 (0.11), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 201 HIS 0.004 0.001 HIS j 89 PHE 0.021 0.001 PHE k 8 TYR 0.028 0.001 TYR R 2 ARG 0.023 0.000 ARG n 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1062 time to evaluate : 6.158 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: B 5 LYS cc_start: 0.8276 (tppt) cc_final: 0.7889 (tptm) REVERT: B 28 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7745 (mttt) REVERT: B 70 ASN cc_start: 0.8569 (m-40) cc_final: 0.8282 (p0) REVERT: B 82 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8334 (mt-10) REVERT: B 100 GLU cc_start: 0.8032 (tt0) cc_final: 0.7670 (tt0) REVERT: B 102 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8682 (mtt90) REVERT: B 183 LYS cc_start: 0.8079 (mttt) cc_final: 0.7700 (mtpt) REVERT: B 185 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8056 (tt0) REVERT: B 270 ARG cc_start: 0.8359 (mmm160) cc_final: 0.7752 (ttt-90) REVERT: C 1 MET cc_start: 0.6460 (ttt) cc_final: 0.6082 (tpt) REVERT: C 74 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8129 (tp30) REVERT: C 88 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6772 (mp0) REVERT: C 106 LYS cc_start: 0.8968 (mttt) cc_final: 0.8679 (mttp) REVERT: D 69 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8273 (ptp-170) REVERT: D 152 GLU cc_start: 0.8397 (tp30) cc_final: 0.8061 (pp20) REVERT: D 163 ASN cc_start: 0.9194 (t0) cc_final: 0.8557 (t0) REVERT: D 198 GLU cc_start: 0.8275 (tt0) cc_final: 0.7963 (mm-30) REVERT: E 133 ARG cc_start: 0.8140 (mpt90) cc_final: 0.7891 (mpt90) REVERT: E 134 GLU cc_start: 0.8335 (tt0) cc_final: 0.7931 (tt0) REVERT: E 161 LYS cc_start: 0.7701 (mttt) cc_final: 0.7457 (mmtp) REVERT: E 164 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8180 (pm20) REVERT: F 86 LYS cc_start: 0.7834 (mttm) cc_final: 0.7318 (ttpp) REVERT: F 95 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6908 (ppt170) REVERT: F 176 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5235 (mmtt) REVERT: G 6 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7498 (tp) REVERT: G 7 ASP cc_start: 0.7791 (t70) cc_final: 0.7317 (t0) REVERT: G 28 ASN cc_start: 0.8283 (m-40) cc_final: 0.8019 (m-40) REVERT: I 48 ILE cc_start: 0.1408 (OUTLIER) cc_final: 0.1055 (tt) REVERT: I 116 MET cc_start: 0.0770 (mmp) cc_final: 0.0081 (ptm) REVERT: J 106 LYS cc_start: 0.8779 (tttp) cc_final: 0.8480 (ttmt) REVERT: K 53 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7499 (mttm) REVERT: K 98 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7832 (ttp80) REVERT: K 106 GLU cc_start: 0.7946 (mp0) cc_final: 0.7684 (mp0) REVERT: K 110 GLU cc_start: 0.7754 (pt0) cc_final: 0.7368 (tp30) REVERT: K 121 GLU cc_start: 0.8366 (tt0) cc_final: 0.8036 (tt0) REVERT: L 78 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7276 (mtp85) REVERT: M 73 ILE cc_start: 0.9491 (mm) cc_final: 0.9260 (mm) REVERT: M 84 LYS cc_start: 0.8574 (mptp) cc_final: 0.7941 (mppt) REVERT: M 127 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: M 136 MET cc_start: 0.6504 (ttm) cc_final: 0.6254 (ttm) REVERT: N 18 GLN cc_start: 0.8538 (tt0) cc_final: 0.8310 (tt0) REVERT: O 13 ARG cc_start: 0.8517 (ttt-90) cc_final: 0.8053 (tpp80) REVERT: O 16 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7564 (mmt-90) REVERT: P 29 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8123 (mmtt) REVERT: P 38 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8111 (mttt) REVERT: P 82 ASP cc_start: 0.8576 (t70) cc_final: 0.8156 (t0) REVERT: P 97 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9172 (mt) REVERT: P 103 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7954 (mtt-85) REVERT: Q 51 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8324 (mtt-85) REVERT: Q 78 LYS cc_start: 0.8930 (mttm) cc_final: 0.8636 (mtmm) REVERT: R 16 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7920 (mm-30) REVERT: R 31 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8130 (mm-30) REVERT: R 60 LYS cc_start: 0.8477 (mttt) cc_final: 0.7720 (mmtp) REVERT: S 95 ARG cc_start: 0.8654 (ttp-170) cc_final: 0.8090 (ttm-80) REVERT: T 1 MET cc_start: 0.6657 (tpt) cc_final: 0.5548 (tpt) REVERT: T 56 GLU cc_start: 0.8405 (tt0) cc_final: 0.8094 (tp30) REVERT: U 10 GLU cc_start: 0.8391 (tt0) cc_final: 0.7942 (tp30) REVERT: U 37 GLU cc_start: 0.8627 (tt0) cc_final: 0.8174 (tp30) REVERT: U 46 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: V 71 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7802 (mmmt) REVERT: V 75 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8369 (tp-100) REVERT: W 44 LYS cc_start: 0.8622 (mttt) cc_final: 0.8322 (mtpt) REVERT: W 66 LYS cc_start: 0.8253 (mttt) cc_final: 0.7882 (mtpt) REVERT: X 45 ARG cc_start: 0.7687 (ptt90) cc_final: 0.7406 (ptt90) REVERT: Y 40 SER cc_start: 0.9382 (m) cc_final: 0.8805 (p) REVERT: Z 11 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8591 (mtt-85) REVERT: Z 37 GLU cc_start: 0.8580 (tp30) cc_final: 0.8008 (mt-10) REVERT: b 40 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8489 (mmt180) REVERT: c 9 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8441 (pt) REVERT: c 17 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7610 (p) REVERT: g 9 MET cc_start: 0.3648 (mtm) cc_final: 0.3297 (mtt) REVERT: g 27 MET cc_start: 0.8299 (mmm) cc_final: 0.8045 (mmm) REVERT: g 64 LYS cc_start: 0.6234 (mtmm) cc_final: 0.5972 (mmmt) REVERT: g 117 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4841 (mp) REVERT: g 137 ARG cc_start: 0.5461 (mmt-90) cc_final: 0.4894 (ttp-170) REVERT: g 178 ASN cc_start: 0.6538 (m-40) cc_final: 0.5922 (t0) REVERT: g 183 VAL cc_start: 0.7708 (t) cc_final: 0.7364 (p) REVERT: g 192 ASP cc_start: 0.8045 (t70) cc_final: 0.7414 (t70) REVERT: g 194 ASP cc_start: 0.6419 (m-30) cc_final: 0.6099 (m-30) REVERT: g 222 ARG