Starting phenix.real_space_refine on Sat Apr 13 04:10:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p09_17330/04_2024/8p09_17330_neut_updated.pdb" } resolution = 3.3 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= 0.004 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 1824 5.49 5 Mg 230 5.21 5 S 234 5.16 5 C 47171 2.51 5 N 15743 2.21 5 O 21082 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 PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 3": "OD1" <-> "OD2" 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 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 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 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 86284 Number of models: 1 Model: "" Number of chains: 47 Chain: "1" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1617 Classifications: {'RNA': 75} Modifications used: {'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: 37147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1741, 37147 Classifications: {'RNA': 1741} Modifications used: {'5*END': 1, 'rna2p_pur': 146, 'rna2p_pyr': 123, 'rna3p': 1, 'rna3p_pur': 765, 'rna3p_pyr': 706} Link IDs: {'rna2p': 269, 'rna3p': 1471} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "3" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 5} 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: {'PCIS': 1, 'PTRANS': 4, '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: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 220 Unusual residues: {' MG': 220} Classifications: {'undetermined': 220} Link IDs: {None: 219} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" 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: 69 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 57 not shown) Time building chain proxies: 35.03, per 1000 atoms: 0.41 Number of scatterers: 86284 At special positions: 0 Unit cell: (231, 237.6, 225.5, 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 1824 15.00 Mg 230 11.99 O 21082 8.00 N 15743 7.00 C 47171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 74 " distance=2.03 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: 31.00 Conformation dependent library (CDL) restraints added in 6.7 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: 180 helices and 63 sheets defined 28.2% alpha, 12.6% beta 514 base pairs and 934 stacking pairs defined. Time for finding SS restraints: 35.42 Creating SS restraints... Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.017A pdb=" N LYS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 118 No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 124 through 142 removed outlier: 3.847A pdb=" N GLU A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.926A pdb=" N ASN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 4.239A pdb=" N ILE A 205 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 208 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.012A pdb=" N ILE A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 removed outlier: 3.607A pdb=" N LEU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 66 Processing helix chain 'C' and resid 81 through 93 removed outlier: 4.361A pdb=" N ARG C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 4.683A pdb=" N TYR C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 186 Processing helix chain 'C' and resid 199 through 202 Processing helix chain 'D' and resid 58 through 61 No H-bonds generated for 'chain 'D' and resid 58 through 61' 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: 3.991A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Proline residue: D 190 - end of helix Processing helix chain 'D' and resid 192 through 202 removed outlier: 3.694A pdb=" N LYS D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.649A pdb=" N LEU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 48 removed outlier: 3.622A pdb=" N LEU E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.584A pdb=" N PHE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.533A pdb=" N ILE E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 132 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 removed outlier: 5.400A pdb=" N LEU E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.352A pdb=" N THR E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) 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 251 Processing helix chain 'F' and resid 7 through 32 removed outlier: 3.568A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 30 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) removed outlier: 5.099A 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 77 removed outlier: 3.611A pdb=" N PHE F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) 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 44 through 49 removed outlier: 3.555A pdb=" N LEU G 48 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG G 49 " --> pdb=" O ILE G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 49' Processing helix chain 'G' and resid 58 through 66 Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' 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 258 removed outlier: 3.936A pdb=" N ASP G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 77 through 80 Processing helix chain 'H' and resid 83 through 91 removed outlier: 3.936A pdb=" N MET H 91 " --> pdb=" O LEU H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 119 removed outlier: 3.692A pdb=" N LEU H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 134 removed outlier: 3.877A pdb=" N SER H 134 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 176 removed outlier: 3.860A pdb=" N VAL H 162 " --> pdb=" O PRO H 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP H 167 " --> pdb=" O ASN H 163 " (cutoff:3.500A) removed outlier: 3.652A 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 removed outlier: 3.751A pdb=" N ALA H 215 " --> pdb=" O LEU H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 24 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' 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 144 Processing helix chain 'I' and resid 182 through 234 removed outlier: 3.972A pdb=" N LYS I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG I 233 " --> pdb=" O ALA I 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 30 Processing helix chain 'J' and resid 34 through 36 No H-bonds generated for 'chain 'J' and resid 34 through 36' Processing helix chain 'J' and resid 66 through 86 removed outlier: 4.457A pdb=" N LYS J 70 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN J 73 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL J 77 " --> pdb=" O LYS J 74 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL J 80 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS J 85 " --> pdb=" O GLU J 82 " (cutoff:3.500A) 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 123 through 133 removed outlier: 3.874A pdb=" N LEU J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'J' and resid 167 through 180 removed outlier: 3.817A pdb=" N VAL J 170 " --> pdb=" O GLU J 167 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU J 171 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR J 172 " --> pdb=" O LYS J 169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER J 174 " --> pdb=" O GLU J 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 107 through 117 Processing helix chain 'K' and resid 128 through 131 No H-bonds generated for 'chain 'K' and resid 128 through 131' 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 160 through 166 removed outlier: 3.943A pdb=" N GLN K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K 166 " --> pdb=" O LEU K 162 " (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 removed outlier: 3.804A pdb=" N GLU K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.766A pdb=" N GLN L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 61 removed outlier: 4.124A pdb=" N VAL L 46 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE L 53 " --> pdb=" O THR L 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 56 " --> pdb=" O LYS L 52 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG