Starting phenix.real_space_refine on Sat Apr 13 03:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p03_17329/04_2024/8p03_17329_neut_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 1825 5.49 5 Mg 178 5.21 5 S 234 5.16 5 C 47192 2.51 5 N 15753 2.21 5 O 21094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 30": "NH1" <-> "NH2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 145": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 200": "NH1" <-> "NH2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 240": "NH1" <-> "NH2" Residue "G ARG 245": "NH1" <-> "NH2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "H ARG 70": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 137": "NH1" <-> "NH2" Residue "H ARG 142": "NH1" <-> "NH2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 151": "NH1" <-> "NH2" Residue "H ARG 160": "NH1" <-> "NH2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H ARG 174": "NH1" <-> "NH2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H ARG 213": "NH1" <-> "NH2" Residue "H ARG 219": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I ARG 94": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I ARG 137": "NH1" <-> "NH2" Residue "I ARG 140": "NH1" <-> "NH2" Residue "I ARG 142": "NH1" <-> "NH2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I ARG 170": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 183": "NH1" <-> "NH2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I ARG 190": "NH1" <-> "NH2" Residue "I ARG 191": "NH1" <-> "NH2" Residue "I ARG 198": "NH1" <-> "NH2" Residue "I ARG 216": "NH1" <-> "NH2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I ARG 231": "NH1" <-> "NH2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 233": "NH1" <-> "NH2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 81": "NH1" <-> "NH2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J ARG 106": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "J ARG 116": "NH1" <-> "NH2" Residue "J ARG 118": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 145": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "K ARG 5": "NH1" <-> "NH2" Residue "K ARG 11": "NH1" <-> "NH2" Residue "K ARG 12": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 56": "NH1" <-> "NH2" Residue "K ARG 59": "NH1" <-> "NH2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "K ARG 92": "NH1" <-> "NH2" Residue "K ARG 110": "NH1" <-> "NH2" Residue "K ARG 123": "NH1" <-> "NH2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K ARG 152": "NH1" <-> "NH2" Residue "K ARG 178": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 200": "NH1" <-> "NH2" Residue "K ARG 205": "NH1" <-> "NH2" Residue "L ARG 5": "NH1" <-> "NH2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "L ARG 127": "NH1" <-> "NH2" Residue "L ARG 131": "NH1" <-> "NH2" Residue "L ARG 133": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "L ARG 150": "NH1" <-> "NH2" Residue "L ARG 162": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "L ARG 172": "NH1" <-> "NH2" Residue "L ARG 175": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 65": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 35": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "N ARG 89": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "N ARG 101": "NH1" <-> "NH2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 132": "NH1" <-> "NH2" Residue "N ARG 139": "NH1" <-> "NH2" Residue "O ARG 33": "NH1" <-> "NH2" Residue "O ARG 36": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 55": "NH1" <-> "NH2" Residue "P ARG 64": "NH1" <-> "NH2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P ARG 99": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 106": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "P ARG 124": "NH1" <-> "NH2" Residue "P ARG 127": "NH1" <-> "NH2" Residue "P ARG 133": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 66": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "Q ARG 98": "NH1" <-> "NH2" Residue "Q ARG 104": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 121": "NH1" <-> "NH2" Residue "Q ARG 128": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q ARG 142": "NH1" <-> "NH2" Residue "Q ARG 146": "NH1" <-> "NH2" Residue "Q ARG 147": "NH1" <-> "NH2" Residue "Q ARG 149": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "R ARG 10": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ARG 42": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 47": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 51": "NH1" <-> "NH2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R ARG 81": "NH1" <-> "NH2" Residue "R ARG 130": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "S PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 15": "NH1" <-> "NH2" Residue "S ARG 27": "NH1" <-> "NH2" Residue "S ARG 37": "NH1" <-> "NH2" Residue "S ARG 45": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 69": "NH1" <-> "NH2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S ARG 125": "NH1" <-> "NH2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "S ARG 138": "NH1" <-> "NH2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 146": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T ARG 33": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ARG 63": "NH1" <-> "NH2" Residue "T ARG 67": "NH1" <-> "NH2" Residue "T ARG 78": "NH1" <-> "NH2" Residue "T ARG 80": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "U ARG 14": "NH1" <-> "NH2" Residue "U ARG 23": "NH1" <-> "NH2" Residue "U ARG 24": "NH1" <-> "NH2" Residue "U ARG 38": "NH1" <-> "NH2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U ARG 46": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "U ARG 75": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 108": "NH1" <-> "NH2" Residue "U ARG 113": "NH1" <-> "NH2" Residue "U ARG 118": "NH1" <-> "NH2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "U ARG 124": "NH1" <-> "NH2" Residue "U ARG 130": "NH1" <-> "NH2" Residue "U ARG 132": "NH1" <-> "NH2" Residue "U ARG 141": "NH1" <-> "NH2" Residue "U ARG 142": "NH1" <-> "NH2" Residue "U ARG 144": "NH1" <-> "NH2" Residue "V ARG 16": "NH1" <-> "NH2" Residue "V ARG 56": "NH1" <-> "NH2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 67": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V ARG 101": "NH1" <-> "NH2" Residue "V ARG 102": "NH1" <-> "NH2" Residue "V ARG 121": "NH1" <-> "NH2" Residue "V ARG 129": "NH1" <-> "NH2" Residue "V ARG 133": "NH1" <-> "NH2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 27": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W ARG 87": "NH1" <-> "NH2" Residue "X ARG 15": "NH1" <-> "NH2" Residue "X ARG 22": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X ARG 61": "NH1" <-> "NH2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 20": "NH1" <-> "NH2" Residue "Y ARG 23": "NH1" <-> "NH2" Residue "Y ARG 28": "NH1" <-> "NH2" Residue "Y ARG 36": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 68": "NH1" <-> "NH2" Residue "Y ARG 78": "NH1" <-> "NH2" Residue "Y ARG 97": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 118": "NH1" <-> "NH2" Residue "Z ARG 5": "NH1" <-> "NH2" Residue "Z ARG 8": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z ARG 18": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "Z ARG 119": "NH1" <-> "NH2" Residue "Z PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 140": "NH1" <-> "NH2" Residue "a ARG 8": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "a ARG 61": "NH1" <-> "NH2" Residue "a ARG 90": "NH1" <-> "NH2" Residue "a ARG 93": "NH1" <-> "NH2" Residue "a ARG 104": "NH1" <-> "NH2" Residue "a ARG 107": "NH1" <-> "NH2" Residue "a ARG 110": "NH1" <-> "NH2" Residue "a ARG 113": "NH1" <-> "NH2" Residue "a ARG 118": "NH1" <-> "NH2" Residue "b ARG 5": "NH1" <-> "NH2" Residue "b ARG 6": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 15": "NH1" <-> "NH2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "b ARG 42": "NH1" <-> "NH2" Residue "b ARG 51": "NH1" <-> "NH2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "c ARG 17": "NH1" <-> "NH2" Residue "c ARG 23": "NH1" <-> "NH2" Residue "c ARG 72": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ARG 81": "NH1" <-> "NH2" Residue "d ARG 5": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 20": "NH1" <-> "NH2" Residue "d ARG 31": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 19": "NH1" <-> "NH2" Residue "e ARG 22": "NH1" <-> "NH2" Residue "e ARG 27": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "f ARG 95": "NH1" <-> "NH2" Residue "f ARG 116": "NH1" <-> "NH2" Residue "f ARG 118": "NH1" <-> "NH2" Residue "f ARG 119": "NH1" <-> "NH2" Residue "f ARG 138": "NH1" <-> "NH2" Residue "g ARG 8": "NH1" <-> "NH2" Residue "g ARG 36": "NH1" <-> "NH2" Residue "g ARG 47": "NH1" <-> "NH2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 99": "NH1" <-> "NH2" Residue "g ARG 100": "NH1" <-> "NH2" Residue "g ARG 118": "NH1" <-> "NH2" Residue "g ARG 125": "NH1" <-> "NH2" Residue "g ARG 155": "NH1" <-> "NH2" Residue "g ARG 245": "NH1" <-> "NH2" Residue "g ARG 308": "NH1" <-> "NH2" Residue "i ARG 82": "NH1" <-> "NH2" Residue "i ARG 87": "NH1" <-> "NH2" Residue "i ARG 102": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "i ARG 108": "NH1" <-> "NH2" Residue "i ARG 109": "NH1" <-> "NH2" Residue "i ARG 114": "NH1" <-> "NH2" Residue "i ARG 115": "NH1" <-> "NH2" Residue "j ARG 12": "NH1" <-> "NH2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 14": "NH1" <-> "NH2" Residue "j ARG 24": "NH1" <-> "NH2" Residue "j ARG 46": "NH1" <-> "NH2" Residue "j ARG 57": "NH1" <-> "NH2" Residue "j ARG 62": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j ARG 82": "NH1" <-> "NH2" Residue "j ARG 101": "NH1" <-> "NH2" Residue "k ARG 7": "NH1" <-> "NH2" Residue "k ARG 22": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 86": "NH1" <-> "NH2" Residue "k ARG 96": "NH1" <-> "NH2" Residue "k ARG 101": "NH1" <-> "NH2" Residue "k ARG 148": "NH1" <-> "NH2" Residue "k ARG 190": "NH1" <-> "NH2" Residue "k ARG 212": "NH1" <-> "NH2" Residue "k ARG 224": "NH1" <-> "NH2" Residue "k ARG 252": "NH1" <-> "NH2" Residue "k ARG 260": "NH1" <-> "NH2" Residue "k ARG 267": "NH1" <-> "NH2" Residue "k ARG 306": "NH1" <-> "NH2" Residue "k ARG 323": "NH1" <-> "NH2" Residue "k ARG 325": "NH1" <-> "NH2" Residue "k ARG 390": "NH1" <-> "NH2" Residue "k ARG 395": "NH1" <-> "NH2" Residue "k ARG 425": "NH1" <-> "NH2" Residue "k ARG 433": "NH1" <-> "NH2" Residue "k ARG 469": "NH1" <-> "NH2" Residue "k ARG 497": "NH1" <-> "NH2" Residue "k ARG 502": "NH1" <-> "NH2" Residue "k ARG 506": "NH1" <-> "NH2" Residue "k ARG 531": "NH1" <-> "NH2" Residue "k ARG 567": "NH1" <-> "NH2" Residue "k ARG 568": "NH1" <-> "NH2" Residue "k ARG 574": "NH1" <-> "NH2" Residue "k ARG 576": "NH1" <-> "NH2" Residue "l ARG 2": "NH1" <-> "NH2" Residue "l ARG 6": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 11": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l ARG 15": "NH1" <-> "NH2" Residue "l ARG 17": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 23": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 76": "NH1" <-> "NH2" Residue "n ARG 80": "NH1" <-> "NH2" Residue "n ARG 85": "NH1" <-> "NH2" Residue "n ARG 104": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 86276 Number of models: 1 Model: "" Number of chains: 44 Chain: "1" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1614 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 2, 'rna3p': 1, 'rna3p_pur': 30, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 62} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "2" Number of atoms: 37193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1743, 37193 Classifications: {'RNA': 1743} Modifications used: {'5*END': 1, 'rna2p_pur': 150, 'rna2p_pyr': 124, 'rna3p': 1, 'rna3p_pur': 763, 'rna3p_pyr': 705} Link IDs: {'rna2p': 274, 'rna3p': 1468} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "3" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 193 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MA6%rna3p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2146 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain: "C" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1637 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1741 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 5, 'TRANS': 209} Chain: "E" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1754 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "G" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "H" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1482 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1924 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain: "K" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1680 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "L" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1542 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "N" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "T" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "U" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1194 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "V" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1113 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "X" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "Y" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Z" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1106 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "a" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1021 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "b" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "c" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "d" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "f" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "g" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2437 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "i" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 464 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "j" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 874 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "k" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4693 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "l" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "n" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 175} Classifications: {'undetermined': 175} Link IDs: {None: 174} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 71 residue: pdb=" P G 1 3 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 3 " occ=0.00 residue: pdb=" P C 1 4 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 1 4 " occ=0.00 residue: pdb=" P A 1 5 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 1 5 " occ=0.00 residue: pdb=" P G 1 6 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 6 " occ=0.00 residue: pdb=" P A 1 7 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 1 7 " occ=0.00 residue: pdb=" P G 1 8 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 8 " occ=0.00 residue: pdb=" P U 1 9 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U 1 9 " occ=0.00 residue: pdb=" P G 1 11 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 11 " occ=0.00 residue: pdb=" P C 1 12 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 1 12 " occ=0.00 residue: pdb=" P G 1 13 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G 1 13 " occ=0.00 residue: pdb=" P C 1 14 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C 1 14 " occ=0.00 residue: pdb=" P A 1 15 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 1 15 " occ=0.00 ... (remaining 59 not shown) Time building chain proxies: 33.01, per 1000 atoms: 0.38 Number of scatterers: 86276 At special positions: 0 Unit cell: (231, 237.6, 227.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 234 16.00 P 1825 15.00 Mg 178 11.99 O 21094 8.00 N 15753 7.00 C 47192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 26 " distance=1.97 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 74 " distance=2.11 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 74 " distance=2.06 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=1.92 Simple disulfide: pdb=" SG CYS b 74 " - pdb=" SG CYS b 77 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.25 Conformation dependent library (CDL) restraints added in 6.2 seconds 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 63 sheets defined 27.8% alpha, 13.3% beta 520 base pairs and 924 stacking pairs defined. Time for finding SS restraints: 30.64 Creating SS restraints... Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.742A pdb=" N LEU A 51 " --> pdb=" O LEU A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 59 through 62 No H-bonds generated for 'chain 'A' and resid 59 through 62' Processing helix chain 'A' and resid 92 through 118 removed outlier: 3.608A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N HIS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.926A pdb=" N VAL A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.856A pdb=" N ASN A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASN A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 254 through 257 No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'C' and resid 12 through 21 removed outlier: 3.647A pdb=" N LEU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 66 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 131 through 139 removed outlier: 4.206A pdb=" N TYR C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 185 Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 158 through 177 removed outlier: 3.522A pdb=" N ILE D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.565A pdb=" N LYS D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'D' and resid 192 through 202 removed outlier: 4.050A pdb=" N LYS D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'E' and resid 42 through 48 Processing helix chain 'E' and resid 56 through 61 removed outlier: 4.019A pdb=" N PHE E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 74 removed outlier: 3.715A pdb=" N ASP E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.645A pdb=" N ARG E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE E 132 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 removed outlier: 5.301A pdb=" N LEU E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 224 removed outlier: 3.882A pdb=" N THR E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 242 through 245 No H-bonds generated for 'chain 'E' and resid 242 through 245' Processing helix chain 'E' and resid 247 through 250 No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'F' and resid 7 through 32 removed outlier: 3.731A pdb=" N ALA F 30 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP F 32 " --> pdb=" O GLU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'G' and resid 16 through 18 No H-bonds generated for 'chain 'G' and resid 16 through 18' Processing helix chain 'G' and resid 38 through 40 No H-bonds generated for 'chain 'G' and resid 38 through 40' Processing helix chain 'G' and resid 44 through 49 Processing helix chain 'G' and resid 58 through 67 removed outlier: 4.424A pdb=" N GLN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 248 through 257 Processing helix chain 'H' and resid 77 through 80 removed outlier: 3.561A pdb=" N GLN H 80 " --> pdb=" O ARG H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 83 through 91 Processing helix chain 'H' and resid 102 through 118 removed outlier: 3.860A pdb=" N ARG H 106 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 107 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 108 " --> pdb=" O THR H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 132 Processing helix chain 'H' and resid 158 through 176 removed outlier: 3.615A pdb=" N ALA H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 196 Processing helix chain 'H' and resid 203 through 217 Processing helix chain 'I' and resid 21 through 26 removed outlier: 4.585A pdb=" N THR I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 138 through 145 Processing helix chain 'I' and resid 182 through 236 removed outlier: 3.845A pdb=" N LYS I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 32 removed outlier: 3.685A pdb=" N ALA J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 73 removed outlier: 4.931A pdb=" N LYS J 70 " --> pdb=" O PRO J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 118 through 120 No H-bonds generated for 'chain 'J' and resid 118 through 120' Processing helix chain 'J' and resid 122 through 133 removed outlier: 3.744A pdb=" N LEU J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 170 through 180 removed outlier: 4.002A pdb=" N SER J 174 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 107 through 117 Processing helix chain 'K' and resid 127 through 129 No H-bonds generated for 'chain 'K' and resid 127 through 129' Processing helix chain 'K' and resid 134 through 137 No H-bonds generated for 'chain 'K' and resid 134 through 137' Processing helix chain 'K' and resid 149 through 152 No H-bonds generated for 'chain 'K' and resid 149 through 152' Processing helix chain 'K' and resid 160 through 168 removed outlier: 4.093A pdb=" N GLN K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 182 No H-bonds generated for 'chain 'K' and resid 179 through 182' Processing helix chain 'K' and resid 192 through 205 Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.539A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 62 removed outlier: 4.156A pdb=" N VAL L 46 " --> pdb=" O GLU L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 82 Processing helix chain 'L' and resid 97 through 99 No H-bonds generated for 'chain 'L' and resid 97 through 99' Processing helix chain 'L' and resid 102 through 105 No H-bonds generated for 'chain 'L' and resid 102 through 105' Processing helix chain 'L' and resid 110 through 117 Processing helix chain 'L' and resid 123 through 132 removed outlier: 3.912A pdb=" N VAL L 128 " --> pdb=" O HIS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 removed outlier: 3.843A pdb=" N LYS L 155 " --> pdb=" O ASP L 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 152 through 155' Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'M' and resid 5 through 18 removed outlier: 4.074A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 54 Processing helix chain 'M' and resid 73 through 82 Processing helix chain 'N' and resid 48 through 51 No H-bonds generated for 'chain 'N' and resid 48 through 51' Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 35 through 43 Processing helix chain 'O' and resid 61 through 72 removed outlier: 3.817A pdb=" N GLU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 120 through 128 removed outlier: 3.945A pdb=" N ILE O 124 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR O 127 " --> pdb=" O ILE O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 42 removed outlier: 3.535A pdb=" N LEU P 40 " --> pdb=" O GLN P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 57 Processing helix chain 'P' and resid 63 through 67 Processing helix chain 'P' and resid 71 through 76 Processing helix chain 'P' and resid 86 through 104 removed outlier: 3.640A pdb=" N LEU P 91 " --> pdb=" O ASP P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 131 removed outlier: 3.829A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR P 131 " --> pdb=" O ARG P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 150 Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'Q' and resid 65 through 67 No H-bonds generated for 'chain 'Q' and resid 65 through 67' Processing helix chain 'Q' and resid 71 through 88 removed outlier: 3.538A pdb=" N ARG Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 122 removed outlier: 4.115A pdb=" N GLN Q 113 " --> pdb=" O PRO Q 110 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA Q 115 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU Q 116 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Q 119 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG Q 121 " --> pdb=" O ALA Q 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 19 No H-bonds generated for 'chain 'R' and resid 17 through 19' Processing helix chain 'R' and resid 22 through 25 No H-bonds generated for 'chain 'R' and resid 22 through 25' Processing helix chain 'R' and resid 30 through 33 No H-bonds generated for 'chain 'R' and resid 30 through 33' Processing helix chain 'R' and resid 39 through 47 Processing helix chain 'R' and resid 56 through 60 Processing helix chain 'R' and resid 87 through 89 No H-bonds generated for 'chain 'R' and resid 87 through 89' Processing helix chain 'R' and resid 116 through 119 Processing helix chain 'S' and resid 39 through 41 No H-bonds generated for 'chain 'S' and resid 39 through 41' Processing helix chain 'S' and resid 45 through 47 No H-bonds generated for 'chain 'S' and resid 45 through 47' Processing helix chain 'S' and resid 53 through 58 Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 79 through 95 removed outlier: 3.516A pdb=" N ALA S 83 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER S 89 " --> pdb=" O ARG S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 115 removed outlier: 4.239A pdb=" N ILE S 108 " --> pdb=" O SER S 104 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR S 115 " --> pdb=" O ILE S 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 19 removed outlier: 3.640A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 38 removed outlier: 4.175A pdb=" N ARG T 33 " --> pdb=" O HIS T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 61 removed outlier: 3.501A pdb=" N THR T 55 " --> pdb=" O ALA T 51 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 82 removed outlier: 3.954A pdb=" N GLU T 77 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG T 81 " --> pdb=" O GLU T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 109 removed outlier: 3.801A pdb=" N LEU T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 32 removed outlier: 4.632A pdb=" N THR U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA U 32 " --> pdb=" O PHE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 47 removed outlier: 3.724A pdb=" N VAL U 43 " --> pdb=" O ARG U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 72 Processing helix chain 'U' and resid 75 through 77 No H-bonds generated for 'chain 'U' and resid 75 through 77' Processing helix chain 'U' and resid 102 through 116 Processing helix chain 'U' and resid 120 through 126 Processing helix chain 'V' and resid 6 through 8 No H-bonds generated for 'chain 'V' and resid 6 through 8' Processing helix chain 'V' and resid 11 through 24 removed outlier: 3.528A pdb=" N ARG V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA V 20 " --> pdb=" O ARG V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 64 Processing helix chain 'V' and resid 72 through 78 removed outlier: 3.822A pdb=" N LYS V 77 " --> pdb=" O GLY V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 110 removed outlier: 3.709A pdb=" N LEU V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 142 Processing helix chain 'W' and resid 29 through 44 Processing helix chain 'W' and resid 95 through 102 Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 66 through 76 removed outlier: 3.949A pdb=" N ARG X 71 " --> pdb=" O ASP X 67 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP X 76 " --> pdb=" O LEU X 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 20 removed outlier: 3.596A pdb=" N ALA Y 17 " --> pdb=" O SER Y 13 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 44 removed outlier: 3.831A pdb=" N HIS Y 44 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 89 No H-bonds generated for 'chain 'Y' and resid 86 through 89' Processing helix chain 'Y' and resid 113 through 119 removed outlier: 3.504A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 23 removed outlier: 4.399A pdb=" N TRP Z 22 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS Z 23 " --> pdb=" O ASP Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 31 Processing helix chain 'Z' and resid 34 through 38 Processing helix chain 'Z' and resid 91 through 93 No H-bonds generated for 'chain 'Z' and resid 91 through 93' Processing helix chain 'a' and resid 37 through 48 removed outlier: 3.687A pdb=" N GLU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 84 Processing helix chain 'a' and resid 88 through 94 removed outlier: 3.559A pdb=" N ARG a 93 " --> pdb=" O HIS a 89 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS a 94 " --> pdb=" O ARG a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 116 removed outlier: 4.237A pdb=" N LYS a 116 " --> pdb=" O ASN a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 125 No H-bonds generated for 'chain 'a' and resid 122 through 125' Processing helix chain 'b' and resid 51 through 54 No H-bonds generated for 'chain 'b' and resid 51 through 54' Processing helix chain 'b' and resid 76 through 80 Processing helix chain 'e' and resid 16 through 18 No H-bonds generated for 'chain 'e' and resid 16 through 18' Processing helix chain 'e' and resid 33 through 35 No H-bonds generated for 'chain 'e' and resid 33 through 35' Processing helix chain 'e' and resid 40 through 50 removed outlier: 3.750A pdb=" N ARG e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP e 49 " --> pdb=" O GLN e 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 116 removed outlier: 3.559A pdb=" N ARG i 114 " --> pdb=" O GLN i 111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE i 116 " --> pdb=" O ASN i 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 65 No H-bonds generated for 'chain 'j' and resid 63 through 65' Processing helix chain 'j' and resid 97 through 105 Processing helix chain 'k' and resid 24 through 28 Processing helix chain 'k' and resid 30 through 33 No H-bonds generated for 'chain 'k' and resid 30 through 33' Processing helix chain 'k' and resid 60 through 63 No H-bonds generated for 'chain 'k' and resid 60 through 63' Processing helix chain 'k' and resid 116 through 123 removed outlier: 3.515A pdb=" N LEU k 120 " --> pdb=" O LYS k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 140 through 146 Processing helix chain 'k' and resid 151 through 160 Processing helix chain 'k' and resid 186 through 189 No H-bonds generated for 'chain 'k' and resid 186 through 189' Processing helix chain 'k' and resid 195 through 204 removed outlier: 4.028A pdb=" N ILE k 199 " --> pdb=" O LYS k 195 " (cutoff:3.500A) Processing helix chain 'k' and resid 219 through 232 Processing helix chain 'k' and resid 249 through 262 removed outlier: 3.906A pdb=" N LEU k 262 " --> pdb=" O THR k 258 " (cutoff:3.500A) Processing helix chain 'k' and resid 279 through 281 No H-bonds generated for 'chain 'k' and resid 279 through 281' Processing helix chain 'k' and resid 305 through 314 Processing helix chain 'k' and resid 387 through 394 Processing helix chain 'k' and resid 424 through 430 removed outlier: 3.873A pdb=" N HIS k 429 " --> pdb=" O ARG k 425 " (cutoff:3.500A) Processing helix chain 'k' and resid 439 through 445 removed outlier: 3.801A pdb=" N THR k 443 " --> pdb=" O GLN k 440 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL k 445 " --> pdb=" O VAL k 442 " (cutoff:3.500A) Processing helix chain 'k' and resid 451 through 455 Processing helix chain 'k' and resid 464 through 473 Processing helix chain 'k' and resid 494 through 509 Processing helix chain 'k' and resid 522 through 526 Processing helix chain 'k' and resid 551 through 561 removed outlier: 3.880A pdb=" N SER k 560 " --> pdb=" O ASN k 556 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN k 561 " --> pdb=" O LYS k 557 " (cutoff:3.500A) Processing helix chain 'k' and resid 586 through 591 Processing helix chain 'l' and resid 2 through 23 Processing helix chain 'n' and resid 52 through 59 removed outlier: 3.690A pdb=" N CYS n 59 " --> pdb=" O TYR n 55 " (cutoff:3.500A) Processing helix chain 'n' and resid 70 through 76 Processing helix chain 'n' and resid 82 through 93 removed outlier: 4.072A pdb=" N ALA n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 43 through 47 removed outlier: 5.918A pdb=" N SER A 35 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL A 24 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP A 84 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 76 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR A 82 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.583A pdb=" N MET A 237 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'C' and resid 145 through 148 removed outlier: 6.327A pdb=" N ILE C 159 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS C 148 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 161 " --> pdb=" O CYS C 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 38 through 41 removed outlier: 6.995A pdb=" N ILE C 48 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.743A pdb=" N GLY D 102 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE D 87 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE D 100 " --> pdb=" O ILE D 87 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 28 through 34 removed outlier: 3.731A pdb=" N GLY D 45 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 120 through 129 removed outlier: 6.103A pdb=" N TYR D 133 