cc_start: 0.6247 (mtm-85) cc_final: 0.5904 (mtm-85) REVERT: h 69 HIS cc_start: 0.7656 (m90) cc_final: 0.7244 (m170) REVERT: h 89 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6763 (ptpp) REVERT: h 132 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7405 (ttt90) REVERT: h 135 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7923 (mmtp) REVERT: h 136 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7812 (ttm110) REVERT: i 44 ARG cc_start: 0.6187 (ttp-170) cc_final: 0.5983 (ttp-170) REVERT: i 73 ARG cc_start: 0.7983 (tpt-90) cc_final: 0.7373 (ttp-110) REVERT: i 185 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8002 (mtpp) REVERT: j 10 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5324 (pm20) REVERT: j 13 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7122 (mt-10) REVERT: j 26 LYS cc_start: 0.8975 (ttpm) cc_final: 0.8679 (ttmm) REVERT: j 45 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7617 (mtp85) REVERT: j 62 LYS cc_start: 0.8465 (mttt) cc_final: 0.8145 (mttt) REVERT: j 68 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7369 (mtt180) REVERT: j 86 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8300 (mttm) REVERT: k 1 MET cc_start: 0.7934 (mpt) cc_final: 0.7344 (mpt) REVERT: k 14 GLN cc_start: 0.8092 (mp10) cc_final: 0.7754 (mp10) REVERT: k 36 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.6958 (mt) REVERT: k 81 ASN cc_start: 0.7468 (t0) cc_final: 0.7200 (t0) REVERT: k 90 MET cc_start: 0.7459 (ttp) cc_final: 0.6802 (ttt) REVERT: l 4 ARG cc_start: 0.5343 (tpt170) cc_final: 0.4816 (tpt170) REVERT: l 56 LYS cc_start: 0.6997 (mttt) cc_final: 0.6481 (mmtt) REVERT: l 67 GLU cc_start: 0.7828 (tp30) cc_final: 0.7533 (mt-10) REVERT: l 68 ASN cc_start: 0.7575 (t0) cc_final: 0.6449 (t0) REVERT: l 106 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7518 (pt0) REVERT: l 110 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8471 (mttm) REVERT: l 148 ASN cc_start: 0.8077 (m-40) cc_final: 0.7819 (m-40) REVERT: m 66 PHE cc_start: 0.8843 (t80) cc_final: 0.8562 (t80) REVERT: m 69 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7825 (mtpp) REVERT: m 96 MET cc_start: 0.8761 (mtt) cc_final: 0.8381 (ttm) REVERT: n 119 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8130 (mtp85) REVERT: p 15 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6082 (mm-40) REVERT: p 34 ILE cc_start: 0.8496 (mm) cc_final: 0.8259 (mm) REVERT: p 77 TYR cc_start: 0.8977 (m-80) cc_final: 0.8514 (m-80) REVERT: p 85 MET cc_start: 0.8048 (mtt) cc_final: 0.7741 (mtp) REVERT: p 100 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7805 (mp) REVERT: p 106 ARG cc_start: 0.7778 (ttp-110) cc_final: 0.7471 (ttp-170) REVERT: q 10 LYS cc_start: 0.8175 (tttt) cc_final: 0.7957 (tmmt) REVERT: q 12 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.5834 (mtt90) REVERT: q 56 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7817 (ttm110) REVERT: q 75 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7596 (pt0) REVERT: q 94 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (mtt-85) REVERT: r 74 SER cc_start: 0.8676 (t) cc_final: 0.8290 (p) REVERT: r 75 MET cc_start: 0.7874 (mtp) cc_final: 0.7628 (mtp) REVERT: r 92 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7584 (mtm180) REVERT: s 90 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7794 (ttm-80) REVERT: t 37 ASN cc_start: 0.8597 (m-40) cc_final: 0.8192 (m-40) REVERT: t 58 ARG cc_start: 0.8474 (ttt180) cc_final: 0.7957 (ttt-90) REVERT: t 71 LYS cc_start: 0.8173 (tttt) cc_final: 0.7918 (tttt) REVERT: u 1 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.5651 (pp-130) REVERT: u 24 SER cc_start: 0.8867 (t) cc_final: 0.8514 (p) REVERT: x 63 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7848 (p) REVERT: y 57 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8080 (mt) REVERT: z 17 ARG cc_start: 0.7338 (ttm110) cc_final: 0.6472 (mmm160) REVERT: z 21 ARG cc_start: 0.6912 (tpt170) cc_final: 0.6449 (mmm160) REVERT: z 25 LYS cc_start: 0.7452 (mmtt) cc_final: 0.7185 (mmtt) REVERT: z 33 ARG cc_start: 0.7806 (tmt170) cc_final: 0.7133 (mtt180) REVERT: z 34 ARG cc_start: 0.7351 (ttt-90) cc_final: 0.7093 (ttt180) outliers start: 192 outliers final: 122 residues processed: 1181 average time/residue: 1.5094 time to fit residues: 3044.7507 Evaluate side-chains 1187 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1036 time to evaluate : 6.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 132 ASN Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 94 ARG Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 617 optimal weight: 6.9990 chunk 398 optimal weight: 10.0000 chunk 595 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 634 optimal weight: 3.9990 chunk 679 optimal weight: 0.5980 chunk 493 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 784 optimal weight: 0.3980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN D 115 GLN E 127 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 43 ASN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN V 12 GLN i 89 ASN k 55 HIS ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 ASN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 158767 Z= 0.305 Angle : 0.644 15.553 237307 Z= 0.341 Chirality : 0.037 0.398 30211 Planarity : 0.006 0.138 12843 Dihedral : 23.196 178.972 78944 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 4.23 % Allowed : 21.33 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.17 (0.11), residues: 5867 helix: 1.86 (0.11), residues: 2053 sheet: -0.57 (0.15), residues: 1117 loop : -0.95 (0.11), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 62 HIS 0.006 0.001 HIS B 230 PHE 0.019 0.002 PHE k 8 TYR 0.026 0.002 TYR R 2 ARG 0.009 0.001 ARG j 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1030 time to evaluate : 6.172 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: B 5 LYS cc_start: 0.8292 (tppt) cc_final: 0.7889 (tptm) REVERT: B 28 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7745 (mttt) REVERT: B 70 ASN cc_start: 0.8593 (m-40) cc_final: 0.8276 (p0) REVERT: B 82 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8376 (mt-10) REVERT: B 183 LYS cc_start: 0.8192 (mttt) cc_final: 0.7811 (mtpt) REVERT: B 270 ARG cc_start: 0.8489 (mmm160) cc_final: 0.7800 (ttt-90) REVERT: B 271 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7921 (ptt-90) REVERT: C 1 MET cc_start: 0.6558 (ttt) cc_final: 0.6223 (ttm) REVERT: C 88 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6684 (mp0) REVERT: D 69 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8188 (ptp-170) REVERT: D 152 GLU cc_start: 0.8474 (tp30) cc_final: 0.8109 (pm20) REVERT: D 163 ASN cc_start: 0.9222 (t0) cc_final: 0.8565 (t0) REVERT: D 198 GLU cc_start: 0.8280 (tt0) cc_final: 0.7961 (mm-30) REVERT: E 133 ARG cc_start: 0.8215 (mpt90) cc_final: 0.7943 (mpt90) REVERT: E 134 GLU cc_start: 0.8343 (tt0) cc_final: 0.7937 (tt0) REVERT: E 161 LYS cc_start: 0.7804 (mttt) cc_final: 0.7480 (mmtp) REVERT: E 164 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8149 (pm20) REVERT: F 10 VAL cc_start: 0.6575 (OUTLIER) cc_final: 0.6236 (t) REVERT: F 86 LYS cc_start: 0.7809 (mttm) cc_final: 0.7306 (ttpp) REVERT: F 95 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6896 (ppt170) REVERT: F 176 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5394 (mmtt) REVERT: G 7 ASP cc_start: 0.7838 (t70) cc_final: 0.7338 (t0) REVERT: G 28 ASN cc_start: 0.8349 (m-40) cc_final: 0.8109 (m-40) REVERT: I 48 ILE cc_start: 0.1459 (OUTLIER) cc_final: 0.1108 (tt) REVERT: I 116 MET cc_start: 0.0839 (mmp) cc_final: 0.0012 (ptm) REVERT: J 1 MET cc_start: 0.7242 (pmm) cc_final: 0.6951 (pmm) REVERT: J 106 LYS cc_start: 0.8836 (tttp) cc_final: 0.8588 (ttmm) REVERT: K 53 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7497 (mttm) REVERT: K 98 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7884 (ttp80) REVERT: K 106 GLU cc_start: 0.7891 (mp0) cc_final: 0.7608 (mp0) REVERT: K 110 GLU cc_start: 0.7772 (pt0) cc_final: 0.7368 (tp30) REVERT: K 121 GLU cc_start: 0.8411 (tt0) cc_final: 0.8057 (tt0) REVERT: L 78 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7381 (mtp85) REVERT: M 73 ILE cc_start: 0.9487 (mm) cc_final: 0.9269 (mm) REVERT: M 84 LYS cc_start: 0.8574 (mptp) cc_final: 0.7895 (mppt) REVERT: M 127 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: M 136 MET cc_start: 0.6793 (ttm) cc_final: 0.6552 (ttm) REVERT: N 18 GLN cc_start: 0.8639 (tt0) cc_final: 0.8398 (tt0) REVERT: O 13 ARG cc_start: 0.8559 (ttt-90) cc_final: 0.8089 (tpp80) REVERT: O 16 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7567 (mmt-90) REVERT: P 29 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8154 (mmtt) REVERT: P 38 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8084 (mttt) REVERT: P 82 ASP cc_start: 0.8598 (t70) cc_final: 0.8166 (t0) REVERT: P 97 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9206 (mt) REVERT: P 103 ARG cc_start: 0.8271 (mtt90) cc_final: 0.8029 (mtt-85) REVERT: P 111 LYS cc_start: 0.8368 (pttp) cc_final: 0.8108 (ptmm) REVERT: Q 51 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8460 (mtt-85) REVERT: R 16 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7972 (mm-30) REVERT: R 31 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8183 (mm-30) REVERT: R 60 LYS cc_start: 0.8480 (mttt) cc_final: 0.7730 (mmtp) REVERT: R 85 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8534 (ttmm) REVERT: S 95 ARG cc_start: 0.8681 (ttp-170) cc_final: 0.8110 (ttm-80) REVERT: T 1 MET cc_start: 0.6636 (tpt) cc_final: 0.5649 (tpt) REVERT: T 56 GLU cc_start: 0.8413 (tt0) cc_final: 0.8098 (tp30) REVERT: U 46 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7466 (mt0) REVERT: V 71 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7772 (mmmt) REVERT: W 44 LYS cc_start: 0.8651 (mttt) cc_final: 0.8367 (mtpt) REVERT: W 66 LYS cc_start: 0.8261 (mttt) cc_final: 0.7884 (mtpt) REVERT: W 68 LYS cc_start: 0.8403 (tptt) cc_final: 0.7914 (tttt) REVERT: W 78 LYS cc_start: 0.8882 (mttt) cc_final: 0.8545 (mttm) REVERT: X 45 ARG cc_start: 0.7664 (ptt90) cc_final: 0.7375 (ptt90) REVERT: Y 40 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.8855 (p) REVERT: Z 11 ARG cc_start: 0.8929 (mtt-85) cc_final: 0.8602 (mtt-85) REVERT: Z 37 GLU cc_start: 0.8579 (tp30) cc_final: 0.8324 (tp30) REVERT: c 9 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8476 (pt) REVERT: g 9 MET cc_start: 0.3688 (mtm) cc_final: 0.3321 (mtt) REVERT: g 27 MET cc_start: 0.8263 (mmm) cc_final: 0.7965 (mmm) REVERT: g 64 LYS cc_start: 0.6193 (mtmm) cc_final: 0.5940 (mmmt) REVERT: g 117 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4806 (mp) REVERT: g 137 ARG cc_start: 0.5460 (mmt-90) cc_final: 0.4878 (ttp-170) REVERT: g 169 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7610 (mp0) REVERT: g 178 ASN cc_start: 0.6343 (m-40) cc_final: 0.5756 (t0) REVERT: g 183 VAL cc_start: 0.7795 (t) cc_final: 0.7540 (p) REVERT: g 192 ASP cc_start: 0.7998 (t70) cc_final: 0.7340 (t70) REVERT: g 194 ASP cc_start: 0.6434 (m-30) cc_final: 0.6097 (m-30) REVERT: h 69 HIS cc_start: 0.7628 (m90) cc_final: 0.7265 (m170) REVERT: h 89 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6723 (ptpp) REVERT: h 132 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7347 (ttt90) REVERT: h 135 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7944 (mmtp) REVERT: h 136 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: i 73 ARG cc_start: 0.7972 (tpt-90) cc_final: 0.7335 (ttp-110) REVERT: i 185 LYS cc_start: 0.8282 (mtmm) cc_final: 0.8010 (mtpp) REVERT: j 10 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5330 (pm20) REVERT: j 13 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7017 (mt-10) REVERT: j 26 LYS cc_start: 0.8998 (ttpm) cc_final: 0.8701 (ttmm) REVERT: j 45 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7578 (mtp85) REVERT: j 68 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7362 (mtt180) REVERT: k 1 MET cc_start: 0.7824 (mpt) cc_final: 0.7227 (mpt) REVERT: k 14 GLN cc_start: 0.8123 (mp10) cc_final: 0.7780 (mp10) REVERT: k 81 ASN cc_start: 0.7507 (t0) cc_final: 0.7217 (t0) REVERT: k 90 MET cc_start: 0.7513 (ttp) cc_final: 0.6923 (ttt) REVERT: l 4 ARG cc_start: 0.5556 (tpt170) cc_final: 0.4929 (tpt170) REVERT: l 56 LYS cc_start: 0.7036 (mttt) cc_final: 0.6519 (mmtt) REVERT: l 67 GLU cc_start: 0.7890 (tp30) cc_final: 0.7517 (mt-10) REVERT: l 68 ASN cc_start: 0.7634 (t0) cc_final: 0.6445 (t0) REVERT: l 106 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7542 (pt0) REVERT: l 110 LYS cc_start: 0.8903 (ttmt) cc_final: 0.8511 (mttm) REVERT: l 148 ASN cc_start: 0.8119 (m-40) cc_final: 0.7865 (m-40) REVERT: m 49 PHE cc_start: 0.8977 (p90) cc_final: 0.8724 (p90) REVERT: m 66 PHE cc_start: 0.8839 (t80) cc_final: 0.8531 (t80) REVERT: m 69 LYS cc_start: 0.8143 (ptpp) cc_final: 0.7870 (mtpp) REVERT: m 94 LYS cc_start: 0.8482 (mttm) cc_final: 0.8096 (mtmm) REVERT: m 96 MET cc_start: 0.8801 (mtt) cc_final: 0.8441 (ttm) REVERT: n 119 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8175 (mtp85) REVERT: p 15 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.6083 (mm-40) REVERT: p 34 ILE cc_start: 0.8503 (mm) cc_final: 0.8211 (mm) REVERT: p 53 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8192 (mmm160) REVERT: p 77 TYR cc_start: 0.8987 (m-80) cc_final: 0.8542 (m-80) REVERT: p 85 MET cc_start: 0.8080 (mtt) cc_final: 0.7762 (mtp) REVERT: p 100 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7941 (mp) REVERT: p 106 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7511 (ttp-170) REVERT: q 10 LYS cc_start: 0.8184 (tttt) cc_final: 0.7963 (tmmt) REVERT: q 12 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.6444 (mtt90) REVERT: q 56 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7809 (ttp80) REVERT: q 94 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7883 (mtt-85) REVERT: r 74 SER cc_start: 0.8625 (t) cc_final: 0.8273 (p) REVERT: r 75 MET cc_start: 0.7875 (mtp) cc_final: 0.7629 (mtp) REVERT: r 92 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7599 (mtm180) REVERT: s 90 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7608 (ttm110) REVERT: t 17 ARG cc_start: 0.6932 (ptt-90) cc_final: 0.6584 (ptm-80) REVERT: t 37 ASN cc_start: 0.8601 (m-40) cc_final: 0.8182 (m-40) REVERT: t 58 ARG cc_start: 0.8584 (ttt180) cc_final: 0.8051 (ttt-90) REVERT: u 1 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.5745 (pp-130) REVERT: u 24 SER cc_start: 0.8920 (t) cc_final: 0.8557 (p) REVERT: x 63 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7894 (p) REVERT: y 57 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8084 (mp) REVERT: z 17 ARG cc_start: 0.7369 (ttm110) cc_final: 0.6526 (mmm160) REVERT: z 21 ARG cc_start: 0.6966 (tpt170) cc_final: 0.6516 (mmm160) REVERT: z 25 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7365 (mmtt) REVERT: z 33 ARG cc_start: 0.7831 (tmt170) cc_final: 0.7171 (mtt180) REVERT: z 34 ARG cc_start: 0.7365 (ttt-90) cc_final: 0.7074 (ttt180) outliers start: 206 outliers final: 158 residues processed: 1162 average time/residue: 1.3854 time to fit residues: 2723.3617 Evaluate side-chains 1205 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1019 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 21 ARG Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 172 GLU Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 132 ASN Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 94 ARG Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 66 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 907 optimal weight: 1.9990 chunk 955 optimal weight: 0.7980 chunk 871 optimal weight: 3.9990 chunk 929 optimal weight: 10.0000 chunk 559 optimal weight: 6.9990 chunk 404 optimal weight: 20.0000 chunk 729 optimal weight: 0.9980 chunk 285 optimal weight: 8.9990 chunk 840 optimal weight: 9.9990 chunk 879 optimal weight: 0.7980 chunk 926 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN D 115 GLN E 127 ASN R 18 GLN R 43 ASN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN V 12 GLN ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 55 HIS ** l 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 158767 Z= 0.185 Angle : 0.607 15.386 237307 Z= 0.326 Chirality : 0.034 0.397 30211 Planarity : 0.006 0.131 12843 Dihedral : 23.240 179.090 78942 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 4.00 % Allowed : 21.52 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.24 (0.11), residues: 5867 helix: 1.91 (0.11), residues: 2053 sheet: -0.54 (0.15), residues: 1118 loop : -0.91 (0.11), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 62 HIS 0.007 0.001 HIS U 45 PHE 0.019 0.001 PHE k 8 TYR 0.026 0.001 TYR R 2 ARG 0.010 0.000 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1042 time to evaluate : 6.193 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: B 5 LYS cc_start: 0.8286 (tppt) cc_final: 0.7880 (tptm) REVERT: B 28 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7746 (mttt) REVERT: B 70 ASN cc_start: 0.8574 (m-40) cc_final: 0.8318 (p0) REVERT: B 82 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 183 LYS cc_start: 0.8145 (mttt) cc_final: 0.7771 (mtpt) REVERT: B 185 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8119 (tt0) REVERT: B 270 ARG cc_start: 0.8442 (mmm160) cc_final: 0.7768 (ttt-90) REVERT: B 271 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7879 (ptt-90) REVERT: C 1 MET