L 58 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 84 removed outlier: 3.536A pdb=" N ARG L 79 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 removed outlier: 3.931A pdb=" N LEU L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 94 through 99' Processing helix chain 'L' and resid 102 through 108 removed outlier: 3.908A pdb=" N GLU L 107 " --> pdb=" O GLU L 103 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 116 Processing helix chain 'L' and resid 123 through 132 removed outlier: 3.677A pdb=" N ARG L 127 " --> pdb=" O ILE L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 156 No H-bonds generated for 'chain 'L' and resid 154 through 156' Processing helix chain 'L' and resid 174 through 178 removed outlier: 3.571A pdb=" N ALA L 178 " --> pdb=" O LYS L 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 174 through 178' Processing helix chain 'M' and resid 5 through 18 removed outlier: 3.544A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 36 No H-bonds generated for 'chain 'M' and resid 34 through 36' Processing helix chain 'M' and resid 42 through 55 removed outlier: 3.544A pdb=" N SER M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 82 Processing helix chain 'N' and resid 48 through 52 Processing helix chain 'O' and resid 14 through 25 removed outlier: 4.878A pdb=" N GLN O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 42 Processing helix chain 'O' and resid 61 through 71 Processing helix chain 'O' and resid 82 through 89 Processing helix chain 'O' and resid 123 through 129 Processing helix chain 'P' and resid 32 through 42 Processing helix chain 'P' and resid 47 through 57 Processing helix chain 'P' and resid 63 through 66 No H-bonds generated for 'chain 'P' and resid 63 through 66' Processing helix chain 'P' and resid 71 through 76 removed outlier: 3.689A pdb=" N LEU P 75 " --> pdb=" O ILE P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 104 removed outlier: 3.622A pdb=" N LYS P 100 " --> pdb=" O VAL P 96 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS P 101 " --> pdb=" O ALA P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 132 removed outlier: 3.672A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR P 131 " --> pdb=" O ARG P 127 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS P 132 " --> pdb=" O TYR P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 150 removed outlier: 3.909A pdb=" N ALA P 148 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL P 150 " --> pdb=" O ALA P 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 61 No H-bonds generated for 'chain 'Q' and resid 58 through 61' 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 86 removed outlier: 3.685A pdb=" N GLN Q 79 " --> pdb=" O MET Q 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 120 removed outlier: 3.622A pdb=" N LEU Q 119 " --> pdb=" O ALA Q 115 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 27 Processing helix chain 'R' and resid 30 through 34 Processing helix chain 'R' and resid 39 through 46 Processing helix chain 'R' and resid 54 through 60 Processing helix chain 'R' and resid 109 through 111 No H-bonds generated for 'chain 'R' and resid 109 through 111' Processing helix chain 'R' and resid 117 through 119 No H-bonds generated for 'chain 'R' and resid 117 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 51 removed outlier: 5.137A pdb=" N TYR S 49 " --> pdb=" O THR S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 58 Processing helix chain 'S' and resid 77 through 99 removed outlier: 3.529A pdb=" N ILE S 81 " --> pdb=" O HIS S 77 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA S 83 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER S 89 " --> pdb=" O ARG S 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA S 94 " --> pdb=" O LYS S 90 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN S 97 " --> pdb=" O VAL S 93 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS S 98 " --> pdb=" O ALA S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 113 removed outlier: 4.120A pdb=" N GLU S 107 " --> pdb=" O ALA S 103 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE S 108 " --> pdb=" O SER S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 19 removed outlier: 3.648A pdb=" N ALA T 13 " --> pdb=" O VAL T 9 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG T 14 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE T 17 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 38 removed outlier: 3.778A pdb=" N ARG T 33 " --> pdb=" O HIS T 29 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU T 36 " --> pdb=" O LYS T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 61 removed outlier: 3.787A pdb=" N THR T 55 " --> pdb=" O ALA T 51 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS T 56 " --> pdb=" O GLY T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 83 removed outlier: 3.655A pdb=" N GLU T 76 " --> pdb=" O LYS T 72 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU T 77 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG T 81 " --> pdb=" O GLU T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 107 Processing helix chain 'U' and resid 26 through 32 removed outlier: 3.886A pdb=" N THR U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA U 32 " --> pdb=" O PHE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 47 removed outlier: 3.676A pdb=" N VAL U 43 " --> pdb=" O ARG U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'U' and resid 63 through 72 removed outlier: 3.519A pdb=" N ILE U 70 " --> pdb=" O ARG U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 116 Processing helix chain 'U' and resid 120 through 127 Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.790A pdb=" N LYS V 24 " --> pdb=" O ALA V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 66 Processing helix chain 'V' and resid 72 through 78 removed outlier: 4.022A pdb=" N LYS V 77 " --> pdb=" O GLY V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 110 removed outlier: 3.536A pdb=" N GLY V 109 " --> pdb=" O GLN V 105 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 141 removed outlier: 3.507A pdb=" N ARG V 129 " --> pdb=" O PRO V 125 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE V 134 " --> pdb=" O ASP V 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 44 Processing helix chain 'W' and resid 95 through 102 Processing helix chain 'X' and resid 58 through 61 No H-bonds generated for 'chain 'X' and resid 58 through 61' Processing helix chain 'X' and resid 65 through 74 Processing helix chain 'Y' and resid 6 through 18 Processing helix chain 'Y' and resid 32 through 43 Processing helix chain 'Y' and resid 87 through 90 No H-bonds generated for 'chain 'Y' and resid 87 through 90' Processing helix chain 'Y' and resid 113 through 119 removed outlier: 4.165A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 23 removed outlier: 3.630A pdb=" N ASP Z 19 " --> pdb=" O SER Z 15 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP Z 22 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS Z 23 " --> pdb=" O ASP Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 31 removed outlier: 3.764A pdb=" N ALA Z 30 " --> pdb=" O GLN Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 38 Processing helix chain 'Z' and resid 90 through 92 No H-bonds generated for 'chain 'Z' and resid 90 through 92' Processing helix chain 'Z' and resid 130 through 135 Processing helix chain 'a' and resid 37 through 48 removed outlier: 4.027A pdb=" N LYS a 43 " --> pdb=" O GLU a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 85 Processing helix chain 'a' and resid 88 through 93 Processing helix chain 'a' and resid 104 through 116 removed outlier: 4.411A pdb=" N LYS a 116 " --> pdb=" O ASN a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 126 removed outlier: 3.541A pdb=" N GLY a 126 " --> pdb=" O ALA a 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 55 removed outlier: 3.722A pdb=" N GLU b 55 " --> pdb=" O ARG b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 80 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' 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 46 