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 219 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N HIS D 136 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N MET D 217 " --> pdb=" O HIS D 136 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE D 138 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL D 215 " --> pdb=" O PHE D 138 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 115 through 121 removed outlier: 6.633A pdb=" N ALA E 106 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL E 83 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 161 through 164 removed outlier: 4.145A pdb=" N LEU E 169 " --> pdb=" O TRP E 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP E 204 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 40 through 42 Processing sheet with id= L, first strand: chain 'F' and resid 148 through 155 removed outlier: 4.216A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 70 through 72 Processing sheet with id= N, first strand: chain 'G' and resid 121 through 125 removed outlier: 3.616A pdb=" N ASP G 171 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP G 163 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE G 169 " --> pdb=" O ASP G 163 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 146 through 148 removed outlier: 3.645A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE G 130 " --> pdb=" O HIS G 138 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 207 through 211 Processing sheet with id= Q, first strand: chain 'H' and resid 138 through 142 Processing sheet with id= R, first strand: chain 'I' and resid 12 through 17 removed outlier: 6.659A pdb=" N VAL I 49 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 72 through 77 Processing sheet with id= T, first strand: chain 'I' and resid 54 through 57 removed outlier: 3.833A pdb=" N GLY I 54 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL I 108 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 47 through 52 removed outlier: 3.573A pdb=" N ALA J 47 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS J 91 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE J 62 " --> pdb=" O HIS J 91 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL J 93 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL J 64 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE J 95 " --> pdb=" O VAL J 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 141 through 146 Processing sheet with id= W, first strand: chain 'K' and resid 42 through 46 Processing sheet with id= X, first strand: chain 'K' and resid 62 through 67 Processing sheet with id= Y, first strand: chain 'K' and resid 173 through 175 Processing sheet with id= Z, first strand: chain 'K' and resid 78 through 81 removed outlier: 6.576A pdb=" N LEU K 103 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 20 through 24 Processing sheet with id= AB, first strand: chain 'N' and resid 101 through 112 removed outlier: 3.658A pdb=" N ARG N 101 " --> pdb=" O ILE N 96 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG N 89 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL N 77 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP N 91 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLY N 75 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 15.786A pdb=" N LEU N 93 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 16.588A pdb=" N LEU N 73 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS N 144 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY N 129 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL N 142 " --> pdb=" O GLY N 129 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 50 through 52 removed outlier: 4.216A pdb=" N LEU O 52 " --> pdb=" O ILE O 77 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 34 through 36 Processing sheet with id= AE, first strand: chain 'Q' and resid 95 through 97 Processing sheet with id= AF, first strand: chain 'R' and resid 93 through 97 Processing sheet with id= AG, first strand: chain 'S' and resid 9 through 15 Processing sheet with id= AH, first strand: chain 'U' and resid 13 through 15 Processing sheet with id= AI, first strand: chain 'V' and resid 81 through 83 Processing sheet with id= AJ, first strand: chain 'V' and resid 113 through 115 Processing sheet with id= AK, first strand: chain 'W' and resid 85 through 93 removed outlier: 3.653A pdb=" N THR W 25 " --> pdb=" O GLU W 111 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 59 through 66 Processing sheet with id= AM, first strand: chain 'X' and resid 35 through 37 Processing sheet with id= AN, first strand: chain 'Y' and resid 24 through 27 Processing sheet with id= AO, first strand: chain 'Y' and resid 71 through 74 removed outlier: 7.005A pdb=" N VAL Y 103 " --> pdb=" O LEU Y 126 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 101 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE Y 101 " --> pdb=" O PHE Y 128 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Z' and resid 80 through 84 removed outlier: 3.840A pdb=" N GLU Z 53 " --> pdb=" O ARG Z 71 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN Z 73 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL Z 51 " --> pdb=" O GLN Z 73 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA Z 103 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL Z 122 " --> pdb=" O ALA Z 103 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'a' and resid 6 through 10 Processing sheet with id= AR, first strand: chain 'a' and resid 13 through 15 Processing sheet with id= AS, first strand: chain 'b' and resid 36 through 43 Processing sheet with id= AT, first strand: chain 'c' and resid 32 through 35 removed outlier: 3.569A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'd' and resid 55 through 58 removed outlier: 6.705A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'd' and resid 19 through 21 removed outlier: 3.919A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'f' and resid 106 through 110 removed outlier: 6.955A pdb=" N LYS f 113 " --> pdb=" O ASP f 109 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 4 through 7 Processing sheet with id= AY, first strand: chain 'g' and resid 18 through 23 removed outlier: 6.790A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 99 through 101 removed outlier: 3.567A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU g 87 " --> pdb=" O PHE g 101 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 119 through 123 removed outlier: 3.827A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASN g 133 " --> pdb=" O CYS g 138 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N CYS g 138 " --> pdb=" O ASN g 133 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 174 through 178 Processing sheet with id= BC, first strand: chain 'g' and resid 206 through 209 removed outlier: 3.621A pdb=" N TYR g 228 " --> pdb=" O LEU g 218 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'g' and resid 239 through 241 removed outlier: 3.540A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'j' and resid 47 through 51 removed outlier: 6.231A pdb=" N MET j 50 " --> pdb=" O VAL j 38 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL j 38 " --> pdb=" O MET j 50 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY j 80 " --> pdb=" O VAL j 91 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL j 91 " --> pdb=" O GLY j 80 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'k' and resid 6 through 8 removed outlier: 3.619A pdb=" N THR k 6 " --> pdb=" O LEU k 75 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'k' and resid 285 through 288 removed outlier: 6.463A pdb=" N ILE k 269 " --> pdb=" O LEU k 106 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU k 108 " --> pdb=" O ILE k 269 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL k 271 " --> pdb=" O LEU k 108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE k 238 " --> pdb=" O ILE k 270 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL k 272 " --> pdb=" O PHE k 238 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE k 240 " --> pdb=" O VAL k 272 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'k' and resid 289 through 292 Processing sheet with id= BI, first strand: chain 'k' and resid 362 through 364 removed outlier: 6.593A pdb=" N THR k 543 " --> pdb=" O ALA k 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'k' and resid 531 through 533 removed outlier: 3.949A pdb=" N ARG k 531 " --> pdb=" O ILE k 374 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA k 515 " --> pdb=" O MET k 375 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N MET k 377 " --> pdb=" O ALA k 515 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL k 517 " --> pdb=" O MET k 377 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'n' and resid 98 through 102 removed outlier: 6.725A pdb=" N ILE n 108 " --> pdb=" O VAL n 100 " (cutoff:3.500A) 1265 hydrogen bonds defined for protein. 3570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1300 hydrogen bonds 2066 hydrogen bond angles 0 basepair planarities 520 basepair parallelities 924 stacking parallelities Total time for adding SS restraints: 62.87 Time building geometry restraints manager: 32.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 18898 1.33 - 1.46: 32571 1.46 - 1.59: 36555 1.59 - 1.72: 3120 1.72 - 1.85: 356 Bond restraints: 91500 Sorted by residual: bond pdb=" O3' U 1 72 " pdb=" P A 1 73 " ideal model delta sigma weight residual 1.607 1.417 0.190 1.50e-02 4.44e+03 1.61e+02 bond pdb=" C4 I2T 21244 " pdb=" C5 I2T 21244 " ideal model delta sigma weight residual 1.632 1.451 0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" N1 I2T 21244 " pdb=" C2 I2T 21244 " ideal model delta sigma weight residual 1.551 1.371 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" N1 I2T 21244 " pdb=" C6 I2T 21244 " ideal model delta sigma weight residual 1.547 1.367 0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" O3' C 21245 " pdb=" P A 21246 " ideal model delta sigma weight residual 1.607 1.478 0.129 1.50e-02 4.44e+03 7.42e+01 ... (remaining 91495 not shown) Histogram of bond angle deviations from ideal: 20.25 - 43.44: 1 43.44 - 66.63: 0 66.63 - 89.82: 0 89.82 - 113.01: 61325 113.01 - 136.21: 70928 Bond angle restraints: 132254 Sorted by residual: angle pdb=" O3' U 1 72 " pdb=" P A 1 73 " pdb=" OP2 A 1 73 " ideal model delta sigma weight residual 108.00 20.25 87.75 3.00e+00 1.11e-01 8.56e+02 angle pdb=" C4' G 21515 " pdb=" C3' G 21515 " pdb=" O3' G 21515 " ideal model delta sigma weight residual 113.00 98.91 14.09 1.50e+00 4.44e-01 8.82e+01 angle pdb=" P G 2 270 " pdb=" O5' G 2 270 " pdb=" C5' G 2 270 " ideal model delta sigma weight residual 120.90 106.84 14.06 1.50e+00 4.44e-01 8.78e+01 angle pdb=" P G 21765 " pdb=" O5' G 21765 " pdb=" C5' G 21765 " ideal model delta sigma weight residual 120.90 106.85 14.05 1.50e+00 4.44e-01 8.78e+01 angle pdb=" O3' U 1 72 " pdb=" P A 1 73 " pdb=" OP1 A 1 73 " ideal model delta sigma weight residual 108.00 132.54 -24.54 3.00e+00 1.11e-01 6.69e+01 ... (remaining 132249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 52870 35.95 - 71.89: 4799 71.89 - 107.84: 518 107.84 - 143.79: 14 143.79 - 179.74: 25 Dihedral angle restraints: 58226 sinusoidal: 41224 harmonic: 17002 Sorted by residual: dihedral pdb=" CB CYS b 23 " pdb=" SG CYS b 23 " pdb=" SG CYS b 26 " pdb=" CB CYS b 26 " ideal model delta sinusoidal sigma weight residual 93.00 5.77 87.23 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" O4' C 21135 " pdb=" C1' C 21135 " pdb=" N1 C 21135 " pdb=" C2 C 21135 " ideal model delta sinusoidal sigma weight residual -160.00 19.74 -179.74 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 21473 " pdb=" C1' U 21473 " pdb=" N1 U 21473 " pdb=" C2 U 21473 " ideal model delta sinusoidal sigma weight residual -160.00 19.10 -179.10 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 58223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 15760 0.161 - 0.321: 469 0.321 - 0.482: 34 0.482 - 0.643: 6 0.643 - 0.803: 2 Chirality restraints: 16271 Sorted by residual: chirality pdb=" P G 2 270 " pdb=" OP1 G 2 270 " pdb=" OP2 G 2 270 " pdb=" O5' G 2 270 " both_signs ideal model delta sigma weight residual True 2.41 -3.21 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" P G 21765 " pdb=" OP1 G 21765 " pdb=" OP2 G 21765 " pdb=" O5' G 21765 " both_signs ideal model delta sigma weight residual True 2.41 -3.21 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" P U 21724 " pdb=" OP1 U 21724 " pdb=" OP2 U 21724 " pdb=" O5' U 21724 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 16268 not shown) Planarity restraints: 10023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 21105 " 0.355 2.00e-02 2.50e+03 1.90e-01 8.12e+02 pdb=" N1 C 21105 " 0.007 2.00e-02 2.50e+03 pdb=" C2 C 21105 " -0.054 2.00e-02 2.50e+03 pdb=" O2 C 21105 " -0.238 2.00e-02 2.50e+03 pdb=" N3 C 21105 " 0.085 2.00e-02 2.50e+03 pdb=" C4 C 21105 " 0.059 2.00e-02 2.50e+03 pdb=" N4 C 21105 " 0.202 2.00e-02 2.50e+03 pdb=" C5 C 21105 " -0.205 2.00e-02 2.50e+03 pdb=" C6 C 21105 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 201 " 0.075 2.00e-02 2.50e+03 1.41e-01 5.97e+02 pdb=" N9 G 2 201 " -0.081 2.00e-02 2.50e+03 pdb=" C8 G 2 201 " 0.131 2.00e-02 2.50e+03 pdb=" N7 G 2 201 " 0.154 2.00e-02 2.50e+03 pdb=" C5 G 2 201 " -0.072 2.00e-02 2.50e+03 pdb=" C6 G 2 201 " -0.085 2.00e-02 2.50e+03 pdb=" O6 G 2 201 " 0.053 2.00e-02 2.50e+03 pdb=" N1 G 2 201 " -0.053 2.00e-02 2.50e+03 pdb=" C2 G 2 201 " -0.080 2.00e-02 2.50e+03 pdb=" N2 G 2 201 " 0.314 2.00e-02 2.50e+03 pdb=" N3 G 2 201 " -0.185 2.00e-02 2.50e+03 pdb=" C4 G 2 201 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 542 " 0.320 2.00e-02 2.50e+03 1.32e-01 5.26e+02 pdb=" N9 G 2 542 " -0.040 2.00e-02 2.50e+03 pdb=" C8 G 2 542 " -0.110 2.00e-02 2.50e+03 pdb=" N7 G 2 542 " -0.110 2.00e-02 2.50e+03 pdb=" C5 G 2 542 " -0.067 2.00e-02 2.50e+03 pdb=" C6 G 2 542 " 0.042 2.00e-02 2.50e+03 pdb=" O6 G 2 542 " 0.224 2.00e-02 2.50e+03 pdb=" N1 G 2 542 " 0.019 2.00e-02 2.50e+03 pdb=" C2 G 2 542 " -0.076 2.00e-02 2.50e+03 pdb=" N2 G 2 542 " -0.007 2.00e-02 2.50e+03 pdb=" N3 G 2 542 " -0.093 2.00e-02 2.50e+03 pdb=" C4 G 2 542 " -0.101 2.00e-02 2.50e+03 ... (remaining 10020 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 75 2.23 - 2.89: 30452 2.89 - 3.56: 118257 3.56 - 4.23: 237042 4.23 - 4.90: 346179 Nonbonded interactions: 732005 Sorted by model distance: nonbonded pdb=" O3' U 1 55 " pdb=" OD1 ASN A 179 " model vdw 1.556 3.040 nonbonded pdb=" OP2 C 1 56 " pdb=" OD1 ASN A 178 " model vdw 1.684 3.040 nonbonded pdb=" O4 U 1 72 " pdb=" N6 A 1 73 " model vdw 1.708 2.520 nonbonded pdb=" C3' U 1 72 " pdb=" OP2 A 1 73 " model vdw 1.788 2.776 nonbonded pdb=" OP1 U 21648 " pdb="MG MG 22064 " model vdw 1.913 2.170 ... (remaining 732000 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=0.00 max=1.00 mean=0.98 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.060 Extract box with map and model: 14.920 Check model and map are aligned: 0.920 Set scattering table: 0.600 Process input model: 215.410 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.250 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 241.