cc_start: 0.6534 (ttt) cc_final: 0.6199 (ttm) REVERT: C 88 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6675 (mp0) REVERT: D 69 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8169 (ptp-170) REVERT: D 152 GLU cc_start: 0.8451 (tp30) cc_final: 0.8097 (pm20) REVERT: D 163 ASN cc_start: 0.9185 (t0) cc_final: 0.8535 (t0) REVERT: D 198 GLU cc_start: 0.8276 (tt0) cc_final: 0.7956 (mm-30) REVERT: E 17 MET cc_start: 0.8230 (mmm) cc_final: 0.8000 (mmt) REVERT: E 133 ARG cc_start: 0.8197 (mpt90) cc_final: 0.7914 (mpt90) REVERT: E 134 GLU cc_start: 0.8367 (tt0) cc_final: 0.7972 (tt0) REVERT: E 161 LYS cc_start: 0.7765 (mttt) cc_final: 0.7413 (mmtp) REVERT: E 164 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8143 (pm20) REVERT: F 86 LYS cc_start: 0.7805 (mttm) cc_final: 0.7292 (ttpp) REVERT: F 95 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6902 (ppt170) REVERT: F 133 LEU cc_start: 0.8925 (pt) cc_final: 0.8701 (mp) REVERT: F 176 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.5371 (mmtt) REVERT: G 6 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7374 (tp) REVERT: G 7 ASP cc_start: 0.7790 (t70) cc_final: 0.7302 (t0) REVERT: G 28 ASN cc_start: 0.8322 (m-40) cc_final: 0.8060 (m-40) REVERT: I 48 ILE cc_start: 0.1451 (OUTLIER) cc_final: 0.1098 (tt) REVERT: I 116 MET cc_start: 0.0787 (mmp) cc_final: 0.0113 (ppp) REVERT: J 1 MET cc_start: 0.7197 (pmm) cc_final: 0.6927 (pmm) REVERT: J 106 LYS cc_start: 0.8819 (tttp) cc_final: 0.8461 (ttpt) REVERT: K 53 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7529 (mttm) REVERT: K 98 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7824 (ttp80) REVERT: K 106 GLU cc_start: 0.7900 (mp0) cc_final: 0.7635 (mp0) REVERT: K 121 GLU cc_start: 0.8387 (tt0) cc_final: 0.8036 (tt0) REVERT: L 78 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: M 16 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8163 (mmt90) REVERT: M 73 ILE cc_start: 0.9467 (mm) cc_final: 0.9234 (mm) REVERT: M 84 LYS cc_start: 0.8582 (mptp) cc_final: 0.7922 (mppt) REVERT: M 127 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8068 (mtpp) REVERT: M 136 MET cc_start: 0.6596 (ttm) cc_final: 0.6324 (ttm) REVERT: N 18 GLN cc_start: 0.8582 (tt0) cc_final: 0.8358 (tt0) REVERT: O 13 ARG cc_start: 0.8526 (ttt-90) cc_final: 0.8065 (tpp80) REVERT: O 16 ARG cc_start: 0.7828 (mmm160) cc_final: 0.7581 (mmt-90) REVERT: P 29 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8110 (mmtt) REVERT: P 38 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8099 (mttt) REVERT: P 82 ASP cc_start: 0.8570 (t70) cc_final: 0.8135 (t0) REVERT: P 97 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9177 (mt) REVERT: P 103 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7997 (mtt-85) REVERT: Q 51 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8404 (mtt-85) REVERT: R 16 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7989 (mm-30) REVERT: R 31 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8174 (mm-30) REVERT: R 60 LYS cc_start: 0.8489 (mttt) cc_final: 0.7738 (mmtp) REVERT: S 95 ARG cc_start: 0.8681 (ttp-170) cc_final: 0.8109 (ttm-80) REVERT: T 1 MET cc_start: 0.6624 (tpt) cc_final: 0.6011 (tpt) REVERT: T 56 GLU cc_start: 0.8407 (tt0) cc_final: 0.8106 (tp30) REVERT: U 46 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: V 71 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7787 (mmmt) REVERT: W 44 LYS cc_start: 0.8620 (mttt) cc_final: 0.8342 (mtpt) REVERT: W 66 LYS cc_start: 0.8255 (mttt) cc_final: 0.7880 (mtpt) REVERT: W 68 LYS cc_start: 0.8419 (tptt) cc_final: 0.7906 (tttt) REVERT: W 78 LYS cc_start: 0.8870 (mttt) cc_final: 0.8516 (mttm) REVERT: X 45 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7335 (ptt90) REVERT: Y 40 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.8849 (p) REVERT: Z 11 ARG cc_start: 0.8919 (mtt-85) cc_final: 0.8590 (mtt-85) REVERT: Z 37 GLU cc_start: 0.8573 (tp30) cc_final: 0.7997 (mt-10) REVERT: c 9 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8465 (pt) REVERT: g 9 MET cc_start: 0.3665 (mtm) cc_final: 0.3307 (mtt) REVERT: g 27 MET cc_start: 0.8238 (mmm) cc_final: 0.7965 (mmm) REVERT: g 49 MET cc_start: 0.6953 (mtp) cc_final: 0.6730 (mtm) REVERT: g 64 LYS cc_start: 0.6198 (mtmm) cc_final: 0.5947 (mmmt) REVERT: g 117 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4790 (mp) REVERT: g 137 ARG cc_start: 0.5460 (mmt-90) cc_final: 0.4878 (ttp-170) REVERT: g 178 ASN cc_start: 0.6529 (m-40) cc_final: 0.5895 (t0) REVERT: g 183 VAL cc_start: 0.7706 (t) cc_final: 0.7428 (p) REVERT: g 192 ASP cc_start: 0.7993 (t70) cc_final: 0.7327 (t70) REVERT: g 194 ASP cc_start: 0.6425 (m-30) cc_final: 0.6094 (m-30) REVERT: g 222 ARG cc_start: 0.6113 (mtm-85) cc_final: 0.5753 (mtm-85) REVERT: h 69 HIS cc_start: 0.7608 (m90) cc_final: 0.7249 (m170) REVERT: h 89 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6711 (ptpp) REVERT: h 132 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7360 (ttt90) REVERT: h 135 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7963 (mmtp) REVERT: h 136 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7848 (mtm-85) REVERT: i 73 ARG cc_start: 0.7966 (tpt-90) cc_final: 0.7340 (ttp-110) REVERT: i 185 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8004 (mtpp) REVERT: j 10 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5403 (pm20) REVERT: j 13 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7109 (mt-10) REVERT: j 26 LYS cc_start: 0.8994 (ttpm) cc_final: 0.8694 (ttmm) REVERT: j 68 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7373 (mtt180) REVERT: j 86 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8318 (mttm) REVERT: k 1 MET cc_start: 0.7824 (mpt) cc_final: 0.7194 (mpt) REVERT: k 2 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7401 (mtt180) REVERT: k 14 GLN