removed outlier: 3.971A pdb=" N ARG e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR e 46 " --> pdb=" O CYS e 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 40 through 46' Processing helix chain 'i' and resid 85 through 89 Processing helix chain 'i' and resid 104 through 116 removed outlier: 3.717A pdb=" N TYR i 112 " --> pdb=" O ARG i 109 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG i 114 " --> pdb=" O GLN i 111 " (cutoff:3.500A) removed outlier: 3.639A 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 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 Processing helix chain 'k' and resid 151 through 160 removed outlier: 3.841A pdb=" N THR k 157 " --> pdb=" O GLN k 153 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 179 No H-bonds generated for 'chain 'k' and resid 176 through 179' Processing helix chain 'k' and resid 186 through 191 Processing helix chain 'k' and resid 195 through 203 Processing helix chain 'k' and resid 207 through 210 removed outlier: 3.666A pdb=" N LYS k 210 " --> pdb=" O THR k 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 207 through 210' Processing helix chain 'k' and resid 219 through 232 Processing helix chain 'k' and resid 251 through 262 removed outlier: 4.732A 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 313 Processing helix chain 'k' and resid 387 through 392 Processing helix chain 'k' and resid 424 through 427 No H-bonds generated for 'chain 'k' and resid 424 through 427' Processing helix chain 'k' and resid 439 through 446 removed outlier: 4.391A pdb=" N ASP k 444 " --> pdb=" O GLN k 440 " (cutoff:3.500A) Processing helix chain 'k' and resid 451 through 454 Processing helix chain 'k' and resid 459 through 461 No H-bonds generated for 'chain 'k' and resid 459 through 461' Processing helix chain 'k' and resid 464 through 475 Processing helix chain 'k' and resid 494 through 511 removed outlier: 4.227A pdb=" N ALA k 511 " --> pdb=" O PHE k 507 " (cutoff:3.500A) Processing helix chain 'k' and resid 523 through 528 Processing helix chain 'k' and resid 551 through 562 Processing helix chain 'k' and resid 584 through 591 removed outlier: 4.136A pdb=" N LYS k 589 " --> pdb=" O ASP k 585 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 24 Processing helix chain 'n' and resid 52 through 61 Processing helix chain 'n' and resid 70 through 76 Processing helix chain 'n' and resid 82 through 94 removed outlier: 3.792A pdb=" N ALA n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 19 through 23 removed outlier: 7.043A pdb=" N ASP A 84 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 76 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR A 82 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 44 through 46 Processing sheet with id= C, first strand: chain 'A' and resid 226 through 228 removed outlier: 3.617A pdb=" N VAL A 236 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= E, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.117A pdb=" N ILE C 145 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE C 159 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS C 148 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE C 161 " --> pdb=" O CYS C 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.064A pdb=" N ILE C 48 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.894A pdb=" N GLY D 102 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE D 87 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE D 100 " --> pdb=" O ILE D 87 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 120 through 128 removed outlier: 3.554A pdb=" N ASP D 209 " --> pdb=" O PHE D 142 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 28 through 34 removed outlier: 3.653A pdb=" N GLY D 45 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.675A pdb=" N LYS D 219 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N HIS D 136 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET D 217 " --> pdb=" O HIS D 136 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N PHE D 138 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL D 215 " --> pdb=" O PHE D 138 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 115 through 121 removed outlier: 3.598A pdb=" N LYS E 119 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS E 85 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA E 106 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL E 83 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLY E 108 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP E 81 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 161 through 165 removed outlier: 3.565A pdb=" N LEU E 169 " --> pdb=" O TRP E 204 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 39 through 42 Processing sheet with id= N, first strand: chain 'F' and resid 148 through 155 removed outlier: 3.858A pdb=" N GLY F 140 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 70 through 72 Processing sheet with id= P, first strand: chain 'G' and resid 102 through 104 removed outlier: 4.909A pdb=" N ILE G 102 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA G 110 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 121 through 125 removed outlier: 3.657A pdb=" N ASP G 171 " --> pdb=" O GLN G 161 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 139 through 142 Processing sheet with id= S, first strand: chain 'I' and resid 12 through 17 removed outlier: 6.874A pdb=" N VAL I 49 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 72 through 77 Processing sheet with id= U, first strand: chain 'J' and resid 47 through 52 removed outlier: 3.620A pdb=" N VAL J 93 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 184 through 189 removed outlier: 4.503A pdb=" N ASP J 184 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY J 141 " --> pdb=" O HIS J 157 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 42 through 47 Processing sheet with id= X, first strand: chain 'K' and resid 62 through 67 removed outlier: 3.647A pdb=" N PHE K 65 " --> pdb=" O ARG K 74 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 187 through 189 Processing sheet with id= Z, first strand: chain 'M' and resid 20 through 24 removed outlier: 3.601A pdb=" N ALA M 23 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 101 through 112 removed outlier: 5.745A pdb=" N ARG N 89 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL N 77 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASP N 91 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLY N 75 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 15.998A pdb=" N LEU N 93 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 17.353A pdb=" N LEU N 73 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY N 129 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL N 142 " --> pdb=" O GLY N 129 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 31 through 33 removed outlier: 3.542A pdb=" N LEU O 52 " --> pdb=" O ILE O 77 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 28 through 30 removed outlier: 7.279A pdb=" N ALA Q 92 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'Q' and resid 33 through 35 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 76 through 78 Processing sheet with id= AG, first strand: chain 'S' and resid 9 through 15 Processing sheet with id= AH, first strand: chain 'V' and resid 81 through 83 Processing sheet with id= AI, first strand: chain 'W' and resid 111 through 114 removed outlier: 4.680A pdb=" N LYS W 86 " --> pdb=" O MET W 56 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'W' and resid 59 through 66 Processing sheet with id= AK, first strand: chain 'X' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'Y' and resid 24 through 27 Processing sheet with id= AM, first strand: chain 'Y' and resid 71 through 74 removed outlier: 7.154A pdb=" N VAL Y 103 " --> pdb=" O LEU Y 126 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 101 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE Y 101 " --> pdb=" O PHE Y 128 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Z' and resid 80 through 84 removed outlier: 6.631A pdb=" N GLN Z 73 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL Z 51 " --> pdb=" O GLN Z 73 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS Z 124 " --> pdb=" O LEU Z 101 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA Z 103 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL Z 122 " --> pdb=" O ALA Z 103 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'a' and resid 7 through 10 Processing sheet with id= AP, first strand: chain 'a' and resid 13 through 15 Processing sheet with id= AQ, first strand: chain 'b' and resid 20 through 22 Processing sheet with id= AR, first strand: chain 'b' and resid 36 through 43 Processing sheet with id= AS, first strand: chain 'c' and resid 32 through 34 Processing sheet with id= AT, first strand: chain 'd' and resid 42 through 46 removed outlier: 3.529A pdb=" N LYS d 16 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'f' and resid 106 through 110 removed outlier: 6.800A pdb=" N LYS f 113 " --> pdb=" O ASP f 109 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 18 through 22 removed outlier: 6.620A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 99 through 102 removed outlier: 3.691A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 108 through 113 removed outlier: 7.034A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 153 through 156 removed outlier: 3.746A pdb=" N ILE g 165 " --> pdb=" O TRP g 177 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR g 186 " --> pdb=" O VAL g 176 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 215 through 217 Processing sheet with id= BA, first strand: chain 'g' and resid 239 through 241 removed outlier: 3.699A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 4 through 12 removed outlier: 6.852A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU g 306 " --> pdb=" O TYR g 302 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'j' and resid 33 through 37 removed outlier: 3.502A pdb=" N LEU j 93 " --> pdb=" O LEU j 78 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY j 80 " --> pdb=" O VAL j 91 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL j 91 " --> pdb=" O GLY j 80 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU j 58 " --> pdb=" O ALA j 89 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N VAL j 91 " --> pdb=" O LEU j 58 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N HIS j 60 " --> pdb=" O VAL j 91 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU j 93 " --> pdb=" O HIS j 60 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'k' and resid 6 through 10 removed outlier: 3.707A pdb=" N THR k 6 " --> pdb=" O LEU k 75 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'k' and resid 285 through 288 removed outlier: 3.524A pdb=" N PHE k 285 " --> pdb=" O VAL k 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL k 109 " --> pdb=" O CYS k 287 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE k 269 " --> pdb=" O LEU k 106 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU k 108 " --> pdb=" O ILE k 269 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL k 271 " --> pdb=" O LEU k 108 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'k' and resid 289 through 292 Processing sheet with id= BG, first strand: chain 'k' and resid 362 through 364 removed outlier: 6.665A pdb=" N THR k 543 " --> pdb=" O ALA k 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'k' and resid 375 through 377 removed outlier: 3.553A pdb=" N VAL k 517 " --> pdb=" O MET k 375 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'k' and resid 409 through 411 removed outlier: 6.757A pdb=" N VAL k 482 " --> pdb=" O SER k 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'k' and resid 566 through 569 Processing sheet with id= BK, first strand: chain 'n' and resid 98 through 102 removed outlier: 3.857A pdb=" N LYS n 98 " --> pdb=" O THR n 110 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL n 100 " --> pdb=" O ILE n 108 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE n 108 " --> pdb=" O VAL n 100 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1284 hydrogen bonds 2070 hydrogen bond angles 0 basepair planarities 514 basepair parallelities 934 stacking parallelities Total time for adding SS restraints: 67.98 Time building geometry restraints manager: 33.99 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: 15961 1.33 - 1.46: 34006 1.46 - 1.59: 38161 1.59 - 1.72: 2966 1.72 - 1.85: 356 Bond restraints: 91450 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 1.60e+02 bond pdb=" O3' C 21245 " pdb=" P A 21246 " ideal model delta sigma weight residual 1.607 1.423 0.184 1.50e-02 4.44e+03 1.50e+02 bond pdb=" C2' I2T 21244 " pdb=" O2' I2T 21244 " ideal model delta sigma weight residual 1.420 1.239 0.181 1.50e-02 4.44e+03 1.46e+02 bond pdb=" C4 I2T 21244 " pdb=" C5 I2T 21244 " ideal model delta sigma weight residual 1.632 1.444 0.188 2.00e-02 2.50e+03 8.82e+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 8.13e+01 ... (remaining 91445 not shown) Histogram of bond angle deviations from ideal: 20.26 - 43.42: 1 43.42 - 66.58: 0 66.58 - 89.74: 1 89.74 - 112.90: 61045 112.90 - 136.05: 71128 Bond angle restraints: 132175 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 20.26 87.74 3.00e+00 1.11e-01 8.55e+02 angle pdb=" C3' U 1 28 " pdb=" O3' U 1 28 " pdb=" P G 1 29 " ideal model delta sigma weight residual 120.20 105.87 14.33 1.50e+00 4.44e-01 9.13e+01 angle pdb=" O3' C 2 73 " pdb=" C3' C 2 73 " pdb=" C2' C 2 73 " ideal model delta sigma weight residual 109.50 123.71 -14.21 1.50e+00 4.44e-01 8.97e+01 angle pdb=" P A 1 2 " pdb=" O5' A 1 2 " pdb=" C5' A 1 2 " ideal model delta sigma weight residual 120.90 106.88 14.02 1.50e+00 4.44e-01 8.73e+01 angle pdb=" O LYS V 143 " pdb=" C LYS V 143 " pdb=" N LYS V 144 " ideal model delta sigma weight residual 122.55 110.99 11.56 1.24e+00 6.50e-01 8.69e+01 ... (remaining 132170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 52880 35.89 - 71.79: 4747 71.79 - 107.68: 506 107.68 - 143.57: 22 143.57 - 179.47: 25 Dihedral angle restraints: 58180 sinusoidal: 41178 harmonic: 17002 Sorted by residual: dihedral pdb=" O4' U 2 819 " pdb=" C1' U 2 819 " pdb=" N1 U 2 819 " pdb=" C2 U 2 819 " ideal model delta sinusoidal sigma weight residual 200.00 22.31 177.69 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21513 " pdb=" C1' C 21513 " pdb=" N1 C 21513 " pdb=" C2 C 21513 " ideal model delta sinusoidal sigma weight residual 200.00 24.85 175.15 1 1.50e+01 4.44e-03 8.52e+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 200.00 28.09 171.91 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 58177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 15589 0.160 - 0.320: 633 0.320 - 0.480: 37 0.480 - 0.640: 3 0.640 - 0.800: 1 Chirality restraints: 16263 Sorted by residual: chirality pdb=" P A 1 2 " pdb=" OP1 A 1 2 " pdb=" OP2 A 1 2 " pdb=" O5' A 1 2 " 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=" C33 I2T 21244 " pdb=" C32 I2T 21244 " pdb=" C34 I2T 21244 " pdb=" N34 I2T 21244 " both_signs ideal model delta sigma weight residual False -2.60 -1.97 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA LEU S 51 " pdb=" N LEU S 51 " pdb=" C LEU S 51 " pdb=" CB LEU S 51 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 16260 not shown) Planarity restraints: 10021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 74 " -0.501 2.00e-02 2.50e+03 2.08e-01 1.30e+03 pdb=" N9 G 2 74 " 0.067 2.00e-02 2.50e+03 pdb=" C8 G 2 74 " 0.247 2.00e-02 2.50e+03 pdb=" N7 G 2 74 " 0.207 2.00e-02 2.50e+03 pdb=" C5 G 2 74 " 0.085 2.00e-02 2.50e+03 pdb=" C6 G 2 74 " -0.108 2.00e-02 2.50e+03 pdb=" O6 G 2 74 " -0.301 2.00e-02 2.50e+03 pdb=" N1 G 2 74 " -0.079 2.00e-02 2.50e+03 pdb=" C2 G 2 74 " 0.039 2.00e-02 2.50e+03 pdb=" N2 G 2 74 " 0.168 2.00e-02 2.50e+03 pdb=" N3 G 2 74 " 0.064 2.00e-02 2.50e+03 pdb=" C4 G 2 74 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21548 " -0.355 2.00e-02 2.50e+03 1.89e-01 8.03e+02 pdb=" N1 C 21548 " -0.017 2.00e-02 2.50e+03 pdb=" C2 C 21548 " 0.055 2.00e-02 2.50e+03 pdb=" O2 C 21548 " 0.210 2.00e-02 2.50e+03 pdb=" N3 C 21548 " -0.027 2.00e-02 2.50e+03 pdb=" C4 C 21548 " -0.048 2.00e-02 2.50e+03 pdb=" N4 C 21548 " -0.236 2.00e-02 