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.190 91500 Z= 0.514 Angle : 1.213 87.752 132254 Z= 0.749 Chirality : 0.064 0.803 16271 Planarity : 0.016 0.223 10023 Dihedral : 22.162 179.737 47241 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 6.25 % Allowed : 17.91 % Favored : 75.84 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.43 % 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: -3.79 (0.09), residues: 5824 helix: -2.30 (0.10), residues: 1731 sheet: -2.00 (0.15), residues: 991 loop : -2.86 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.221 0.012 TRP g 247 HIS 0.018 0.002 HIS k 208 PHE 0.107 0.006 PHE R 15 TYR 0.134 0.007 TYR R 30 ARG 0.018 0.001 ARG I 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1082 time to evaluate : 4.952 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: A 100 ASP cc_start: 0.5624 (m-30) cc_final: 0.5326 (m-30) REVERT: A 144 ARG cc_start: 0.1922 (OUTLIER) cc_final: 0.0249 (mpp-170) REVERT: C 9 GLN cc_start: 0.7042 (tt0) cc_final: 0.6713 (mt0) REVERT: D 110 MET cc_start: 0.7529 (tpt) cc_final: 0.7087 (tpt) REVERT: F 56 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6451 (mm110) REVERT: F 57 ASN cc_start: 0.8243 (m-40) cc_final: 0.8038 (m-40) REVERT: F 227 LYS cc_start: 0.7627 (tptm) cc_final: 0.7154 (tttt) REVERT: G 214 ASN cc_start: 0.8702 (m-40) cc_final: 0.8404 (m-40) REVERT: H 70 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7733 (mtm180) REVERT: H 93 MET cc_start: 0.8353 (ttm) cc_final: 0.8089 (ttm) REVERT: H 155 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7422 (p0) REVERT: H 219 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7481 (ttm170) REVERT: I 82 SER cc_start: 0.8583 (p) cc_final: 0.8302 (m) REVERT: I 132 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7644 (mtm110) REVERT: I 155 GLN cc_start: 0.7899 (pt0) cc_final: 0.7679 (pt0) REVERT: J 32 MET cc_start: 0.3980 (mpp) cc_final: 0.3584 (ptt) REVERT: L 66 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7690 (ttmm) REVERT: L 79 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7972 (ttt-90) REVERT: M 3 MET cc_start: 0.9022 (mtp) cc_final: 0.8743 (mtt) REVERT: N 157 LYS cc_start: -0.2047 (OUTLIER) cc_final: -0.2687 (ptmt) REVERT: O 12 MET cc_start: 0.4020 (tpp) cc_final: 0.3416 (mmm) REVERT: Q 143 LYS cc_start: 0.8540 (tttp) cc_final: 0.8278 (tttt) REVERT: R 111 MET cc_start: 0.8590 (mtt) cc_final: 0.8369 (mtt) REVERT: S 62 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7962 (mtt180) REVERT: S 145 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: T 79 GLU cc_start: 0.7028 (tp30) cc_final: 0.6764 (tp30) REVERT: T 87 GLU cc_start: 0.0866 (OUTLIER) cc_final: -0.0238 (mm-30) REVERT: T 126 MET cc_start: 0.3926 (mmt) cc_final: 0.2223 (mtp) REVERT: U 144 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5362 (ppt170) REVERT: V 130 ASP cc_start: 0.8108 (m-30) cc_final: 0.7840 (m-30) REVERT: W 19 ARG cc_start: 0.5636 (mtt180) cc_final: 0.4658 (mtp85) REVERT: W 44 LYS cc_start: 0.7384 (tppt) cc_final: 0.7142 (ttpt) REVERT: W 62 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7445 (mtt-85) REVERT: Y 5 ASN cc_start: 0.8685 (t0) cc_final: 0.8473 (t0) REVERT: Y 9 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7269 (p0) REVERT: Y 111 MET cc_start: 0.8356 (ptp) cc_final: 0.8110 (ptp) REVERT: Y 112 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7539 (p0) REVERT: Z 60 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7966 (mtmt) REVERT: Z 64 SER cc_start: 0.8810 (t) cc_final: 0.8479 (t) REVERT: Z 127 ASN cc_start: 0.7453 (m-40) cc_final: 0.7083 (m110) REVERT: b 84 VAL cc_start: 0.8980 (m) cc_final: 0.8731 (m) REVERT: c 8 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8505 (tt) REVERT: c 36 LYS cc_start: 0.8046 (tppp) cc_final: 0.7800 (tptp) REVERT: f 140 TYR cc_start: 0.7792 (t80) cc_final: 0.6826 (t80) REVERT: j 33 GLN cc_start: 0.7918 (tt0) cc_final: 0.7516 (tt0) REVERT: k 22 ARG cc_start: 0.4190 (mmt90) cc_final: 0.3208 (ttt180) REVERT: k 33 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4110 (mmt180) REVERT: k 64 LYS cc_start: 0.5806 (tttp) cc_final: 0.4951 (mtpp) REVERT: k 116 LYS cc_start: 0.2265 (pmtt) cc_final: 0.1001 (mtmm) REVERT: k 121 LYS cc_start: 0.4973 (mttt) cc_final: 0.4341 (mtmt) REVERT: k 206 LEU cc_start: 0.5010 (mt) cc_final: 0.4792 (mp) REVERT: k 331 PHE cc_start: 0.0662 (OUTLIER) cc_final: 0.0137 (m-80) REVERT: k 353 MET cc_start: 0.2984 (tpp) cc_final: 0.2775 (tpt) REVERT: k 505 LYS cc_start: 0.4491 (tptp) cc_final: 0.3941 (mttt) REVERT: k 524 MET cc_start: -0.0011 (ttm) cc_final: -0.0584 (ttm) REVERT: k 569 ASP cc_start: 0.4662 (OUTLIER) cc_final: 0.4187 (m-30) REVERT: l 10 MET cc_start: 0.7345 (ttp) cc_final: 0.7124 (ttp) REVERT: l 20 MET cc_start: 0.8018 (tmm) cc_final: 0.7726 (tmm) outliers start: 319 outliers final: 209 residues processed: 1333 average time/residue: 0.8706 time to fit residues: 1910.3481 Evaluate side-chains 1117 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 893 time to evaluate : 4.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 132 ARG Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 58 GLU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 143 SER Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain S residue 35 ASN Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 70 CYS Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 10 ASP Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain Y residue 9 ASP Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 90 CYS Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 8 LEU Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 209 SER Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 50 ILE Chi-restraints excluded: chain k residue 154 ASN Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 336 THR Chi-restraints excluded: chain k residue 378 LEU Chi-restraints excluded: chain k residue 437 THR Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 454 ILE Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 564 ILE Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain k residue 596 PHE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 635 optimal weight: 7.9990 chunk 570 optimal weight: 6.9990 chunk 316 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 384 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 590 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 439 optimal weight: 7.9990 chunk 683 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 68 ASN ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN A 178 ASN A 181 ASN C 84 GLN C 110 ASN C 132 GLN D 43 ASN E 97 GLN E 113 HIS E 254 HIS F 56 GLN F 226 GLN G 8 HIS G 138 HIS G 142 HIS G 214 ASN H 66 HIS H 89 ASN H 97 ASN H 125 GLN H 129 ASN H 180 ASN I 13 GLN I 105 ASN I 110 ASN J 25 GLN J 39 GLN J 157 HIS K 35 ASN K 52 ASN K 111 GLN L 113 GLN L 132 GLN L 154 GLN M 32 HIS N 11 GLN N 83 GLN N 121 GLN ** O 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 HIS O 73 GLN Q 79 GLN R 32 GLN R 104 GLN S 35 ASN S 77 HIS S 86 GLN T 48 ASN U 42 HIS U 76 GLN U 120 HIS V 11 GLN V 12 GLN X 21 ASN X 49 GLN Z 77 ASN Z 92 ASN ** Z 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 HIS b 43 ASN c 49 HIS c 51 GLN e 5 GLN f 91 ASN g 4 GLN g 20 GLN g 76 GLN g 117 ASN g 187 ASN i 111 GLN i 132 ASN j 19 ASN j 37 GLN k 414 GLN k 429 HIS k 510 HIS k 549 GLN n 46 ASN n 106 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 91500 Z= 0.284 Angle : 0.685 13.718 132254 Z= 0.351 Chirality : 0.042 0.304 16271 Planarity : 0.005 0.062 10023 Dihedral : 22.634 179.473 35465 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.22 % Favored : 90.76 % Rotamer: Outliers : 6.76 % Allowed : 20.26 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.10), residues: 5824 helix: -1.22 (0.12), residues: 1724 sheet: -1.51 (0.15), residues: 1025 loop : -2.56 (0.10), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 204 HIS 0.011 0.001 HIS O 48 PHE 0.020 0.002 PHE L 147 TYR 0.028 0.002 TYR O 114 ARG 0.007 0.001 ARG W 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 904 time to evaluate : 4.972 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: A 30 MET cc_start: 0.7061 (mtt) cc_final: 0.6818 (mtp) REVERT: A 53 ARG cc_start: 0.7905 (mpp80) cc_final: 0.7355 (mtt-85) REVERT: A 119 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5130 (tp) REVERT: A 136 TRP cc_start: 0.4908 (OUTLIER) cc_final: 0.4496 (m-10) REVERT: C 7 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8368 (t) REVERT: C 9 GLN cc_start: 0.6971 (tt0) cc_final: 0.6698 (mt0) REVERT: C 34 MET cc_start: 0.8469 (mmm) cc_final: 0.7841 (mtm) REVERT: C 165 ASN cc_start: 0.7706 (t0) cc_final: 0.7467 (t0) REVERT: D 110 MET cc_start: 0.7532 (tpt) cc_final: 0.6986 (tpt) REVERT: E 94 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7715 (ttm-80) REVERT: E 225 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: F 57 ASN cc_start: 0.8265 (m-40) cc_final: 0.8061 (m-40) REVERT: F 217 ILE cc_start: 0.3390 (OUTLIER) cc_final: 0.3136 (tt) REVERT: F 227 LYS cc_start: 0.7684 (tptm) cc_final: 0.7227 (tttt) REVERT: G 200 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7680 (mtt-85) REVERT: G 214 ASN cc_start: 0.8725 (m110) cc_final: 0.8463 (m-40) REVERT: H 70 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7791 (mtm180) REVERT: H 93 MET cc_start: 0.8462 (ttm) cc_final: 0.8150 (ttm) REVERT: H 138 GLU cc_start: 0.7654 (tt0) cc_final: 0.7405 (tt0) REVERT: H 155 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7425 (p0) REVERT: H 219 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7734 (ttm170) REVERT: I 82 SER cc_start: 0.8589 (p) cc_final: 0.8290 (m) REVERT: I 219 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: J 18 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5542 (tm-30) REVERT: J 32 MET cc_start: 0.4114 (mpp) cc_final: 0.3798 (ptt) REVERT: L 66 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7734 (ttmm) REVERT: M 3 MET cc_start: 0.8919 (mtp) cc_final: 0.8651 (mtt) REVERT: P 3 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7320 (tpp-160) REVERT: P 105 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8342 (p0) REVERT: Q 83 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: S 145 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: T 45 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7869 (mttt) REVERT: T 80 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7774 (ttm170) REVERT: T 87 GLU cc_start: 0.1048 (OUTLIER) cc_final: 0.0680 (mt-10) REVERT: T 126 MET cc_start: 0.3426 (mmt) cc_final: 0.1900 (mtp) REVERT: U 91 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7588 (mmtt) REVERT: U 108 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7275 (ttp80) REVERT: V 112 MET cc_start: 0.8163 (tpp) cc_final: 0.7766 (tpp) REVERT: V 130 ASP cc_start: 0.8026 (m-30) cc_final: 0.7785 (m-30) REVERT: W 19 ARG cc_start: 0.5580 (mtt180) cc_final: 0.4605 (mtp85) REVERT: W 44 LYS cc_start: 0.7475 (tppt) cc_final: 0.7084 (ttpt) REVERT: W 62 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7457 (mtt-85) REVERT: X 76 ASP cc_start: 0.7710 (t70) cc_final: 0.7493 (t0) REVERT: Y 111 MET cc_start: 0.8294 (ptp) cc_final: 0.8092 (ptp) REVERT: Z 127 ASN cc_start: 0.7515 (m-40) cc_final: 0.7128 (m110) REVERT: b 84 VAL cc_start: 0.8894 (m) cc_final: 0.8690 (m) REVERT: c 36 LYS cc_start: 0.8064 (tppp) cc_final: 0.7800 (tptp) REVERT: c 81 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7768 (ttt180) REVERT: f 140 TYR cc_start: 0.7746 (t80) cc_final: 0.6735 (t80) REVERT: g 5 MET cc_start: 0.7025 (mmt) cc_final: 0.6720 (mmt) REVERT: g 145 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: j 33 GLN cc_start: 0.7992 (tt0) cc_final: 0.7656 (tt0) REVERT: j 62 ARG cc_start: 0.8784 (ptt180) cc_final: 0.8502 (ptt90) REVERT: j 82 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6026 (mtp180) REVERT: k 22 ARG cc_start: 0.4015 (mmt90) cc_final: 0.2935 (ttm-80) REVERT: k 64 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.4737 (mtmm) REVERT: k 206 LEU cc_start: 0.4807 (mt) cc_final: 0.4594 (mp) REVERT: k 331 PHE cc_start: 0.0717 (OUTLIER) cc_final: 0.0194 (m-80) REVERT: k 353 MET cc_start: 0.2767 (tpp) cc_final: 0.2543 (tpt) REVERT: k 385 LYS cc_start: 0.3605 (OUTLIER) cc_final: 0.3296 (pmtt) REVERT: k 505 LYS cc_start: 0.4534 (tptp) cc_final: 0.3971 (tttt) REVERT: k 555 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6465 (mtp) REVERT: k 569 ASP cc_start: 0.4709 (OUTLIER) cc_final: 0.4220 (m-30) REVERT: k 587 GLU cc_start: 0.6985 (pm20) cc_final: 0.6784 (mt-10) REVERT: l 10 MET cc_start: 0.7337 (ttp) cc_final: 0.7123 (ttp) REVERT: l 20 MET cc_start: 0.8181 (tmm) cc_final: 0.7955 (tmm) outliers start: 345 outliers final: 240 residues processed: 1160 average time/residue: 0.8780 time to fit residues: 1722.0625 Evaluate side-chains 1111 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 849 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 87 ARG Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 10 ASP Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 209 SER Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 96 GLN Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 50 ILE Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 157 THR Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 336 THR Chi-restraints excluded: chain k residue 364 ILE Chi-restraints excluded: chain k residue 365 VAL Chi-restraints excluded: chain k residue 378 LEU Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 454 ILE Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 543 THR Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 380 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 569 optimal weight: 3.9990 chunk 465 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 685 optimal weight: 0.0670 chunk 740 optimal weight: 0.4980 chunk 610 optimal weight: 4.9990 chunk 679 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 549 optimal weight: 9.9990 overall best weight: 3.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN E 97 GLN I 105 ASN I 110 ASN L 132 GLN ** O 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 GLN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN R 104 GLN V 12 GLN Z 77 ASN ** Z 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS f 91 ASN ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 91500 Z= 0.240 Angle : 0.630 11.957 132254 Z= 0.324 Chirality : 0.040 0.282 16271 Planarity : 0.005 0.058 10023 Dihedral : 22.494 179.548 35319 Min Nonbonded Distance : 1.022 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.88 % Favored : 91.11 % Rotamer: Outliers : 7.25 % Allowed : 21.18 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.10), residues: 5824 helix: -0.79 (0.12), residues: 1726 sheet: -1.25 (0.16), residues: 1009 loop : -2.41 (0.10), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 204 HIS 0.013 0.001 HIS O 48 PHE 0.019 0.001 PHE k 147 TYR 0.022 0.002 TYR O 114 ARG 0.017 0.000 ARG k 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 917 time to evaluate : 5.014 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: A 136 TRP cc_start: 0.5030 (OUTLIER) cc_final: 0.4659 (m-10) REVERT: C 9 GLN cc_start: 0.6984 (tt0) cc_final: 0.6704 (mt0) REVERT: C 34 MET cc_start: 0.8323 (mmm) cc_final: 0.7821 (mtm) REVERT: D 110 MET cc_start: 0.7575 (tpt) cc_final: 0.7061 (tpt) REVERT: E 94 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7754 (ttm-80) REVERT: E 225 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: F 217 ILE cc_start: 0.3403 (OUTLIER) cc_final: 0.3154 (tt) REVERT: F 227 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6892 (tttt) REVERT: G 200 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7670 (mtt-85) REVERT: H 70 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7769 (mtm180) REVERT: H 93 MET cc_start: 0.8397 (ttm) cc_final: 0.8049 (ttm) REVERT: H 138 GLU cc_start: 0.7623 (tt0) cc_final: 0.7360 (tt0) REVERT: H 155 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7424 (p0) REVERT: H 219 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7709 (ttm170) REVERT: I 82 SER cc_start: 0.8566 (p) cc_final: 0.8277 (m) REVERT: I 219 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: J 32 MET cc_start: 0.4070 (mpp) cc_final: 0.3726 (ptt) REVERT: K 135 GLU cc_start: 0.5532 (mp0) cc_final: 0.4635 (tm-30) REVERT: L 66 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7733 (ttmm) REVERT: M 70 TYR cc_start: 0.8473 (m-80) cc_final: 0.8260 (m-10) REVERT: M 74 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: M 80 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6589 (ttm170) REVERT: N 126 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7876 (m) REVERT: P 3 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7745 (tpp-160) REVERT: P 105 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8300 (p0) REVERT: Q 75 MET cc_start: 0.7950 (ptm) cc_final: 0.7571 (ptp) REVERT: Q 83 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: Q 98 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7949 (mmm160) REVERT: R 70 MET cc_start: 0.6651 (mpp) cc_final: 0.6230 (mpp) REVERT: S 41 MET cc_start: 0.7989 (mtt) cc_final: 0.7612 (mmp) REVERT: S 145 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.6233 (m-80) REVERT: T 45 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7853 (mttt) REVERT: T 80 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7594 (ttm170) REVERT: T 126 MET cc_start: 0.3608 (mmt) cc_final: 0.2042 (mtp) REVERT: U 72 GLN cc_start: 0.7988 (mt0) cc_final: 0.7735 (mt0) REVERT: U 108 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7217 (ttp80) REVERT: V 38 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7921 (ttmt) REVERT: V 112 MET cc_start: 0.8116 (tpp) cc_final: 0.7806 (tpp) REVERT: V 130 ASP cc_start: 0.7987 (m-30) cc_final: 0.7779 (m-30) REVERT: W 19 ARG cc_start: 0.5455 (mtt180) cc_final: 0.4527 (mtp85) REVERT: W 44 LYS cc_start: 0.7458 (tppt) cc_final: 0.7070 (ttpt) REVERT: W 62 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7445 (mtt-85) REVERT: W 92 HIS cc_start: 0.6315 (m90) cc_final: 0.6000 (m90) REVERT: Y 18 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7338 (tp30) REVERT: Z 127 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7123 (m110) REVERT: a 74 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7773 (mtp) REVERT: b 84 VAL cc_start: 0.8899 (m) cc_final: 0.8654 (m) REVERT: b 87 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7937 (mtt180) REVERT: b 94 ASP cc_start: 0.8075 (t0) cc_final: 0.7835 (t0) REVERT: c 81 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7827 (ttt180) REVERT: d 37 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7049 (p0) REVERT: d 64 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: f 90 LYS cc_start: 0.4756 (OUTLIER) cc_final: 0.2393 (ptpt) REVERT: f 91 ASN cc_start: 0.5469 (OUTLIER) cc_final: 0.4513 (p0) REVERT: f 140 TYR cc_start: 0.7747 (t80) cc_final: 0.6749 (t80) REVERT: g 145 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: j 82 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.5988 (mtp180) REVERT: k 22 ARG cc_start: 0.4060 (mmt90) cc_final: 0.2984 (ttm-80) REVERT: k 33 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.4100 (mmt180) REVERT: k 64 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.4823 (mtmm) REVERT: k 206 LEU cc_start: 0.4702 (mt) cc_final: 0.4436 (mp) REVERT: k 246 TYR cc_start: 0.3636 (OUTLIER) cc_final: 0.3217 (p90) REVERT: k 331 PHE cc_start: 0.0910 (OUTLIER) cc_final: 0.0306 (m-80) REVERT: k 353 MET cc_start: 0.3285 (tpp) cc_final: 0.3015 (tpt) REVERT: k 385 LYS cc_start: 0.3716 (OUTLIER) cc_final: 0.2470 (pmtt) REVERT: k 505 LYS cc_start: 0.4409 (tptp) cc_final: 0.3819 (tttt) REVERT: k 506 ARG cc_start: 0.3760 (OUTLIER) cc_final: 0.2773 (tmm-80) REVERT: k 555 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6533 (mtp) REVERT: l 10 MET cc_start: 0.7327 (ttp) cc_final: 0.7112 (ttp) outliers start: 370 outliers final: 246 residues processed: 1172 average time/residue: 0.8470 time to fit residues: 1666.2874 Evaluate side-chains 1132 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 854 time to evaluate : 4.