cc_start: 0.8112 (mp10) cc_final: 0.7769 (mp10) REVERT: k 81 ASN cc_start: 0.7527 (t0) cc_final: 0.7247 (t0) REVERT: k 90 MET cc_start: 0.7484 (ttp) cc_final: 0.7122 (mtp) REVERT: l 4 ARG cc_start: 0.5535 (tpt170) cc_final: 0.4901 (tpt170) REVERT: l 56 LYS cc_start: 0.7017 (mttt) cc_final: 0.6508 (mmtt) REVERT: l 67 GLU cc_start: 0.7856 (tp30) cc_final: 0.7538 (mt-10) REVERT: l 68 ASN cc_start: 0.7601 (t0) cc_final: 0.6471 (t0) REVERT: l 106 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7535 (pt0) REVERT: l 110 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8576 (mttm) REVERT: l 148 ASN cc_start: 0.8113 (m-40) cc_final: 0.7857 (m-40) REVERT: m 49 PHE cc_start: 0.8980 (p90) cc_final: 0.8688 (p90) REVERT: m 66 PHE cc_start: 0.8829 (t80) cc_final: 0.8531 (t80) REVERT: m 69 LYS cc_start: 0.8144 (ptpp) cc_final: 0.7869 (mtpp) REVERT: m 88 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7448 (mtm-85) REVERT: m 96 MET cc_start: 0.8773 (mtt) cc_final: 0.8403 (ttm) REVERT: n 119 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8156 (mtp85) REVERT: p 15 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.6072 (mm-40) REVERT: p 53 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8204 (mmm160) REVERT: p 77 TYR cc_start: 0.8984 (m-80) cc_final: 0.8517 (m-80) REVERT: p 85 MET cc_start: 0.8061 (mtt) cc_final: 0.7750 (mtp) REVERT: p 100 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7941 (mp) REVERT: p 106 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7460 (ttp-170) REVERT: q 10 LYS cc_start: 0.8222 (tttt) cc_final: 0.8005 (tmmt) REVERT: q 12 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.6338 (mtt90) REVERT: q 56 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7841 (ttm110) REVERT: q 75 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7566 (pt0) REVERT: q 94 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7896 (mtt-85) REVERT: r 74 SER cc_start: 0.8643 (t) cc_final: 0.8262 (p) REVERT: r 75 MET cc_start: 0.7878 (mtp) cc_final: 0.7675 (mtp) REVERT: r 92 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7620 (mtm180) REVERT: s 90 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7640 (ttm110) REVERT: t 37 ASN cc_start: 0.8606 (m-40) cc_final: 0.8197 (m-40) REVERT: t 58 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8016 (ttt-90) REVERT: u 1 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.5704 (pp-130) REVERT: u 24 SER cc_start: 0.8900 (t) cc_final: 0.8533 (p) REVERT: x 63 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7847 (p) REVERT: y 57 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8077 (mp) REVERT: z 17 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6486 (mmm160) REVERT: z 21 ARG cc_start: 0.6909 (tpt170) cc_final: 0.6459 (mmm160) REVERT: z 25 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7361 (mmtt) REVERT: z 33 ARG cc_start: 0.7828 (tmt170) cc_final: 0.7168 (mtt180) REVERT: z 34 ARG cc_start: 0.7346 (ttt-90) cc_final: 0.7051 (ttt180) outliers start: 195 outliers final: 150 residues processed: 1164 average time/residue: 1.3871 time to fit residues: 2733.4028 Evaluate side-chains 1206 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1026 time to evaluate : 6.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 151 LYS Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 132 ASN Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 31 MET Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 88 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 94 ARG Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 610 optimal weight: 1.9990 chunk 983 optimal weight: 0.8980 chunk 599 optimal weight: 6.9990 chunk 466 optimal weight: 2.9990 chunk 683 optimal weight: 4.9990 chunk 1031 optimal weight: 6.9990 chunk 949 optimal weight: 5.9990 chunk 821 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 634 optimal weight: 4.9990 chunk 503 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN D 115 GLN E 127 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 43 ASN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN U 46 GLN V 12 GLN i 89 ASN k 55 HIS ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 158767 Z= 0.291 Angle : 0.636 15.532 237307 Z= 0.337 Chirality : 0.036 0.391 30211 Planarity : 0.006 0.136 12843 Dihedral : 23.180 179.602 78942 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 4.25 % Allowed : 21.41 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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 (0.11), residues: 5867 helix: 1.83 (0.11), residues: 2058 sheet: -0.48 (0.15), residues: 1112 loop : -0.93 (0.11), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 62 HIS 0.006 0.001 HIS B 230 PHE 0.022 0.001 PHE l 62 TYR 0.031 0.002 TYR n 7 ARG 0.010 0.001 ARG J 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1032 time to evaluate : 5.573 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: B 5 LYS cc_start: 0.8292 (tppt) cc_final: 0.7889 (tptm) REVERT: B 28 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7755 (mttt) REVERT: B 70 ASN cc_start: 0.8584 (m-40) cc_final: 0.8313 (p0) REVERT: B 82 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8378 (mt-10) REVERT: B 183 LYS cc_start: 0.8183 (mttt) cc_final: 0.7809 (mtpt) REVERT: B 185 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8114 (tt0) REVERT: B 270 ARG cc_start: 0.8466 (mmm160) cc_final: 0.7783 (ttt-90) REVERT: B 271 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7919 (ptt-90) REVERT: C 1 MET cc_start: 0.6548 (ttt) cc_final: 0.6203 (ttm) REVERT: C 88 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6690 (mp0) REVERT: D 69 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8168 (ptp-170) REVERT: D 152 GLU cc_start: 0.8468 (tp30) cc_final: 0.8121 (pm20) REVERT: D 163 ASN cc_start: 0.9214 (t0) cc_final: 