2.50e+03 pdb=" C5 C 21548 " 0.187 2.00e-02 2.50e+03 pdb=" C6 C 21548 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 78 " -0.387 2.00e-02 2.50e+03 1.85e-01 7.70e+02 pdb=" N1 C 2 78 " 0.118 2.00e-02 2.50e+03 pdb=" C2 C 2 78 " 0.025 2.00e-02 2.50e+03 pdb=" O2 C 2 78 " 0.195 2.00e-02 2.50e+03 pdb=" N3 C 2 78 " -0.071 2.00e-02 2.50e+03 pdb=" C4 C 2 78 " -0.046 2.00e-02 2.50e+03 pdb=" N4 C 2 78 " -0.182 2.00e-02 2.50e+03 pdb=" C5 C 2 78 " 0.122 2.00e-02 2.50e+03 pdb=" C6 C 2 78 " 0.225 2.00e-02 2.50e+03 ... (remaining 10018 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 11 1.88 - 2.63: 2180 2.63 - 3.39: 105934 3.39 - 4.14: 240409 4.14 - 4.90: 377199 Nonbonded interactions: 725733 Sorted by model distance: nonbonded pdb="MG MG 22031 " pdb="MG MG 22032 " model vdw 1.119 1.300 nonbonded pdb="MG MG 21945 " pdb="MG MG 21946 " model vdw 1.121 1.300 nonbonded pdb="MG MG 21909 " pdb="MG MG 21910 " model vdw 1.137 1.300 nonbonded pdb="MG MG 21937 " pdb="MG MG 21938 " model vdw 1.139 1.300 nonbonded pdb=" OP1 C 1 56 " pdb=" OD1 ASN A 179 " model vdw 1.650 3.040 ... (remaining 725728 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: 0.010 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 15.460 Check model and map are aligned: 1.070 Set scattering table: 0.660 Process input model: 235.830 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 261.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.011 0.190 91450 Z= 0.706 Angle : 1.386 87.736 132175 Z= 0.850 Chirality : 0.073 0.800 16263 Planarity : 0.018 0.269 10021 Dihedral : 22.245 179.466 47207 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.78 % Favored : 88.07 % Rotamer: Outliers : 9.33 % Allowed : 19.17 % Favored : 71.51 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.85 % 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: -4.21 (0.09), residues: 5824 helix: -2.71 (0.09), residues: 1721 sheet: -2.08 (0.15), residues: 984 loop : -3.15 (0.09), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.014 TRP K 8 HIS 0.026 0.003 HIS a 63 PHE 0.099 0.007 PHE J 135 TYR 0.170 0.011 TYR K 21 ARG 0.013 0.001 ARG b 95 *********************** 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 1696 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 476 poor density : 1220 time to evaluate : 5.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.6356 (OUTLIER) cc_final: 0.5236 (t) REVERT: A 125 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: A 126 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6410 (tt0) REVERT: A 266 ARG cc_start: -0.0778 (OUTLIER) cc_final: -0.1326 (mtm180) REVERT: C 42 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8485 (mtpt) REVERT: D 47 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.9012 (p) REVERT: D 87 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8874 (pp) REVERT: D 186 ASN cc_start: 0.8492 (m-40) cc_final: 0.6446 (m-40) REVERT: E 35 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6830 (tmmm) REVERT: E 100 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7420 (mtp180) REVERT: E 225 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: F 94 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7416 (ptt-90) REVERT: G 54 TYR cc_start: 0.8873 (m-80) cc_final: 0.8614 (m-80) REVERT: G 254 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8527 (pttm) REVERT: H 175 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7966 (tm-30) REVERT: I 41 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7225 (tp) REVERT: I 45 TRP cc_start: 0.7768 (m-90) cc_final: 0.7371 (m-90) REVERT: I 155 GLN cc_start: 0.7746 (mt0) cc_final: 0.7071 (mm110) REVERT: J 51 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7759 (pp) REVERT: J 120 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8359 (mmt90) REVERT: J 143 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6895 (mtm180) REVERT: J 162 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7223 (mm110) REVERT: J 171 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: K 53 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8331 (mppt) REVERT: K 62 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8797 (t) REVERT: K 181 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8565 (mt0) REVERT: L 103 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: M 70 TYR cc_start: 0.8289 (m-10) cc_final: 0.7984 (m-80) REVERT: O 84 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7709 (mppt) REVERT: R 41 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8132 (mm-40) REVERT: R 66 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7721 (mt-10) REVERT: S 29 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.7869 (p0) REVERT: S 50 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8648 (mmtt) REVERT: S 111 ILE cc_start: 0.9276 (mm) cc_final: 0.9036 (mt) REVERT: T 36 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7876 (tm-30) REVERT: T 74 GLN cc_start: 0.8969 (tt0) cc_final: 0.8640 (tt0) REVERT: U 28 PHE cc_start: 0.8523 (m-80) cc_final: 0.8283 (m-10) REVERT: U 54 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8690 (ptpp) REVERT: U 55 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8423 (mtt-85) REVERT: V 35 ASP cc_start: 0.8678 (p0) cc_final: 0.8471 (p0) REVERT: V 50 GLU cc_start: 0.7131 (tp30) cc_final: 0.6926 (tp30) REVERT: V 85 ASN cc_start: 0.8959 (m-40) cc_final: 0.8551 (m-40) REVERT: V 98 SER cc_start: 0.9449 (t) cc_final: 0.8858 (m) REVERT: V 130 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7990 (t0) REVERT: W 21 ARG cc_start: 0.8470 (ttm170) cc_final: 0.7588 (ttp-170) REVERT: W 33 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7732 (mm-30) REVERT: W 59 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8268 (mttp) REVERT: W 61 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8568 (mt) REVERT: X 21 ASN cc_start: 0.8586 (t0) cc_final: 0.8002 (t0) REVERT: X 33 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: X 34 MET cc_start: 0.8690 (tpp) cc_final: 0.8331 (tpp) REVERT: Y 85 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: Y 124 LYS cc_start: 0.9026 (mttm) cc_final: 0.8807 (mttp) REVERT: Z 1 MET cc_start: 0.3141 (ttp) cc_final: 0.2723 (ttt) REVERT: Z 3 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8153 (ptmm) REVERT: Z 53 GLU cc_start: 0.8689 (pp20) cc_final: 0.7959 (pp20) REVERT: Z 90 CYS cc_start: 0.8187 (m) cc_final: 0.7794 (m) REVERT: Z 139 GLU cc_start: 0.7982 (pp20) cc_final: 0.7649 (pp20) REVERT: b 37 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7813 (mmtm) REVERT: b 39 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.9106 (t80) REVERT: c 14 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8283 (tm-30) REVERT: c 42 LYS cc_start: 0.7942 (mttp) cc_final: 0.7723 (mptt) REVERT: c 81 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7506 (mtm-85) REVERT: c 82 LYS cc_start: 0.8600 (mtpp) cc_final: 0.7668 (mtpp) REVERT: f 85 TYR cc_start: 0.3242 (OUTLIER) cc_final: 0.2881 (m-80) REVERT: g 52 TYR cc_start: 0.8011 (t80) cc_final: 0.7760 (t80) REVERT: g 116 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8435 (p0) REVERT: g 271 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8393 (mttp) REVERT: i 98 LYS cc_start: 0.5606 (ttpp) cc_final: 0.5246 (tttt) REVERT: j 44 ASN cc_start: 0.8136 (m-40) cc_final: 0.7833 (m110) REVERT: j 90 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7019 (p0) REVERT: j 101 ARG cc_start: 0.7833 (ptp-110) cc_final: 0.7622 (ptp-110) REVERT: k 17 LYS cc_start: 0.8611 (tptt) cc_final: 0.8219 (tppt) REVERT: k 63 LYS cc_start: 0.6127 (mptt) cc_final: 0.5799 (tppt) REVERT: k 81 LYS cc_start: 0.5781 (mmmt) cc_final: 0.5547 (mptt) REVERT: k 82 GLU cc_start: 0.6773 (mt-10) cc_final: 0.5742 (mt-10) REVERT: k 96 ARG cc_start: 0.4877 (ttt180) cc_final: 0.4317 (ptt-90) REVERT: k 148 ARG cc_start: 0.7491 (ptt180) cc_final: 0.6118 (ttt180) REVERT: k 158 LYS cc_start: 0.6632 (mttt) cc_final: 0.6131 (mtpt) REVERT: k 202 GLN cc_start: 0.6376 (pt0) cc_final: 0.5605 (tm-30) REVERT: k 223 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6161 (tt0) REVERT: k 242 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5118 (mt-10) REVERT: k 260 ARG cc_start: 0.6344 (ttt90) cc_final: 0.5933 (ttt-90) REVERT: k 282 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7799 (tm) REVERT: k 298 VAL cc_start: 0.7280 (t) cc_final: 0.7071 (t) REVERT: k 309 ILE cc_start: 0.6899 (mm) cc_final: 0.6675 (mm) REVERT: k 316 TYR cc_start: 0.3361 (p90) cc_final: 0.2785 (p90) REVERT: k 345 MET cc_start: 0.3491 (ptp) cc_final: 0.3054 (ptp) REVERT: k 452 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7497 (tt0) REVERT: k 481 ASP cc_start: 0.0905 (OUTLIER) cc_final: 0.0679 (t0) REVERT: k 491 TYR cc_start: 0.5305 (m-80) cc_final: 0.5017 (m-80) REVERT: k 551 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.5881 (tp) REVERT: n 76 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7499 (mtp85) REVERT: n 79 ILE cc_start: 0.9003 (mm) cc_final: 0.8773 (mt) REVERT: n 112 ASN cc_start: 0.7327 (t0) cc_final: 0.7126 (t0) outliers start: 476 outliers final: 289 residues processed: 1598 average time/residue: 0.8446 time to fit residues: 2245.7795 Evaluate side-chains 1319 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 990 time to evaluate : 5.