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 10 ASP Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 91 ASN Chi-restraints excluded: chain f residue 104 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 50 ILE Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 145 THR Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 246 TYR Chi-restraints excluded: chain k residue 287 CYS Chi-restraints excluded: chain k residue 322 LEU Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 336 THR Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 364 ILE Chi-restraints excluded: chain k residue 374 ILE Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 440 GLN Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 543 THR Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 583 ILE Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 676 optimal weight: 10.0000 chunk 515 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 326 optimal weight: 1.9990 chunk 459 optimal weight: 1.9990 chunk 687 optimal weight: 1.9990 chunk 727 optimal weight: 8.9990 chunk 359 optimal weight: 4.9990 chunk 651 optimal weight: 0.0970 chunk 196 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN I 105 ASN I 110 ASN L 132 GLN ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 GLN ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN P 58 HIS ** Q 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN S 48 GLN S 80 GLN Z 77 ASN ** Z 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 GLN ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 91500 Z= 0.164 Angle : 0.575 11.720 132254 Z= 0.295 Chirality : 0.038 0.263 16271 Planarity : 0.004 0.052 10023 Dihedral : 22.369 179.620 35288 Min Nonbonded Distance : 1.132 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.53 % Favored : 91.45 % Rotamer: Outliers : 6.43 % Allowed : 22.89 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.10), residues: 5824 helix: -0.41 (0.12), residues: 1716 sheet: -0.98 (0.16), residues: 978 loop : -2.22 (0.10), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 204 HIS 0.007 0.001 HIS O 48 PHE 0.026 0.001 PHE k 558 TYR 0.018 0.001 TYR K 113 ARG 0.010 0.000 ARG H 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 887 time to evaluate : 5.021 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: A 127 LEU cc_start: 0.4730 (OUTLIER) cc_final: 0.4530 (tt) REVERT: A 130 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.4843 (tt) REVERT: A 136 TRP cc_start: 0.5092 (OUTLIER) cc_final: 0.4724 (m-10) REVERT: C 34 MET cc_start: 0.8248 (mmm) cc_final: 0.7888 (mtm) REVERT: D 110 MET cc_start: 0.7549 (tpt) cc_final: 0.7148 (tpt) REVERT: E 94 ARG cc_start: 0.8170 (ttp-170) cc_final: 0.7659 (ttm-80) REVERT: E 249 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7385 (t-90) REVERT: F 217 ILE cc_start: 0.3336 (OUTLIER) cc_final: 0.3098 (tt) REVERT: F 227 LYS cc_start: 0.7543 (tptm) cc_final: 0.7120 (tttt) REVERT: G 3 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8263 (mtm180) REVERT: G 200 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7566 (mtt180) REVERT: H 70 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7765 (mtm180) REVERT: H 219 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7825 (ttm110) REVERT: I 82 SER cc_start: 0.8452 (p) cc_final: 0.8216 (m) REVERT: I 219 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: J 28 LEU cc_start: 0.4257 (OUTLIER) cc_final: 0.3567 (mt) REVERT: J 32 MET cc_start: 0.3999 (OUTLIER) cc_final: 0.3748 (ptt) REVERT: J 113 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.4702 (mtpt) REVERT: K 135 GLU cc_start: 0.5645 (mp0) cc_final: 0.4679 (tm-30) REVERT: L 66 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7746 (ttmm) REVERT: N 1 MET cc_start: 0.1195 (mmt) cc_final: 0.0893 (mmt) REVERT: N 97 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6947 (ttp-110) REVERT: P 3 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7886 (tpp-160) REVERT: P 105 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8102 (p0) REVERT: Q 75 MET cc_start: 0.7907 (ptm) cc_final: 0.7544 (ptp) REVERT: Q 83 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: Q 98 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7867 (mmm160) REVERT: R 70 MET cc_start: 0.6624 (mpp) cc_final: 0.6191 (mpp) REVERT: S 41 MET cc_start: 0.8001 (mtt) cc_final: 0.7583 (mmp) REVERT: S 62 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7757 (mtt180) REVERT: T 45 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7917 (mttt) REVERT: T 80 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7643 (ttm170) REVERT: T 126 MET cc_start: 0.3158 (mmt) cc_final: 0.1639 (mtp) REVERT: U 8 LYS cc_start: 0.4596 (OUTLIER) cc_final: 0.4195 (pttm) REVERT: U 24 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8057 (ttp-170) REVERT: U 92 ASP cc_start: 0.6841 (t0) cc_final: 0.6213 (m-30) REVERT: U 108 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7168 (ttp80) REVERT: U 144 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5686 (ppt170) REVERT: V 38 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7877 (ttmt) REVERT: V 112 MET cc_start: 0.8082 (tpp) cc_final: 0.7783 (tpp) REVERT: W 19 ARG cc_start: 0.5583 (mtt180) cc_final: 0.4596 (mtp85) REVERT: W 44 LYS cc_start: 0.7456 (tppt) cc_final: 0.7077 (ttpt) REVERT: W 62 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7383 (mtt-85) REVERT: Y 105 THR cc_start: 0.8665 (t) cc_final: 0.8362 (t) REVERT: Z 119 ARG cc_start: 0.8317 (mtp180) cc_final: 0.8116 (mtm180) REVERT: Z 127 ASN cc_start: 0.7468 (m-40) cc_final: 0.7077 (m110) REVERT: a 11 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8025 (ptpt) REVERT: a 74 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: b 46 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: b 87 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7516 (mtt180) REVERT: b 94 ASP cc_start: 0.8065 (t0) cc_final: 0.7765 (t0) REVERT: d 37 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7067 (p0) REVERT: d 64 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: f 90 LYS cc_start: 0.4101 (OUTLIER) cc_final: 0.2145 (pttt) REVERT: f 140 TYR cc_start: 0.7712 (t80) cc_final: 0.6818 (t80) REVERT: g 145 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: j 62 ARG cc_start: 0.8666 (ptt90) cc_final: 0.8431 (ptt180) REVERT: j 82 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6070 (mtp180) REVERT: k 22 ARG cc_start: 0.3991 (mmt90) cc_final: 0.2879 (ttm-80) REVERT: k 33 ARG cc_start: 0.5571 (OUTLIER) cc_final: 0.4264 (mmt180) REVERT: k 64 LYS cc_start: 0.6092 (tttp) cc_final: 0.4758 (mtmm) REVERT: k 80 GLU cc_start: 0.5956 (tp30) cc_final: 0.5136 (tt0) REVERT: k 101 ARG cc_start: 0.3314 (mmm160) cc_final: 0.3027 (mtp85) REVERT: k 204 LEU cc_start: 0.3137 (OUTLIER) cc_final: 0.2655 (tt) REVERT: k 206 LEU cc_start: 0.4596 (mt) cc_final: 0.4177 (mt) REVERT: k 353 MET cc_start: 0.2983 (tpp) cc_final: 0.2729 (tpt) REVERT: k 385 LYS cc_start: 0.3733 (OUTLIER) cc_final: 0.2567 (pmtt) REVERT: k 425 ARG cc_start: 0.2893 (tpt-90) cc_final: 0.2410 (mtm180) REVERT: k 505 LYS cc_start: 0.4529 (tptp) cc_final: 0.3804 (tttt) REVERT: k 506 ARG cc_start: 0.3604 (OUTLIER) cc_final: 0.2732 (tmm-80) REVERT: k 535 PHE cc_start: 0.4465 (OUTLIER) cc_final: 0.3683 (m-80) outliers start: 328 outliers final: 219 residues processed: 1113 average time/residue: 0.9155 time to fit residues: 1722.9331 Evaluate side-chains 1106 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 853 time to evaluate : 5.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 10 ASP Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 90 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 16 LYS Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 104 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 215 GLN Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 204 LEU Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 336 THR Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 364 ILE Chi-restraints excluded: chain k residue 378 LEU Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 535 PHE Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 606 optimal weight: 6.9990 chunk 413 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 541 optimal weight: 8.9990 chunk 300 optimal weight: 9.9990 chunk 621 optimal weight: 8.9990 chunk 503 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 371 optimal weight: 4.9990 chunk 653 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 ASN G 161 GLN I 13 GLN I 105 ASN I 110 ASN L 132 GLN N 121 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN R 32 GLN S 80 GLN Z 77 ASN ** Z 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 91500 Z= 0.415 Angle : 0.733 12.173 132254 Z= 0.370 Chirality : 0.046 0.355 16271 Planarity : 0.006 0.059 10023 Dihedral : 22.470 179.849 35253 Min Nonbonded Distance : 0.974 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.94 % Favored : 90.04 % Rotamer: Outliers : 8.13 % Allowed : 22.50 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.10), residues: 5824 helix: -0.65 (0.12), residues: 1718 sheet: -1.11 (0.16), residues: 1008 loop : -2.29 (0.10), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 204 HIS 0.010 0.002 HIS e 10 PHE 0.024 0.002 PHE L 147 TYR 0.023 0.002 TYR A 33 ARG 0.014 0.001 ARG k 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 856 time to evaluate : 5.052 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: A 9 TYR cc_start: 0.5289 (m-10) cc_final: 0.5078 (m-80) REVERT: A 127 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4503 (tt) REVERT: A 136 TRP cc_start: 0.5147 (OUTLIER) cc_final: 0.4481 (m-10) REVERT: C 9 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7123 (tm-30) REVERT: C 34 MET cc_start: 0.8315 (mmm) cc_final: 0.7917 (mtm) REVERT: D 110 MET cc_start: 0.7627 (tpt) cc_final: 0.7032 (tpt) REVERT: D 162 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8029 (mtp85) REVERT: E 94 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7812 (ttm-80) REVERT: E 210 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8657 (tp) REVERT: E 225 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: E 249 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7532 (t-90) REVERT: F 217 ILE cc_start: 0.3635 (OUTLIER) cc_final: 0.3360 (tt) REVERT: G 200 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7719 (mtt-85) REVERT: H 179 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7711 (mtp180) REVERT: H 219 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7908 (ttm170) REVERT: I 82 SER cc_start: 0.8569 (p) cc_final: 0.8292 (m) REVERT: I 219 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: J 18 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: J 28 LEU cc_start: 0.4088 (OUTLIER) cc_final: 0.3196 (mm) REVERT: J 32 MET cc_start: 0.4214 (mpp) cc_final: 0.3804 (ptt) REVERT: J 84 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5858 (tm-30) REVERT: J 113 LYS cc_start: 0.5692 (OUTLIER) cc_final: 0.4751 (mtpt) REVERT: K 135 GLU cc_start: 0.5461 (mp0) cc_final: 0.4496 (tm-30) REVERT: L 66 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7858 (ttmm) REVERT: M 80 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6482 (ttm170) REVERT: N 1 MET cc_start: 0.1302 (mmt) cc_final: 0.1063 (mmt) REVERT: N 5 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8815 (mm-40) REVERT: P 3 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7548 (tpp-160) REVERT: P 105 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8462 (p0) REVERT: Q 83 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: R 70 MET cc_start: 0.6769 (mpp) cc_final: 0.5986 (mtp) REVERT: S 62 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8194 (mtt180) REVERT: S 96 TYR cc_start: 0.8698 (m-80) cc_final: 0.8451 (m-10) REVERT: S 145 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: T 45 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7867 (mttt) REVERT: T 126 MET cc_start: 0.2544 (mmt) cc_final: 0.1221 (mtt) REVERT: U 8 LYS cc_start: 0.4644 (OUTLIER) cc_final: 0.4100 (pttm) REVERT: U 24 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8074 (ttp-170) REVERT: U 91 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7611 (tppt) REVERT: U 108 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7292 (ttp80) REVERT: V 13 GLU cc_start: 0.7054 (mp0) cc_final: 0.6822 (mp0) REVERT: V 38 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7917 (ttmt) REVERT: W 19 ARG cc_start: 0.5560 (mtt180) cc_final: 0.4973 (mtp85) REVERT: W 44 LYS cc_start: 0.7487 (tppt) cc_final: 0.7104 (ttpt) REVERT: W 62 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7338 (mtt-85) REVERT: X 41 LYS cc_start: 0.7883 (tptp) cc_final: 0.7674 (tptp) REVERT: Y 105 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8573 (t) REVERT: Z 127 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7157 (m110) REVERT: a 11 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8043 (ptpt) REVERT: a 74 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: b 46 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: b 87 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7948 (mtt180) REVERT: b 94 ASP cc_start: 0.8081 (t0) cc_final: 0.7831 (t0) REVERT: d 37 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7049 (p0) REVERT: d 64 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: f 90 LYS cc_start: 0.4469 (OUTLIER) cc_final: 0.2530 (pttt) REVERT: f 140 TYR cc_start: 0.7794 (t80) cc_final: 0.6796 (t80) REVERT: g 145 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: g 271 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7162 (tptt) REVERT: g 285 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: i 132 ASN cc_start: 0.8573 (m-40) cc_final: 0.8354 (m-40) REVERT: j 40 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6752 (ptpt) REVERT: j 82 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6199 (mtp180) REVERT: k 22 ARG cc_start: 0.4009 (mmt90) cc_final: 0.2905 (ttm-80) REVERT: k 64 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.4613 (mtmm) REVERT: k 80 GLU cc_start: 0.6031 (tp30) cc_final: 0.5186 (tt0) REVERT: k 288 CYS cc_start: 0.4352 (OUTLIER) cc_final: 0.3582 (t) REVERT: k 290 TYR cc_start: 0.2956 (m-80) cc_final: 0.2358 (m-80) REVERT: k 300 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7390 (p) REVERT: k 331 PHE cc_start: 0.1716 (OUTLIER) cc_final: 0.0827 (m-80) REVERT: k 353 MET cc_start: 0.3201 (tpp) cc_final: 0.2884 (tpt) REVERT: k 385 LYS cc_start: 0.3859 (OUTLIER) cc_final: 0.2926 (pmtt) REVERT: k 505 LYS cc_start: 0.4613 (tptp) cc_final: 0.3776 (ttpt) REVERT: k 506 ARG cc_start: 0.3584 (OUTLIER) cc_final: 0.2711 (tmm-80) REVERT: k 523 ILE cc_start: 0.4442 (OUTLIER) cc_final: 0.3862 (tt) REVERT: k 535 PHE cc_start: 0.4424 (OUTLIER) cc_final: 0.3889 (t80) REVERT: k 555 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6554 (mtp) REVERT: n 111 ARG cc_start: 0.7840 (ptt-90) cc_final: 0.7466 (ptt180) outliers start: 415 outliers final: 307 residues processed: 1164 average time/residue: 0.8430 time to fit residues: 1651.4402 Evaluate side-chains 1185 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 830 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 51 ARG Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 35 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 272 GLN Chi-restraints excluded: chain g residue 285 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 114 ARG Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain j residue 40 LYS Chi-restraints excluded: chain j residue 50 MET Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 61 CYS Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 99 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 145 THR Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 288 CYS Chi-restraints excluded: chain k residue 300 THR Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 322 LEU Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 333 VAL Chi-restraints excluded: chain k residue 336 THR Chi-restraints excluded: chain k residue 354 LYS Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 365 VAL Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 440 GLN Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 454 ILE Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 523 ILE Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 535 PHE Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 564 ILE Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 583 ILE Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 74 SER Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 244 optimal weight: 5.9990 chunk 655 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 427 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 728 optimal weight: 8.9990 chunk 604 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 13 GLN I 105 ASN I 110 ASN J 76 GLN L 132 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN R 32 GLN V 12 GLN V 126 GLN ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 561 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 91500 Z= 0.266 Angle : 0.637 11.975 132254 Z= 0.325 Chirality : 0.041 0.268 16271 Planarity : 0.005 0.064 10023 Dihedral : 22.415 179.734 35243 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.03 % Favored : 90.95 % Rotamer: Outliers : 7.86 % Allowed : 23.32 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.10), residues: 5824 helix: -0.47 (0.12), residues: 1714 sheet: -0.93 (0.16), residues: 976 loop : -2.24 (0.10), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 204 HIS 0.007 0.001 HIS e 10 PHE 0.020 0.002 PHE k 558 TYR 0.020 0.002 TYR A 39 ARG 0.015 0.000 ARG k 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 873 time to evaluate : 5.059 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: A 9 TYR cc_start: 0.5162 (m-10) cc_final: 0.4776 (m-80) REVERT: A 50 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: A 127 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.4512 (tt) REVERT: A 130 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5116 (tt) REVERT: A 136 TRP cc_start: 0.5264 (OUTLIER) cc_final: 0.4821 (m-10) REVERT: C 34 MET cc_start: 0.8257 (mmm) cc_final: 0.7942 (mtm) REVERT: C 35 GLU cc_start: 0.7581 (tp30) cc_final: 0.7310 (mm-30) REVERT: D 105 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7895 (mp) REVERT: D 110 MET cc_start: 0.7593 (tpt) cc_final: 0.7015 (tpt) REVERT: E 94 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7795 (ttm-80) REVERT: E 225 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: E 249 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7557 (t-90) REVERT: F 217 ILE cc_start: 0.3485 (OUTLIER) cc_final: 0.3229 (tt) REVERT: G 200 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7691 (mtt-85) REVERT: H 179 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7631 (mtp180) REVERT: H 219 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7897 (ttm170) REVERT: I 82 SER cc_start: 0.8561 (p) cc_final: 0.8285 (m) REVERT: J 18 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: J 28 LEU cc_start: 0.4400 (OUTLIER) cc_final: 0.3687 (mt) REVERT: J 32 MET cc_start: 0.4151 (OUTLIER) cc_final: 0.3762 (ptt) REVERT: J 113 LYS cc_start: 0.5650 (OUTLIER) cc_final: 0.4681 (mtpt) REVERT: K 135 GLU cc_start: 0.5273 (mp0) cc_final: 0.4213 (tm-30) REVERT: L 66 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7795 (ttmm) REVERT: M 18 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7703 (mm-30) REVERT: M 25 LYS cc_start: 0.8703 (tttm) cc_final: 0.8459 (tttt) REVERT: M 80 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6549 (ttm170) REVERT: N 1 MET cc_start: 0.1426 (mmt) cc_final: 0.1207 (mmt) REVERT: O 78 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6830 (mtpt) REVERT: P 3 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7734 (tpp-160) REVERT: P 105 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8398 (p0) REVERT: Q 83 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: Q 98 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7899 (mmm160) REVERT: R 70 MET cc_start: 0.6753 (mpp) cc_final: 0.5968 (mtp) REVERT: S 41 MET cc_start: 0.8036 (mtt) cc_final: 0.7644 (mmp) REVERT: S 62 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8042 (mtt180) REVERT: S 145 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: T 1 MET cc_start: 0.5071 (OUTLIER) cc_final: 0.3397 (tpt) REVERT: T 45 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7869 (mttt) REVERT: T 126 MET cc_start: 0.2814 (mmt) cc_final: 0.1570 (mtp) REVERT: U 8 LYS cc_start: 0.4740 (OUTLIER) cc_final: 0.4204 (pttm) REVERT: U 24 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8050 (ttp-170) REVERT: U 61 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: U 77 TYR cc_start: 0.8350 (m-80) cc_final: 0.7914 (m-80) REVERT: U 91 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7575 (tppt) REVERT: U 108 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7248 (ttp80) REVERT: U 144 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5530 (ppt170) REVERT: V 38 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7901 (ttmt) REVERT: W 19 ARG cc_start: 0.5462 (mtt180) cc_final: 0.4933 (mtp85) REVERT: W 62 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7492 (mtt-85) REVERT: Y 28 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8206 (ppt90) REVERT: Y 105 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8518 (t) REVERT: Z 127 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7121 (m110) REVERT: a 11 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8052 (ptpt) REVERT: a 39 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: a 74 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7889 (mtp) REVERT: a 97 TYR cc_start: 0.7927 (t80) cc_final: 0.7705 (t80) REVERT: b 46 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: b 87 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7939 (mtt180) REVERT: d 37 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7022 (p0) REVERT: d 64 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: f 90 LYS cc_start: 0.4335 (OUTLIER) cc_final: 0.2542 (pttt) REVERT: f 140 TYR cc_start: 0.7772 (t80) cc_final: 0.6823 (t80) REVERT: g 5 MET cc_start: 0.6948 (mmt) cc_final: 0.6657 (mmt) REVERT: g 77 PHE cc_start: 0.8161 (m-80) cc_final: 0.7955 (m-80) REVERT: g 271 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7029 (tptt) REVERT: g 285 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8195 (mp10) REVERT: i 132 ASN cc_start: 0.8503 (m-40) cc_final: 0.8268 (m-40) REVERT: j 40 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6826 (ptpt) REVERT: j 82 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6130 (mtp180) REVERT: j 109 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.6985 (tt) REVERT: k 22 ARG cc_start: 0.4052 (mmt90) cc_final: 0.2981 (ttm-80) REVERT: k 33 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.4268 (mmt180) REVERT: k 64 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.4785 (mtmm) REVERT: k 80 GLU cc_start: 0.5960 (tp30) cc_final: 0.5205 (tt0) REVERT: k 101 ARG cc_start: 0.3062 (mmm160) cc_final: 0.2824 (mmm160) REVERT: k 288 CYS cc_start: 0.4151 (OUTLIER) cc_final: 0.3455 (t) REVERT: k 331 PHE cc_start: 0.1754 (OUTLIER) cc_final: 0.0888 (m-80) REVERT: k 353 MET cc_start: 0.3415 (tpp) cc_final: 0.3092 (tpt) REVERT: k 377 MET cc_start: 0.4653 (ttt) cc_final: 0.4437 (ttp) REVERT: k 385 LYS cc_start: 0.3953 (OUTLIER) cc_final: 0.2705 (pmtt) REVERT: k 411 TYR cc_start: 0.3828 (t80) cc_final: 0.3396 (t80) REVERT: k 497 ARG cc_start: 0.6336 (mtm110) cc_final: 0.5745 (mtm-85) REVERT: k 505 LYS cc_start: 0.4532 (tptp) cc_final: 0.3650 (ttpt) REVERT: k 506 ARG cc_start: 0.3570 (OUTLIER) cc_final: 0.2682 (tmm-80) REVERT: k 555 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6474 (mtp) REVERT: n 94 LYS cc_start: 0.7701 (mttm) cc_final: 0.7369 (mttm) REVERT: n 111 ARG cc_start: 0.7949 (ptt-90) cc_final: 0.7582 (ptt180) outliers start: 401 outliers final: 287 residues processed: 1165 average time/residue: 0.8428 time to fit residues: 1642.8329 Evaluate side-chains 1193 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 854 time to evaluate : 5.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 78 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 90 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 26 ASP Chi-restraints excluded: chain a residue 34 THR Chi-restraints excluded: chain a residue 39 GLU Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 104 ARG Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 104 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 29 ASP Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 272 GLN Chi-restraints excluded: chain g residue 285 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 114 ARG Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 40 LYS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 227 CYS Chi-restraints excluded: chain k residue 288 CYS Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 322 LEU Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 336 THR Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 440 GLN Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 583 ILE Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 74 SER Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 702 optimal weight: 0.3980 chunk 82 optimal weight: 20.0000 chunk 415 optimal weight: 2.9990 chunk 532 optimal weight: 10.0000 chunk 412 optimal weight: 7.9990 chunk 613 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 725 optimal weight: 10.0000 chunk 454 optimal weight: 8.9990 chunk 442 optimal weight: 20.0000 chunk 335 optimal weight: 0.9980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 ASN I 110 ASN L 132 GLN ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN R 32 GLN V 12 GLN k 153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 91500 Z= 0.284 Angle : 0.650 13.939 132254 Z= 0.331 Chirality : 0.041 0.270 16271 Planarity : 0.005 0.067 10023 Dihedral : 22.400 179.681 35231 Min Nonbonded Distance : 1.022 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.75 % Favored : 90.23 % Rotamer: Outliers : 8.00 % Allowed : 23.34 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 5824 helix: -0.41 (0.12), residues: 1707 sheet: -0.86 (0.16), residues: 964 loop : -2.21 (0.10), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 204 HIS 0.008 0.001 HIS e 10 PHE 0.020 0.002 PHE k 147 TYR 0.018 0.002 TYR T 21 ARG 0.018 0.000 ARG k 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 408 poor density : 869 time to evaluate : 5.112 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: A 50 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: A 127 LEU cc_start: 0.4817 (OUTLIER) cc_final: 0.4561 (tt) REVERT: A 130 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5080 (tt) REVERT: A 136 TRP cc_start: 0.5208 (OUTLIER) cc_final: 0.4730 (m-10) REVERT: C 9 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6976 (tm-30) REVERT: C 34 MET cc_start: 0.8275 (mmm) cc_final: 0.7932 (mtm) REVERT: C 35 GLU cc_start: 0.7572 (tp30) cc_final: 0.7337 (mm-30) REVERT: D 110 MET cc_start: 0.7585 (tpt) cc_final: 0.7007 (tpt) REVERT: E 94 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7729 (ttm-80) REVERT: E 225 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: E 249 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7612 (t-90) REVERT: F 217 ILE cc_start: 0.3798 (OUTLIER) cc_final: 0.3511 (tt) REVERT: G 200 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7689 (mtt-85) REVERT: H 179 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7690 (mtp180) REVERT: H 219 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7835 (ttm170) REVERT: I 82 SER cc_start: 0.8562 (p) cc_final: 0.8290 (m) REVERT: J 18 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5807 (tm-30) REVERT: J 28 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.3600 (mt) REVERT: J 32 MET cc_start: 0.4111 (OUTLIER) cc_final: 0.3759 (ptt) REVERT: J 84 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.5883 (tm-30) REVERT: J 113 LYS cc_start: 0.5731 (OUTLIER) cc_final: 0.4739 (mtpt) REVERT: K 135 GLU cc_start: 0.5233 (mp0) cc_final: 0.4239 (tm-30) REVERT: L 66 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7767 (ttmm) REVERT: M 18 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7733 (mm-30) REVERT: M 80 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6494 (ttm170) REVERT: O 78 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6831 (ttmt) REVERT: P 3 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7720 (tpp-160) REVERT: P 105 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8380 (p0) REVERT: Q 83 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: Q 98 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7944 (mmm160) REVERT: R 70 MET cc_start: 0.6816 (mpp) cc_final: 0.6007 (mtp) REVERT: S 41 MET cc_start: 0.8038 (mtt) cc_final: 0.7673 (mmp) REVERT: S 62 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8103 (mtt180) REVERT: S 96 TYR cc_start: 0.8670 (m-80) cc_final: 0.8420 (m-10) REVERT: S 145 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: T 45 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (mttt) REVERT: T 126 MET cc_start: 0.2967 (mmt) cc_final: 0.0790 (mtt) REVERT: U 8 LYS cc_start: 0.4725 (OUTLIER) cc_final: 0.4222 (pttm) REVERT: U 24 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8062 (ttp-170) REVERT: U 61 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: U 77 TYR cc_start: 0.8382 (m-80) cc_final: 0.7928 (m-80) REVERT: U 108 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7256 (ttp80) REVERT: U 144 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5432 (ppt170) REVERT: V 38 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7888 (ttmt) REVERT: W 17 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7055 (pp) REVERT: W 19 ARG cc_start: 0.5594 (mtt180) cc_final: 0.5022 (mtp85) REVERT: W 62 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7498 (mtt-85) REVERT: Y 28 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8211 (ppt90) REVERT: Y 105 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8540 (t) REVERT: Y 112 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7660 (p0) REVERT: Z 127 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7120 (m110) REVERT: a 11 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8050 (ptpt) REVERT: a 74 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: a 97 TYR cc_start: 0.7968 (t80) cc_final: 0.7750 (t80) REVERT: b 46 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: b 87 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7951 (mtt180) REVERT: d 37 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7011 (p0) REVERT: d 64 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: f 90 LYS cc_start: 0.4143 (OUTLIER) cc_final: 0.2324 (pttt) REVERT: f 91 ASN cc_start: 0.5599 (p0) cc_final: 0.5264 (p0) REVERT: f 140 TYR cc_start: 0.7746 (t80) cc_final: 0.6777 (t80) REVERT: g 271 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7032 (tptt) REVERT: g 285 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: i 82 ARG cc_start: 0.7234 (ptm-80) cc_final: 0.6962 (ptm160) REVERT: i 132 ASN cc_start: 0.8497 (m-40) cc_final: 0.8226 (m-40) REVERT: j 40 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6717 (ptpt) REVERT: j 82 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6142 (mtp180) REVERT: j 109 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7058 (tt) REVERT: k 22 ARG cc_start: 0.4067 (mmt90) cc_final: 0.2982 (ttm-80) REVERT: k 33 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.3943 (mmm160) REVERT: k 64 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.4776 (mtmm) REVERT: k 80 GLU cc_start: 0.5873 (tp30) cc_final: 0.5237 (tt0) REVERT: k 101 ARG cc_start: 0.3068 (mmm160) cc_final: 0.2833 (mmm160) REVERT: k 127 GLN cc_start: 0.5436 (tp-100) cc_final: 0.4592 (mp10) REVERT: k 155 TYR cc_start: 0.6534 (t80) cc_final: 0.6128 (t80) REVERT: k 288 CYS cc_start: 0.4310 (OUTLIER) cc_final: 0.3451 (t) REVERT: k 331 PHE cc_start: 0.1825 (OUTLIER) cc_final: 0.0976 (m-80) REVERT: k 353 MET cc_start: 0.3366 (tpp) cc_final: 0.3061 (tpt) REVERT: k 385 LYS cc_start: 0.3638 (OUTLIER) cc_final: 0.2395 (pmtt) REVERT: k 497 ARG cc_start: 0.6500 (mtm110) cc_final: 0.6107 (mtm110) REVERT: k 505 LYS cc_start: 0.4318 (tptp) cc_final: 0.3642 (mttt) REVERT: k 506 ARG cc_start: 0.3602 (OUTLIER) cc_final: 0.2686 (tmm-80) REVERT: k 548 PRO cc_start: 0.3519 (Cg_exo) cc_final: 0.3244 (Cg_endo) REVERT: k 555 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6602 (mtp) REVERT: n 111 ARG cc_start: 0.7999 (ptt-90) cc_final: 0.7627 (ptt180) outliers start: 408 outliers final: 310 residues processed: 1169 average time/residue: 0.8409 time to fit residues: 1653.5858 Evaluate side-chains 1217 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 856 time to evaluate : 4.