0.8554 (t0) REVERT: D 198 GLU cc_start: 0.8285 (tt0) cc_final: 0.7962 (mm-30) REVERT: E 133 ARG cc_start: 0.8222 (mpt90) cc_final: 0.7947 (mpt90) REVERT: E 134 GLU cc_start: 0.8371 (tt0) cc_final: 0.7955 (tt0) REVERT: E 161 LYS cc_start: 0.7772 (mttt) cc_final: 0.7413 (mmtp) REVERT: E 164 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8141 (pm20) REVERT: F 10 VAL cc_start: 0.6526 (OUTLIER) cc_final: 0.6186 (t) REVERT: F 86 LYS cc_start: 0.7813 (mttm) cc_final: 0.7303 (ttpp) REVERT: F 95 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6884 (ppt170) REVERT: F 133 LEU cc_start: 0.8893 (pt) cc_final: 0.8693 (mp) REVERT: F 176 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5381 (mmtt) REVERT: G 7 ASP cc_start: 0.7801 (t70) cc_final: 0.7303 (t0) REVERT: G 28 ASN cc_start: 0.8340 (m-40) cc_final: 0.8098 (m-40) REVERT: I 48 ILE cc_start: 0.1483 (OUTLIER) cc_final: 0.1134 (tt) REVERT: I 116 MET cc_start: 0.0808 (mmp) cc_final: 0.0127 (ppp) REVERT: J 106 LYS cc_start: 0.8830 (tttp) cc_final: 0.8461 (ttpt) REVERT: K 53 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7530 (mttm) REVERT: K 106 GLU cc_start: 0.7866 (mp0) cc_final: 0.7598 (mp0) REVERT: K 121 GLU cc_start: 0.8398 (tt0) cc_final: 0.8048 (tt0) REVERT: L 78 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7382 (mtp85) REVERT: M 16 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8129 (mmt90) REVERT: M 73 ILE cc_start: 0.9486 (mm) cc_final: 0.9265 (mm) REVERT: M 84 LYS cc_start: 0.8569 (mptp) cc_final: 0.7897 (mppt) REVERT: M 127 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8088 (mtpp) REVERT: M 136 MET cc_start: 0.6856 (ttm) cc_final: 0.6624 (ttm) REVERT: N 18 GLN cc_start: 0.8635 (tt0) cc_final: 0.8394 (tt0) REVERT: O 13 ARG cc_start: 0.8566 (ttt-90) cc_final: 0.8101 (tpp80) REVERT: O 16 ARG cc_start: 0.7820 (mmm160) cc_final: 0.7562 (mmt-90) REVERT: P 29 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8156 (mmtt) REVERT: P 38 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8060 (mttt) REVERT: P 82 ASP cc_start: 0.8586 (t70) cc_final: 0.8151 (t0) REVERT: P 97 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9210 (mt) REVERT: P 103 ARG cc_start: 0.8267 (mtt90) cc_final: 0.8027 (mtt-85) REVERT: P 111 LYS cc_start: 0.8360 (pttp) cc_final: 0.8102 (ptmm) REVERT: Q 51 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8544 (mtt-85) REVERT: R 16 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8006 (mt-10) REVERT: R 31 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8183 (mm-30) REVERT: R 43 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7881 (m-40) REVERT: R 60 LYS cc_start: 0.8505 (mttt) cc_final: 0.7742 (mmtp) REVERT: S 95 ARG cc_start: 0.8713 (ttp-170) cc_final: 0.8131 (ttm-80) REVERT: T 1 MET cc_start: 0.6686 (tpt) cc_final: 0.6062 (tpt) REVERT: T 56 GLU cc_start: 0.8417 (tt0) cc_final: 0.8116 (tp30) REVERT: U 10 GLU cc_start: 0.8415 (tt0) cc_final: 0.7961 (tp30) REVERT: U 46 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: V 71 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7785 (mmmt) REVERT: W 44 LYS cc_start: 0.8638 (mttt) cc_final: 0.8344 (mtpt) REVERT: W 66 LYS cc_start: 0.8261 (mttt) cc_final: 0.7884 (mtpt) REVERT: W 68 LYS cc_start: 0.8408 (tptt) cc_final: 0.7923 (tttt) REVERT: X 45 ARG cc_start: 0.7660 (ptt90) cc_final: 0.7382 (ptt90) REVERT: Y 40 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.8878 (p) REVERT: Z 11 ARG cc_start: 0.8934 (mtt-85) cc_final: 0.8605 (mtt-85) REVERT: Z 37 GLU cc_start: 0.8579 (tp30) cc_final: 0.8323 (tp30) REVERT: c 9 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8428 (pt) REVERT: g 9 MET cc_start: 0.3673 (mtm) cc_final: 0.3284 (mtt) REVERT: g 27 MET cc_start: 0.8272 (mmm) cc_final: 0.7978 (mmm) REVERT: g 64 LYS cc_start: 0.6205 (mtmm) cc_final: 0.5957 (mmmt) REVERT: g 117 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.4740 (mp) REVERT: g 137 ARG cc_start: 0.5454 (mmt-90) cc_final: 0.4886 (ttp-170) REVERT: g 178 ASN cc_start: 0.6342 (m-40) cc_final: 0.5752 (t0) REVERT: g 183 VAL cc_start: 0.7726 (t) cc_final: 0.7453 (p) REVERT: g 192 ASP cc_start: 0.7995 (t70) cc_final: 0.7330 (t70) REVERT: g 194 ASP cc_start: 0.6347 (m-30) cc_final: 0.6017 (m-30) REVERT: g 222 ARG cc_start: 0.6236 (mtm-85) cc_final: 0.5902 (mtm-85) REVERT: h 59 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6010 (ptm160) REVERT: h 69 HIS cc_start: 0.7626 (m90) cc_final: 0.7265 (m170) REVERT: h 89 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6722 (ptpp) REVERT: h 132 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7371 (ttt90) REVERT: h 135 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7971 (mmtp) REVERT: h 136 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7891 (mtm-85) REVERT: i 73 ARG cc_start: 0.7936 (tpt-90) cc_final: 0.7286 (ttp-110) REVERT: i 185 LYS cc_start: 0.8279 (mtmm) cc_final: 0.8008 (mtpp) REVERT: j 10 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5355 (pm20) REVERT: j 13 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7126 (mt-10) REVERT: j 26 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8688 (ttmm) REVERT: j 52 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8756 (mtpt) REVERT: j 62 LYS cc_start: 0.8505 (mttt) cc_final: 0.8084 (mttp) REVERT: j 68 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7404 (mtt180) REVERT: j 86 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8343 (mttm) REVERT: k 1 MET cc_start: 0.7811 (mpt) cc_final: 0.7159 (mpt) REVERT: k 14 GLN cc_start: 0.8154 (mp10) cc_final: 0.7819 (mp10) REVERT: k 81 ASN cc_start: 0.7554 (t0) cc_final: 0.7271 (t0) REVERT: k 90 MET cc_start: 0.7534 (ttp) cc_final: 0.7141 (mtp) REVERT: l 56 LYS cc_start: 0.7039 (mttt) cc_final: 0.6524 (mmtt) REVERT: l 67 GLU cc_start: 0.7899 (tp30) cc_final: 0.7565 (mt-10) REVERT: l 