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 109 ARG Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 78 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 97 GLN Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 90 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 34 THR Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 85 ASN Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 104 ARG Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 272 GLN Chi-restraints excluded: chain g residue 285 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 114 ARG Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain j residue 40 LYS Chi-restraints excluded: chain j residue 50 MET Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 145 THR Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 227 CYS Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 288 CYS Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 322 LEU Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 354 LYS Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 365 VAL Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 440 GLN Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 457 GLN Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 564 ILE Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 583 ILE Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 4 LYS Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 74 SER Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 449 optimal weight: 9.9990 chunk 289 optimal weight: 0.0670 chunk 433 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 461 optimal weight: 6.9990 chunk 494 optimal weight: 7.9990 chunk 358 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 570 optimal weight: 7.9990 overall best weight: 4.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 ASN I 110 ASN L 132 GLN ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN R 32 GLN V 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 91500 Z= 0.303 Angle : 0.661 12.454 132254 Z= 0.336 Chirality : 0.042 0.271 16271 Planarity : 0.005 0.071 10023 Dihedral : 22.402 179.701 35227 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.41 % Favored : 90.57 % Rotamer: Outliers : 7.92 % Allowed : 23.79 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.10), residues: 5824 helix: -0.41 (0.12), residues: 1704 sheet: -0.87 (0.16), residues: 967 loop : -2.18 (0.10), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP k 140 HIS 0.008 0.001 HIS e 10 PHE 0.020 0.002 PHE L 147 TYR 0.019 0.002 TYR k 246 ARG 0.012 0.000 ARG H 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 862 time to evaluate : 5.067 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: A 50 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: A 127 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4562 (tt) REVERT: A 130 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5152 (tt) REVERT: A 136 TRP cc_start: 0.5345 (OUTLIER) cc_final: 0.4980 (m-10) REVERT: C 9 GLN cc_start: 0.7402 (tm-30) cc_final: 0.7181 (tm-30) REVERT: C 34 MET cc_start: 0.8269 (mmm) cc_final: 0.7947 (mtm) REVERT: C 74 VAL cc_start: 0.9022 (t) cc_final: 0.8814 (t) REVERT: C 84 GLN cc_start: 0.7614 (mt0) cc_final: 0.7384 (mm110) REVERT: C 121 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8773 (tp) REVERT: D 105 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (mp) REVERT: D 110 MET cc_start: 0.7602 (tpt) cc_final: 0.7011 (tpt) REVERT: E 94 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7736 (ttm-80) REVERT: E 225 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: E 249 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7605 (t-90) REVERT: F 217 ILE cc_start: 0.3919 (OUTLIER) cc_final: 0.3624 (tt) REVERT: G 200 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7630 (mtt180) REVERT: H 179 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7657 (mtp180) REVERT: H 219 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7835 (ttm170) REVERT: I 82 SER cc_start: 0.8569 (p) cc_final: 0.8308 (m) REVERT: J 18 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5626 (tm-30) REVERT: J 28 LEU cc_start: 0.4313 (OUTLIER) cc_final: 0.3617 (mt) REVERT: J 32 MET cc_start: 0.4091 (OUTLIER) cc_final: 0.3723 (ptt) REVERT: J 84 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5805 (tm-30) REVERT: J 113 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.4833 (mtpt) REVERT: J 120 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6790 (mpt180) REVERT: K 135 GLU cc_start: 0.5204 (mp0) cc_final: 0.4249 (tm-30) REVERT: L 66 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7772 (ttmm) REVERT: M 18 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7742 (mm-30) REVERT: M 25 LYS cc_start: 0.8710 (tttm) cc_final: 0.8455 (tttt) REVERT: M 80 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6552 (ttm170) REVERT: O 78 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6913 (mtpt) REVERT: P 3 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7700 (tpp-160) REVERT: P 105 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8399 (p0) REVERT: Q 83 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: Q 98 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7975 (mmm160) REVERT: R 70 MET cc_start: 0.6823 (mpp) cc_final: 0.6073 (mtp) REVERT: S 41 MET cc_start: 0.8017 (mtt) cc_final: 0.7654 (mmp) REVERT: S 62 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8129 (mtt180) REVERT: S 145 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: T 45 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7955 (mttt) REVERT: T 126 MET cc_start: 0.3070 (mmt) cc_final: 0.0778 (mtt) REVERT: U 8 LYS cc_start: 0.4496 (OUTLIER) cc_final: 0.3983 (pttm) REVERT: U 24 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8064 (ttp-170) REVERT: U 61 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: U 108 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7263 (ttp80) REVERT: U 144 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5431 (ppt170) REVERT: V 38 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7895 (ttmt) REVERT: W 17 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7013 (pp) REVERT: W 19 ARG cc_start: 0.5515 (mtt180) cc_final: 0.4969 (mtp85) REVERT: W 62 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7391 (mtt-85) REVERT: Y 28 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (ppt90) REVERT: Y 105 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8558 (t) REVERT: Y 112 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7676 (p0) REVERT: Z 127 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7120 (m110) REVERT: a 11 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8048 (ptpt) REVERT: a 74 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7889 (mtp) REVERT: a 97 TYR cc_start: 0.7998 (t80) cc_final: 0.7774 (t80) REVERT: b 46 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6800 (mm-30) REVERT: b 87 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7921 (mtt180) REVERT: d 37 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7026 (p0) REVERT: d 64 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: f 91 ASN cc_start: 0.5520 (p0) cc_final: 0.5178 (p0) REVERT: f 140 TYR cc_start: 0.7744 (t80) cc_final: 0.6779 (t80) REVERT: g 271 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7036 (tptt) REVERT: g 285 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: i 132 ASN cc_start: 0.8490 (m-40) cc_final: 0.8220 (m-40) REVERT: j 40 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6670 (ptpt) REVERT: j 62 ARG cc_start: 0.8794 (ptt90) cc_final: 0.8409 (ptt180) REVERT: j 82 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6120 (mtp180) REVERT: j 109 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7055 (tt) REVERT: k 22 ARG cc_start: 0.4073 (mmt90) cc_final: 0.2985 (ttm-80) REVERT: k 33 ARG cc_start: 0.5317 (OUTLIER) cc_final: 0.3827 (mmm160) REVERT: k 64 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.4729 (mtmm) REVERT: k 80 GLU cc_start: 0.5856 (tp30) cc_final: 0.5206 (tt0) REVERT: k 101 ARG cc_start: 0.3068 (mmm160) cc_final: 0.2839 (mmm160) REVERT: k 127 GLN cc_start: 0.5381 (tp-100) cc_final: 0.4549 (mp10) REVERT: k 155 TYR cc_start: 0.6493 (t80) cc_final: 0.6051 (t80) REVERT: k 288 CYS cc_start: 0.4309 (OUTLIER) cc_final: 0.3251 (t) REVERT: k 331 PHE cc_start: 0.1827 (OUTLIER) cc_final: 0.0982 (m-80) REVERT: k 353 MET cc_start: 0.3325 (tpp) cc_final: 0.3032 (tpt) REVERT: k 385 LYS cc_start: 0.3553 (OUTLIER) cc_final: 0.2358 (pmtt) REVERT: k 505 LYS cc_start: 0.4377 (tptp) cc_final: 0.3766 (mttt) REVERT: k 506 ARG cc_start: 0.3578 (OUTLIER) cc_final: 0.2598 (tmm-80) REVERT: k 548 PRO cc_start: 0.3662 (Cg_exo) cc_final: 0.3363 (Cg_endo) REVERT: k 555 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6635 (mtp) REVERT: n 111 ARG cc_start: 0.7916 (ptt-90) cc_final: 0.7551 (ptt180) outliers start: 404 outliers final: 319 residues processed: 1159 average time/residue: 0.9591 time to fit residues: 1890.4004 Evaluate side-chains 1218 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 846 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 109 ARG Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 78 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 97 GLN Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 90 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 34 THR Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 85 ASN Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 104 ARG Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 104 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain f residue 132 MET Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 272 GLN Chi-restraints excluded: chain g residue 285 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 114 ARG Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 40 LYS Chi-restraints excluded: chain j residue 50 MET Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 145 THR Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 224 ARG Chi-restraints excluded: chain k residue 227 CYS Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 288 CYS Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 322 LEU Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 440 GLN Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 457 GLN Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 564 ILE Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 583 ILE Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 4 LYS Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 74 SER Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 660 optimal weight: 9.9990 chunk 695 optimal weight: 40.0000 chunk 634 optimal weight: 10.0000 chunk 676 optimal weight: 7.9990 chunk 407 optimal weight: 7.9990 chunk 294 optimal weight: 3.9990 chunk 531 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 611 optimal weight: 1.9990 chunk 639 optimal weight: 30.0000 chunk 673 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 110 ASN L 132 GLN N 5 GLN N 121 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN V 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 91500 Z= 0.327 Angle : 0.680 12.032 132254 Z= 0.345 Chirality : 0.043 0.276 16271 Planarity : 0.005 0.071 10023 Dihedral : 22.423 179.901 35222 Min Nonbonded Distance : 1.008 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.96 % Favored : 90.02 % Rotamer: Outliers : 7.84 % Allowed : 23.97 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 5824 helix: -0.48 (0.12), residues: 1709 sheet: -0.93 (0.16), residues: 977 loop : -2.20 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 204 HIS 0.009 0.001 HIS e 10 PHE 0.021 0.002 PHE L 147 TYR 0.020 0.002 TYR k 246 ARG 0.013 0.001 ARG H 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 861 time to evaluate : 5.038 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: A 50 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: A 127 LEU cc_start: 0.4987 (OUTLIER) cc_final: 0.4741 (tt) REVERT: A 130 LEU cc_start: 0.5491 (OUTLIER) cc_final: 0.5050 (tt) REVERT: A 136 TRP cc_start: 0.5231 (OUTLIER) cc_final: 0.4870 (m-10) REVERT: C 9 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7258 (tm-30) REVERT: C 31 ASP cc_start: 0.7656 (p0) cc_final: 0.7064 (m-30) REVERT: C 34 MET cc_start: 0.8349 (mmm) cc_final: 0.8027 (mtm) REVERT: D 105 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7911 (mp) REVERT: D 110 MET cc_start: 0.7611 (tpt) cc_final: 0.7012 (tpt) REVERT: E 94 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7734 (ttm-80) REVERT: E 225 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: E 249 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7645 (t-90) REVERT: F 217 ILE cc_start: 0.4046 (OUTLIER) cc_final: 0.3761 (tt) REVERT: G 200 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7721 (mtt-85) REVERT: H 179 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7670 (mtp180) REVERT: H 219 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7770 (ttm110) REVERT: I 82 SER cc_start: 0.8596 (p) cc_final: 0.8333 (m) REVERT: J 18 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5610 (tm-30) REVERT: J 28 LEU cc_start: 0.4341 (OUTLIER) cc_final: 0.3628 (mt) REVERT: J 32 MET cc_start: 0.4190 (OUTLIER) cc_final: 0.3790 (ptt) REVERT: J 84 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.5829 (tm-30) REVERT: J 120 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6740 (mpt180) REVERT: K 135 GLU cc_start: 0.5229 (mp0) cc_final: 0.4400 (tm-30) REVERT: L 66 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7777 (ttmm) REVERT: M 80 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6584 (ttm170) REVERT: P 3 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7616 (tpp-160) REVERT: P 105 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8433 (p0) REVERT: Q 83 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: R 70 MET cc_start: 0.6901 (mpp) cc_final: 0.6149 (mtp) REVERT: S 31 LEU cc_start: 0.8567 (tt) cc_final: 0.8339 (tt) REVERT: S 41 MET cc_start: 0.8016 (mtt) cc_final: 0.7757 (mmt) REVERT: S 62 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8395 (mtt180) REVERT: S 145 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: T 45 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7974 (mttt) REVERT: T 126 MET cc_start: 0.2701 (mmt) cc_final: 0.0564 (mtt) REVERT: U 8 LYS cc_start: 0.4490 (OUTLIER) cc_final: 0.4045 (pttm) REVERT: U 24 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8070 (ttp-170) REVERT: U 61 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: U 92 ASP cc_start: 0.7034 (t0) cc_final: 0.6647 (t0) REVERT: U 108 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7269 (ttp80) REVERT: U 144 ARG cc_start: 0.6022 (OUTLIER) cc_final: 0.5490 (ppt170) REVERT: V 38 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7892 (ttmt) REVERT: W 17 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7024 (pp) REVERT: W 19 ARG cc_start: 0.5457 (mtt180) cc_final: 0.4916 (mtp85) REVERT: W 62 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7327 (mtt-85) REVERT: Y 28 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8227 (ppt90) REVERT: Y 105 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8594 (t) REVERT: Y 112 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7697 (p0) REVERT: Z 127 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7119 (m110) REVERT: a 11 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8060 (ptpt) REVERT: a 74 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7854 (mtp) REVERT: b 46 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: b 87 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7937 (mtt180) REVERT: d 37 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7036 (p0) REVERT: d 64 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: f 91 ASN cc_start: 0.5284 (p0) cc_final: 0.4957 (p0) REVERT: f 140 TYR cc_start: 0.7746 (t80) cc_final: 0.6752 (t80) REVERT: g 271 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7038 (tptt) REVERT: g 285 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: i 82 ARG cc_start: 0.7287 (ptm-80) cc_final: 0.7003 (ptm160) REVERT: i 132 ASN cc_start: 0.8420 (m-40) cc_final: 0.8180 (t0) REVERT: j 40 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6718 (ptpt) REVERT: j 62 ARG cc_start: 0.8809 (ptt90) cc_final: 0.8488 (ptt180) REVERT: j 82 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6074 (mtp180) REVERT: j 109 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7157 (tt) REVERT: k 22 ARG cc_start: 0.3958 (mmt90) cc_final: 0.2927 (ttm-80) REVERT: k 33 ARG cc_start: 0.5308 (OUTLIER) cc_final: 0.4037 (mmt180) REVERT: k 34 MET cc_start: 0.5714 (mtm) cc_final: 0.5160 (mtp) REVERT: k 64 LYS cc_start: 0.5791 (OUTLIER) cc_final: 0.4707 (mtmm) REVERT: k 101 ARG cc_start: 0.3138 (mmm160) cc_final: 0.2910 (mmm160) REVERT: k 121 LYS cc_start: 0.4659 (mttp) cc_final: 0.3973 (mttp) REVERT: k 127 GLN cc_start: 0.5349 (tp-100) cc_final: 0.4517 (mp10) REVERT: k 155 TYR cc_start: 0.6444 (t80) cc_final: 0.6064 (t80) REVERT: k 288 CYS cc_start: 0.4629 (OUTLIER) cc_final: 0.3341 (t) REVERT: k 331 PHE cc_start: 0.1785 (OUTLIER) cc_final: 0.0968 (m-80) REVERT: k 353 MET cc_start: 0.3375 (tpp) cc_final: 0.3073 (tpt) REVERT: k 505 LYS cc_start: 0.4620 (tptp) cc_final: 0.3883 (mttt) REVERT: k 506 ARG cc_start: 0.3591 (OUTLIER) cc_final: 0.2618 (tmm-80) REVERT: k 548 PRO cc_start: 0.3707 (Cg_exo) cc_final: 0.3403 (Cg_endo) REVERT: k 555 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6735 (mtp) REVERT: n 111 ARG cc_start: 0.7886 (ptt-90) cc_final: 0.7522 (ptt180) outliers start: 400 outliers final: 331 residues processed: 1157 average time/residue: 0.8481 time to fit residues: 1649.5659 Evaluate side-chains 1222 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 843 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 109 ARG Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 97 GLN Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 90 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 34 THR Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 85 ASN Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 104 ARG Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 104 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 272 GLN Chi-restraints excluded: chain g residue 285 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 114 ARG Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain j residue 40 LYS Chi-restraints excluded: chain j residue 50 MET Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 61 CYS Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 143 ILE Chi-restraints excluded: chain k residue 145 THR Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 224 ARG Chi-restraints excluded: chain k residue 227 CYS Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 288 CYS Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 322 LEU Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 333 VAL Chi-restraints excluded: chain k residue 354 LYS Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 410 SER Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 440 GLN Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 457 GLN Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 564 ILE Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 583 ILE Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 4 LYS Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 74 SER Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 444 optimal weight: 10.0000 chunk 715 optimal weight: 7.9990 chunk 436 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 497 optimal weight: 8.9990 chunk 750 optimal weight: 0.9990 chunk 690 optimal weight: 5.9990 chunk 597 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 461 optimal weight: 4.9990 chunk 366 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 110 ASN L 132 GLN N 121 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN R 103 ASN V 12 GLN ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 91500 Z= 0.220 Angle : 0.628 12.239 132254 Z= 0.321 Chirality : 0.040 0.259 16271 Planarity : 0.005 0.071 10023 Dihedral : 22.415 179.809 35222 Min Nonbonded Distance : 1.060 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 7.07 % Allowed : 24.81 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 5824 helix: -0.31 (0.13), residues: 1700 sheet: -0.82 (0.16), residues: 975 loop : -2.16 (0.10), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 204 HIS 0.009 0.001 HIS k 429 PHE 0.018 0.001 PHE k 312 TYR 0.023 0.002 TYR A 9 ARG 0.012 0.000 ARG H 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11648 Ramachandran restraints generated. 5824 Oldfield, 0 Emsley, 5824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 858 time to evaluate : 4.982 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: A 50 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: A 127 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4725 (tt) REVERT: A 130 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5210 (tt) REVERT: A 136 TRP cc_start: 0.5357 (OUTLIER) cc_final: 0.4984 (m-10) REVERT: C 9 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7173 (tm-30) REVERT: C 34 MET cc_start: 0.8287 (mmm) cc_final: 0.7920 (mtm) REVERT: D 105 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7913 (mp) REVERT: D 110 MET cc_start: 0.7585 (tpt) cc_final: 0.7016 (tpt) REVERT: E 94 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7727 (ttm-80) REVERT: E 225 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: E 249 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7623 (t-90) REVERT: F 217 ILE cc_start: 0.3923 (OUTLIER) cc_final: 0.3642 (tt) REVERT: G 200 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7639 (mtt180) REVERT: H 179 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7688 (mtp180) REVERT: H 219 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7742 (ttm110) REVERT: I 82 SER cc_start: 0.8581 (p) cc_final: 0.8310 (m) REVERT: J 18 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5608 (tm-30) REVERT: J 28 LEU cc_start: 0.4116 (OUTLIER) cc_final: 0.3459 (mt) REVERT: J 32 MET cc_start: 0.4068 (OUTLIER) cc_final: 0.3683 (ptt) REVERT: K 135 GLU cc_start: 0.5254 (mp0) cc_final: 0.4322 (tm-30) REVERT: L 66 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7751 (ttmm) REVERT: M 80 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6574 (ttm170) REVERT: O 78 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6812 (mtpt) REVERT: P 3 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7839 (tpp-160) REVERT: P 105 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8380 (p0) REVERT: Q 83 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: Q 117 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7541 (ttt-90) REVERT: R 70 MET cc_start: 0.6802 (mpp) cc_final: 0.6221 (mtp) REVERT: S 31 LEU cc_start: 0.8515 (tt) cc_final: 0.8293 (tt) REVERT: S 41 MET cc_start: 0.7991 (mtt) cc_final: 0.7629 (mmp) REVERT: S 62 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: S 145 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: T 45 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7948 (mttt) REVERT: T 126 MET cc_start: 0.2733 (mmt) cc_final: 0.0521 (mtt) REVERT: U 8 LYS cc_start: 0.4532 (OUTLIER) cc_final: 0.4128 (pttm) REVERT: U 24 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8061 (ttp-170) REVERT: U 61 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: U 92 ASP cc_start: 0.7142 (t0) cc_final: 0.6743 (t0) REVERT: U 108 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7241 (ttp80) REVERT: U 144 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5447 (ppt170) REVERT: V 38 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7877 (ttmt) REVERT: W 17 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7063 (pp) REVERT: W 19 ARG cc_start: 0.5469 (mtt180) cc_final: 0.4934 (mtp85) REVERT: W 62 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7359 (mtt-85) REVERT: Y 28 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8198 (ppt90) REVERT: Y 105 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8543 (t) REVERT: Y 112 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7627 (p0) REVERT: Z 54 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8058 (mtpt) REVERT: Z 127 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7101 (m110) REVERT: a 11 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8013 (ptpt) REVERT: b 46 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: b 87 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7870 (mtt180) REVERT: d 37 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7022 (p0) REVERT: d 64 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: f 91 ASN cc_start: 0.5360 (p0) cc_final: 0.4967 (p0) REVERT: f 140 TYR cc_start: 0.7719 (t80) cc_final: 0.6773 (t80) REVERT: g 5 MET cc_start: 0.6962 (mmt) cc_final: 0.6598 (mmt) REVERT: g 271 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7029 (tptt) REVERT: g 285 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8308 (mp10) REVERT: i 82 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6983 (ptm160) REVERT: i 132 ASN cc_start: 0.8397 (m-40) cc_final: 0.8145 (t0) REVERT: j 40 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6816 (ptpt) REVERT: j 62 ARG cc_start: 0.8807 (ptt90) cc_final: 0.8485 (ptt180) REVERT: j 82 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6037 (mtp180) REVERT: j 109 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7158 (tt) REVERT: k 22 ARG cc_start: 0.4062 (mmt90) cc_final: 0.2988 (ttm-80) REVERT: k 33 ARG cc_start: 0.5339 (OUTLIER) cc_final: 0.4033 (mmt180) REVERT: k 34 MET cc_start: 0.5714 (mtm) cc_final: 0.5146 (mtp) REVERT: k 64 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.4797 (mtmm) REVERT: k 80 GLU cc_start: 0.5821 (tp30) cc_final: 0.5243 (tt0) REVERT: k 101 ARG cc_start: 0.3098 (mmm160) cc_final: 0.2879 (mmm160) REVERT: k 121 LYS cc_start: 0.4702 (mttp) cc_final: 0.4005 (mttp) REVERT: k 127 GLN cc_start: 0.5342 (tp-100) cc_final: 0.4518 (mp10) REVERT: k 155 TYR cc_start: 0.6432 (t80) cc_final: 0.5978 (t80) REVERT: k 288 CYS cc_start: 0.4568 (OUTLIER) cc_final: 0.3333 (t) REVERT: k 331 PHE cc_start: 0.1810 (OUTLIER) cc_final: 0.1010 (m-80) REVERT: k 353 MET cc_start: 0.3357 (tpp) cc_final: 0.3104 (tpt) REVERT: k 385 LYS cc_start: 0.3339 (OUTLIER) cc_final: 0.2592 (pmtt) REVERT: k 425 ARG cc_start: 0.2261 (tpt90) cc_final: 0.1891 (mtt180) REVERT: k 505 LYS cc_start: 0.4612 (tptp) cc_final: 0.3866 (mttt) REVERT: k 506 ARG cc_start: 0.3637 (OUTLIER) cc_final: 0.2700 (tmm-80) REVERT: k 548 PRO cc_start: 0.3704 (Cg_exo) cc_final: 0.3398 (Cg_endo) REVERT: k 555 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6782 (mtp) REVERT: n 111 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.7549 (ptt180) outliers start: 361 outliers final: 299 residues processed: 1124 average time/residue: 0.8550 time to fit residues: 1610.6827 Evaluate side-chains 1200 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 852 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 TRP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 TRP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 109 ARG Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 78 LYS Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 3 ARG Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 107 LYS Chi-restraints excluded: chain P residue 132 LYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 83 GLN Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 ARG Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 117 ARG Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 145 TYR Chi-restraints excluded: chain T residue 45 LYS Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 24 ARG Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 54 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 90 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 25 ILE Chi-restraints excluded: chain a residue 34 THR Chi-restraints excluded: chain a residue 85 ASN Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 104 ARG Chi-restraints excluded: chain b residue 26 CYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain b residue 87 ARG Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 104 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 119 ARG Chi-restraints excluded: chain f residue 151 ASN Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 242 SER Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 272 GLN Chi-restraints excluded: chain g residue 285 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 114 ARG Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 39 ILE Chi-restraints excluded: chain j residue 40 LYS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 72 ASN Chi-restraints excluded: chain j residue 82 ARG Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 33 ARG Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 61 CYS Chi-restraints excluded: chain k residue 64 LYS Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 88 CYS Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 143 ILE Chi-restraints excluded: chain k residue 145 THR Chi-restraints excluded: chain k residue 173 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 288 CYS Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 322 LEU Chi-restraints excluded: chain k residue 331 PHE Chi-restraints excluded: chain k residue 333 VAL Chi-restraints excluded: chain k residue 354 LYS Chi-restraints excluded: chain k residue 362 LEU Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 440 GLN Chi-restraints excluded: chain k residue 441 PHE Chi-restraints excluded: chain k residue 442 VAL Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 457 GLN Chi-restraints excluded: chain k residue 506 ARG Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 555 MET Chi-restraints excluded: chain k residue 564 ILE Chi-restraints excluded: chain k residue 569 ASP Chi-restraints excluded: chain k residue 583 ILE Chi-restraints excluded: chain k residue 584 LYS Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 4 LYS Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 61 GLU Chi-restraints excluded: chain n residue 74 SER Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 474 optimal weight: 3.9990 chunk 636 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 550 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 598 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 614 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 110 ASN L 132 GLN N 121 GLN O 48 HIS ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 HIS P 36 GLN R 32 GLN S 142 GLN V 12 GLN X 35 ASN g 226 HIS ** i 132 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 = 0.3929 r_free = 0.3929 target = 0.154539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111452 restraints weight = 129405.326| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.61 r_work: 0.3211 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 91500 Z= 0.190 Angle : 0.594 11.696 132254 Z= 0.303 Chirality : 0.038 0.253 16271 Planarity : 0.004 0.070 10023 Dihedral : 22.313 179.333 35222 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 6.70 % Allowed : 25.26 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5824 helix: -0.13 (0.13), residues: 1696 sheet: -0.70 (0.16), residues: 962 loop : -2.11 (0.10), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 204 HIS 0.006 0.001 HIS e 10 PHE 0.017 0.001 PHE k 312 TYR 0.034 0.001 TYR T 84 ARG 0.013 0.000 ARG H 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25269.35 seconds wall clock time: 439 minutes 57.07 seconds (26397.07 seconds total)