68 ASN cc_start: 0.7634 (t0) cc_final: 0.6461 (t0) REVERT: l 106 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7534 (pt0) REVERT: l 110 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8555 (mttm) REVERT: l 148 ASN cc_start: 0.8123 (m-40) cc_final: 0.7867 (m-40) REVERT: m 49 PHE cc_start: 0.8984 (p90) cc_final: 0.8733 (p90) REVERT: m 66 PHE cc_start: 0.8842 (t80) cc_final: 0.8536 (t80) REVERT: m 69 LYS cc_start: 0.8144 (ptpp) cc_final: 0.7876 (mtpp) REVERT: m 88 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7415 (mtm-85) REVERT: m 96 MET cc_start: 0.8804 (mtt) cc_final: 0.8439 (ttm) REVERT: n 119 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8168 (mtp85) REVERT: o 37 ARG cc_start: 0.6271 (tpp-160) cc_final: 0.5461 (mmm160) REVERT: p 15 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.6114 (mm-40) REVERT: p 34 ILE cc_start: 0.8520 (mm) cc_final: 0.8226 (mm) REVERT: p 53 ARG cc_start: 0.8406 (mmm160) cc_final: 0.8158 (mmm160) REVERT: p 77 TYR cc_start: 0.8983 (m-80) cc_final: 0.8533 (m-80) REVERT: p 85 MET cc_start: 0.8079 (mtt) cc_final: 0.7773 (mtp) REVERT: p 100 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7963 (mp) REVERT: p 106 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7459 (ttp-170) REVERT: q 10 LYS cc_start: 0.8181 (tttt) cc_final: 0.7962 (tmmt) REVERT: q 12 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.6411 (mtt90) REVERT: q 56 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7804 (ttp80) REVERT: q 94 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7884 (mtt-85) REVERT: r 74 SER cc_start: 0.8680 (t) cc_final: 0.8284 (p) REVERT: r 75 MET cc_start: 0.7902 (mtp) cc_final: 0.7659 (mtp) REVERT: r 92 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7634 (mtm180) REVERT: s 90 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7611 (ttm110) REVERT: t 17 ARG cc_start: 0.6893 (ptt-90) cc_final: 0.6572 (ptm-80) REVERT: t 37 ASN cc_start: 0.8570 (m-40) cc_final: 0.8156 (m-40) REVERT: t 58 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8034 (ttt-90) REVERT: u 1 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.5708 (pp-130) REVERT: u 24 SER cc_start: 0.8916 (t) cc_final: 0.8545 (p) REVERT: x 63 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7828 (p) REVERT: y 57 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8105 (mp) REVERT: z 17 ARG cc_start: 0.7274 (ttm110) cc_final: 0.6445 (mmm160) REVERT: z 21 ARG cc_start: 0.6898 (tpt170) cc_final: 0.6443 (mmm160) REVERT: z 25 LYS cc_start: 0.7641 (mmtt) cc_final: 0.7361 (mmtt) REVERT: z 33 ARG cc_start: 0.7831 (tmt170) cc_final: 0.7173 (mtt180) REVERT: z 34 ARG cc_start: 0.7353 (ttt-90) cc_final: 0.7058 (ttt180) outliers start: 207 outliers final: 166 residues processed: 1164 average time/residue: 1.4197 time to fit residues: 2795.2527 Evaluate side-chains 1218 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1019 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 40 ARG Chi-restraints excluded: chain c residue 5 ILE Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 204 ASP Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain h residue 135 LYS Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 143 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 172 GLU Chi-restraints excluded: chain j residue 10 GLU Chi-restraints excluded: chain j residue 12 GLN Chi-restraints excluded: chain j residue 26 LYS Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain j residue 97 GLN Chi-restraints excluded: chain j residue 130 SER Chi-restraints excluded: chain j residue 132 ASN Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 88 ARG Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 15 GLN Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain q residue 12 ARG Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 94 ARG Chi-restraints excluded: chain q residue 104 CYS Chi-restraints excluded: chain r residue 3 ARG Chi-restraints excluded: chain r residue 9 ILE Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 117 LYS Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 38 ASP Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 66 LEU Chi-restraints excluded: chain t residue 84 ARG Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain w residue 14 THR Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain z residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1035 random chunks: chunk 652 optimal weight: 0.9980 chunk 874 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 757 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 822 optimal weight: 4.9990 chunk 344 optimal weight: 8.9990 chunk 844 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN E 127 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN O 98 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 43 ASN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN V 12 GLN g 120 GLN k 55 HIS o 58 ASN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.096029 restraints weight = 198196.940| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 0.94 r_work: 0.2725 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 158767 Z= 0.349 Angle : 0.669 15.587 237307 Z= 0.352 Chirality : 0.038 0.391 30211 Planarity : 0.006 0.139 12843 Dihedral : 23.187 179.464 78942 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 4.43 % Allowed : 21.25 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.13 (0.11), residues: 5867 helix: 1.74 (0.11), residues: 2065 sheet: -0.51 (0.15), residues: 1099 loop : -0.95 (0.11), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 62 HIS 0.016 0.001 HIS U 45 PHE 0.019 0.002 PHE k 8 TYR 0.027 0.002 TYR R 2 ARG 0.010 0.001 ARG J 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44166.84 seconds wall clock time: 768 minutes 54.15 seconds (46134.15 seconds total)