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 128 LYS Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 GLN Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 155 LYS Chi-restraints excluded: chain L residue 163 SER Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 116 CYS Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 58 HIS Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 CYS Chi-restraints excluded: chain S residue 29 ASN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 7 GLU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 17 ASN Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 7 GLU Chi-restraints excluded: chain X residue 9 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 33 GLN Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain b residue 37 LYS Chi-restraints excluded: chain b residue 39 PHE Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 74 CYS Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 42 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 85 TYR Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 71 ILE Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 144 ASP Chi-restraints excluded: chain g residue 146 SER Chi-restraints excluded: chain g residue 157 SER Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 292 SER Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 197 GLN Chi-restraints excluded: chain k residue 223 GLN Chi-restraints excluded: chain k residue 262 LEU Chi-restraints excluded: chain k residue 269 ILE Chi-restraints excluded: chain k residue 277 SER Chi-restraints excluded: chain k residue 278 VAL Chi-restraints excluded: chain k residue 279 LEU Chi-restraints excluded: chain k residue 282 LEU Chi-restraints excluded: chain k residue 294 SER Chi-restraints excluded: chain k residue 304 SER Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 386 THR Chi-restraints excluded: chain k residue 389 ILE Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 461 THR Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 481 ASP Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 547 SER Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 66 LYS Chi-restraints excluded: chain n residue 108 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 635 optimal weight: 6.9990 chunk 570 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 384 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 chunk 590 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 358 optimal weight: 5.9990 chunk 439 optimal weight: 0.9980 chunk 683 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 40 ASN A 169 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS C 110 ASN C 131 HIS C 132 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 165 ASN E 97 GLN G 98 ASN G 142 HIS G 232 ASN H 51 GLN H 66 HIS H 89 ASN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN H 129 ASN I 186 GLN J 73 GLN ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN K 35 ASN K 52 ASN K 64 ASN K 146 GLN K 155 ASN L 113 GLN L 140 GLN L 154 GLN M 28 HIS M 77 GLN N 83 GLN O 28 HIS ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 HIS P 101 HIS Q 79 GLN S 8 GLN S 11 GLN S 24 HIS ** S 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN T 48 ASN T 62 GLN U 105 ASN U 120 HIS W 18 HIS W 81 GLN X 35 ASN Y 5 ASN Z 23 HIS Z 31 HIS Z 77 ASN a 19 GLN a 106 GLN c 51 GLN g 14 HIS g 56 GLN g 178 ASN g 196 ASN g 226 HIS i 113 ASN i 130 ASN j 44 ASN j 72 ASN k 95 HIS ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 46 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 91450 Z= 0.260 Angle : 0.706 10.394 132175 Z= 0.363 Chirality : 0.043 0.300 16263 Planarity : 0.005 0.071 10021 Dihedral : 22.535 179.760 35648 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.43 % Favored : 91.54 % Rotamer: Outliers : 7.33 % Allowed : 23.32 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -3.18 (0.10), residues: 5824 helix: -1.55 (0.11), residues: 1744 sheet: -1.72 (0.16), residues: 959 loop : -2.62 (0.10), residues: 3121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 204 HIS 0.012 0.001 HIS E 171 PHE 0.026 0.002 PHE c 79 TYR 0.021 0.002 TYR Z 27 ARG 0.010 0.001 ARG g 60 *********************** 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 1412 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1038 time to evaluate : 5.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6426 (p90) REVERT: A 54 ARG cc_start: 0.7414 (ptp90) cc_final: 0.6696 (ptt-90) REVERT: A 125 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: C 42 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8193 (mtpt) REVERT: C 89 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8205 (mmtm) REVERT: D 63 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8578 (mptt) REVERT: D 87 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8749 (pp) REVERT: D 99 ASN cc_start: 0.9087 (t0) cc_final: 0.8739 (t0) REVERT: E 50 VAL cc_start: 0.7480 (m) cc_final: 0.7242 (t) REVERT: E 150 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.7882 (mmtp) REVERT: E 225 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: F 127 MET cc_start: 0.8867 (mmm) cc_final: 0.8505 (mmm) REVERT: F 149 SER cc_start: 0.8548 (p) cc_final: 0.8167 (m) REVERT: H 197 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7572 (ptmm) REVERT: I 155 GLN cc_start: 0.7764 (mt0) cc_final: 0.7059 (mm110) REVERT: J 29 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: J 106 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5636 (mmm160) REVERT: J 162 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7243 (mm110) REVERT: K 62 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8787 (t) REVERT: K 144 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6620 (ttmt) REVERT: K 163 GLU cc_start: 0.8423 (tp30) cc_final: 0.8115 (tp30) REVERT: K 181 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: L 1 MET cc_start: 0.6655 (mtt) cc_final: 0.6379 (mtt) REVERT: M 3 MET cc_start: 0.8587 (ptp) cc_final: 0.8191 (ptp) REVERT: M 5 LYS cc_start: 0.8629 (ttmt) cc_final: 0.7992 (mtmt) REVERT: M 70 TYR cc_start: 0.8221 (m-10) cc_final: 0.7954 (m-80) REVERT: N 31 GLU cc_start: 0.3790 (OUTLIER) cc_final: 0.1978 (pm20) REVERT: N 106 HIS cc_start: 0.9262 (OUTLIER) cc_final: 0.9043 (p90) REVERT: N 113 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8118 (tp) REVERT: O 33 ARG cc_start: 0.7343 (mtt90) cc_final: 0.6950 (mtt90) REVERT: O 35 ILE cc_start: 0.8627 (pt) cc_final: 0.8355 (mt) REVERT: O 84 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7715 (mppt) REVERT: P 4 MET cc_start: 0.8701 (ptp) cc_final: 0.8326 (ptp) REVERT: P 19 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7229 (mtm110) REVERT: P 29 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7896 (p) REVERT: P 56 ASP cc_start: 0.8670 (m-30) cc_final: 0.8355 (m-30) REVERT: Q 80 ASP cc_start: 0.8156 (t0) cc_final: 0.7950 (t0) REVERT: Q 98 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (mmm160) REVERT: R 41 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7599 (mm-40) REVERT: R 61 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8268 (ptp90) REVERT: R 66 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7663 (mt-10) REVERT: R 71 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6741 (tt0) REVERT: S 97 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7669 (tm-30) REVERT: T 36 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7987 (tm-30) REVERT: T 80 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7459 (mmp80) REVERT: T 91 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7774 (tp) REVERT: T 93 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5531 (pm20) REVERT: U 28 PHE cc_start: 0.8478 (m-80) cc_final: 0.8241 (m-10) REVERT: U 40 TYR cc_start: 0.8972 (t80) cc_final: 0.8731 (t80) REVERT: U 51 ASP cc_start: 0.8180 (t0) cc_final: 0.7915 (t0) REVERT: U 54 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8435 (ptpp) REVERT: U 142 ARG cc_start: 0.7475 (mmm160) cc_final: 0.6064 (ptt180) REVERT: V 35 ASP cc_start: 0.8540 (p0) cc_final: 0.8207 (p0) REVERT: V 50 GLU cc_start: 0.7011 (tp30) cc_final: 0.6775 (tp30) REVERT: V 85 ASN cc_start: 0.8962 (m-40) cc_final: 0.8542 (m-40) REVERT: W 19 ARG cc_start: 0.6362 (mmt180) cc_final: 0.6001 (mpt180) REVERT: W 21 ARG cc_start: 0.8481 (ttm170) cc_final: 0.7588 (ttp-170) REVERT: W 33 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7632 (mm-30) REVERT: X 21 ASN cc_start: 0.8552 (t0) cc_final: 0.7912 (t0) REVERT: X 33 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: X 41 LYS cc_start: 0.8888 (ptmm) cc_final: 0.8250 (ptpt) REVERT: Y 4 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.7526 (mtt) REVERT: Z 1 MET cc_start: 0.2676 (OUTLIER) cc_final: 0.2210 (ttt) REVERT: Z 63 ASN cc_start: 0.9224 (p0) cc_final: 0.8874 (p0) REVERT: Z 90 CYS cc_start: 0.8220 (m) cc_final: 0.7821 (m) REVERT: b 19 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7644 (pp30) REVERT: b 89 ARG cc_start: 0.8026 (ttt180) cc_final: 0.7681 (ttt90) REVERT: c 84 HIS cc_start: 0.4876 (OUTLIER) cc_final: 0.4149 (m-70) REVERT: e 48 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8811 (mmmm) REVERT: g 52 TYR cc_start: 0.7922 (t80) cc_final: 0.7676 (t80) REVERT: g 116 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8360 (p0) REVERT: g 189 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7915 (mt) REVERT: g 249 CYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6615 (p) REVERT: g 257 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8615 (mmtp) REVERT: i 99 LYS cc_start: 0.6690 (tptm) cc_final: 0.6344 (tppt) REVERT: i 127 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8070 (tptt) REVERT: j 90 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7333 (p0) REVERT: j 99 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: k 17 LYS cc_start: 0.8603 (tptt) cc_final: 0.7939 (tppt) REVERT: k 63 LYS cc_start: 0.5961 (mptt) cc_final: 0.5752 (tppt) REVERT: k 81 LYS cc_start: 0.5703 (mmmt) cc_final: 0.5195 (mptt) REVERT: k 147 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5163 (p90) REVERT: k 148 ARG cc_start: 0.7373 (ptt180) cc_final: 0.5997 (ttt180) REVERT: k 158 LYS cc_start: 0.6624 (mttt) cc_final: 0.6219 (mtpt) REVERT: k 202 GLN cc_start: 0.6545 (pt0) cc_final: 0.5768 (tm-30) REVERT: k 217 LEU cc_start: 0.5624 (pp) cc_final: 0.5316 (pp) REVERT: k 242 GLU cc_start: 0.6050 (mm-30) cc_final: 0.5708 (mt-10) REVERT: k 335 GLU cc_start: 0.0080 (OUTLIER) cc_final: -0.0196 (mm-30) REVERT: k 338 ASN cc_start: 0.1057 (OUTLIER) cc_final: 0.0803 (m-40) REVERT: k 345 MET cc_start: 0.3355 (ptp) cc_final: 0.2972 (ptp) REVERT: k 436 TYR cc_start: 0.1959 (OUTLIER) cc_final: 0.1629 (t80) REVERT: k 520 HIS cc_start: 0.2725 (OUTLIER) cc_final: 0.2125 (t-90) REVERT: k 524 MET cc_start: 0.4171 (pmm) cc_final: 0.3933 (pmm) REVERT: k 551 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5883 (tt) REVERT: l 20 MET cc_start: 0.7935 (tmm) cc_final: 0.7688 (ttp) REVERT: n 76 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7472 (mtp85) REVERT: n 79 ILE cc_start: 0.9005 (mm) cc_final: 0.8740 (mt) outliers start: 374 outliers final: 219 residues processed: 1308 average time/residue: 0.8761 time to fit residues: 1953.4770 Evaluate side-chains 1228 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 967 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 144 LYS Chi-restraints excluded: chain K residue 148 LYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 181 GLN Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 62 VAL 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 22 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 25 CYS Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 GLN Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 33 GLN Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 49 LYS Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 74 CYS Chi-restraints excluded: chain c residue 3 LEU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 35 VAL Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 4 GLN Chi-restraints excluded: chain e residue 48 LYS Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 127 LYS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 84 THR Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 262 LEU Chi-restraints excluded: chain k residue 278 VAL Chi-restraints excluded: chain k residue 304 SER Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 329 LEU Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 434 ASP Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 468 GLN Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 547 SER Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain n residue 44 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 380 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 569 optimal weight: 2.9990 chunk 465 optimal weight: 0.3980 chunk 188 optimal weight: 20.0000 chunk 685 optimal weight: 7.9990 chunk 740 optimal weight: 10.0000 chunk 610 optimal weight: 3.9990 chunk 679 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 549 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN G 232 ASN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS ** M 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN Q 113 GLN T 26 ASN T 62 GLN W 18 HIS ** W 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 ASN X 35 ASN a 89 HIS d 7 GLN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 ASN k 112 ASN k 175 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 520 HIS k 571 ASN l 22 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 91450 Z= 0.228 Angle : 0.631 11.045 132175 Z= 0.325 Chirality : 0.040 0.282 16263 Planarity : 0.005 0.059 10021 Dihedral : 22.330 179.963 35326 Min Nonbonded Distance : 1.099 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.41 % Favored : 91.57 % Rotamer: Outliers : 7.64 % Allowed : 23.71 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -2.67 (0.10), residues: 5824 helix: -0.95 (0.12), residues: 1746 sheet: -1.53 (0.16), residues: 970 loop : -2.39 (0.10), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 204 HIS 0.010 0.001 HIS E 171 PHE 0.020 0.001 PHE c 79 TYR 0.021 0.001 TYR K 149 ARG 0.009 0.000 ARG f 95 *********************** 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 1384 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 994 time to evaluate : 5.428 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 11 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6419 (p90) REVERT: A 123 LYS cc_start: 0.5398 (pttt) cc_final: 0.4959 (mttp) REVERT: C 42 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8179 (mtpt) REVERT: C 89 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8234 (mmtm) REVERT: D 63 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8524 (mptt) REVERT: D 87 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8645 (pp) REVERT: D 99 ASN cc_start: 0.9089 (t0) cc_final: 0.8726 (t0) REVERT: D 133 TYR cc_start: 0.8464 (m-10) cc_final: 0.8255 (m-10) REVERT: E 33 GLU cc_start: -0.0011 (OUTLIER) cc_final: -0.0236 (mp0) REVERT: E 137 LEU cc_start: 0.9464 (mp) cc_final: 0.9219 (mm) REVERT: E 150 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8285 (mmtp) REVERT: F 127 MET cc_start: 0.8876 (mmm) cc_final: 0.8493 (mmm) REVERT: F 149 SER cc_start: 0.8514 (p) cc_final: 0.8159 (m) REVERT: H 197 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7377 (ptmm) REVERT: H 210 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7887 (tm-30) REVERT: I 105 ASN cc_start: 0.8298 (t0) cc_final: 0.8093 (t0) REVERT: I 155 GLN cc_start: 0.7693 (mt0) cc_final: 0.7000 (mm110) REVERT: I 223 LYS cc_start: 0.7323 (mptt) cc_final: 0.7072 (tmtt) REVERT: J 57 ARG cc_start: 0.6230 (mtm110) cc_final: 0.5937 (mtm110) REVERT: J 106 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5571 (mmm160) REVERT: J 115 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5382 (ttpt) REVERT: J 162 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7218 (mm110) REVERT: K 62 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8809 (t) REVERT: K 92 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7849 (ttt-90) REVERT: K 181 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8401 (mt0) REVERT: L 154 GLN cc_start: 0.8617 (tp40) cc_final: 0.8368 (tp-100) REVERT: M 3 MET cc_start: 0.8545 (ptp) cc_final: 0.8037 (ptp) REVERT: M 5 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8176 (mtmm) REVERT: M 61 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7985 (mt0) REVERT: M 70 TYR cc_start: 0.8178 (m-10) cc_final: 0.7965 (m-80) REVERT: N 31 GLU cc_start: 0.3716 (OUTLIER) cc_final: 0.2063 (pm20) REVERT: N 106 HIS cc_start: 0.9265 (OUTLIER) cc_final: 0.9033 (p90) REVERT: N 113 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8132 (tp) REVERT: O 35 ILE cc_start: 0.8481 (pt) cc_final: 0.8010 (mm) REVERT: O 84 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7702 (mppt) REVERT: P 4 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8348 (ptp) REVERT: P 29 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7873 (p) REVERT: P 56 ASP cc_start: 0.8648 (m-30) cc_final: 0.8223 (m-30) REVERT: Q 80 ASP cc_start: 0.8216 (t0) cc_final: 0.7964 (t0) REVERT: Q 98 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8072 (mmm160) REVERT: R 41 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7615 (mm-40) REVERT: R 61 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8148 (ptp90) REVERT: R 66 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7630 (mt-10) REVERT: R 71 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: S 29 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7798 (p0) REVERT: S 113 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9073 (tt) REVERT: T 36 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7989 (tm-30) REVERT: T 80 ARG cc_start: 0.7724 (ttm170) cc_final: 0.7405 (mmp80) REVERT: T 91 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7613 (tp) REVERT: T 93 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: U 28 PHE cc_start: 0.8356 (m-80) cc_final: 0.8087 (m-10) REVERT: U 40 TYR cc_start: 0.8936 (t80) cc_final: 0.8699 (t80) REVERT: U 76 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7705 (tm-30) REVERT: U 142 ARG cc_start: 0.7162 (mmm160) cc_final: 0.5667 (ttp80) REVERT: V 35 ASP cc_start: 0.8518 (p0) cc_final: 0.8194 (p0) REVERT: V 50 GLU cc_start: 0.6875 (tp30) cc_final: 0.6660 (tp30) REVERT: V 85 ASN cc_start: 0.8970 (m-40) cc_final: 0.8559 (m-40) REVERT: W 21 ARG cc_start: 0.8491 (ttm170) cc_final: 0.7585 (ttp-170) REVERT: W 33 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7688 (mm-30) REVERT: X 21 ASN cc_start: 0.8543 (t0) cc_final: 0.7897 (t0) REVERT: X 33 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: X 41 LYS cc_start: 0.8885 (ptmm) cc_final: 0.8362 (ptpt) REVERT: X 47 ASN cc_start: 0.8808 (p0) cc_final: 0.8449 (p0) REVERT: X 82 ASN cc_start: 0.7666 (t0) cc_final: 0.7461 (t0) REVERT: Y 4 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7670 (mtt) REVERT: Z 1 MET cc_start: 0.2581 (OUTLIER) cc_final: 0.2143 (ttt) REVERT: Z 90 CYS cc_start: 0.8116 (m) cc_final: 0.7876 (m) REVERT: a 11 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8948 (ptpt) REVERT: c 18 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8375 (ptpt) REVERT: c 42 LYS cc_start: 0.7778 (mttp) cc_final: 0.7499 (mptt) REVERT: c 81 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7840 (ttm-80) REVERT: d 43 ILE cc_start: 0.9313 (mp) cc_final: 0.9066 (mt) REVERT: g 116 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8321 (p0) REVERT: g 189 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7961 (mt) REVERT: g 249 CYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6635 (p) REVERT: g 257 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8619 (mmtp) REVERT: g 271 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8248 (mttp) REVERT: j 90 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7316 (p0) REVERT: j 99 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: k 17 LYS cc_start: 0.8590 (tptt) cc_final: 0.7997 (tppt) REVERT: k 63 LYS cc_start: 0.6033 (mptt) cc_final: 0.5801 (tppt) REVERT: k 147 PHE cc_start: 0.6147 (p90) cc_final: 0.4965 (p90) REVERT: k 148 ARG cc_start: 0.7241 (ptt180) cc_final: 0.5907 (ttt180) REVERT: k 158 LYS cc_start: 0.6722 (mttt) cc_final: 0.6270 (mtpt) REVERT: k 242 GLU cc_start: 0.6035 (mm-30) cc_final: 0.5390 (mt-10) REVERT: k 335 GLU cc_start: -0.0211 (OUTLIER) cc_final: -0.0509 (mm-30) REVERT: k 338 ASN cc_start: 0.1128 (OUTLIER) cc_final: 0.0906 (m-40) REVERT: k 345 MET cc_start: 0.3475 (ptp) cc_final: 0.3082 (ptp) REVERT: k 436 TYR cc_start: 0.2062 (OUTLIER) cc_final: 0.1751 (t80) REVERT: k 520 HIS cc_start: 0.2646 (OUTLIER) cc_final: 0.2094 (t70) REVERT: k 524 MET cc_start: 0.4127 (pmm) cc_final: 0.3797 (pmm) REVERT: k 551 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.5998 (tt) REVERT: l 20 MET cc_start: 0.7894 (tmm) cc_final: 0.7579 (ttp) REVERT: n 66 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7900 (ptpt) REVERT: n 76 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7487 (mtp85) REVERT: n 79 ILE cc_start: 0.8940 (mm) cc_final: 0.8726 (mt) outliers start: 390 outliers final: 252 residues processed: 1280 average time/residue: 0.8209 time to fit residues: 1784.5405 Evaluate side-chains 1233 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 940 time to evaluate : 5.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 HIS Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 GLN Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain P residue 4 MET 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 22 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 25 CYS Chi-restraints excluded: chain S residue 29 ASN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 GLN Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 33 GLN Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 74 CYS Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 4 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 84 THR Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 160 LEU Chi-restraints excluded: chain k residue 175 GLN Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 262 LEU Chi-restraints excluded: chain k residue 294 SER Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 329 LEU Chi-restraints excluded: chain k residue 333 VAL Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 376 VAL Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 387 THR Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 434 ASP Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 468 GLN Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain k residue 598 ASP Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 64 ASN Chi-restraints excluded: chain n residue 66 LYS 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: 7.9990 chunk 515 optimal weight: 6.9990 chunk 355 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 chunk 459 optimal weight: 2.9990 chunk 687 optimal weight: 7.9990 chunk 727 optimal weight: 0.0370 chunk 359 optimal weight: 8.9990 chunk 651 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 overall best weight: 3.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS G 232 ASN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN L 75 ASN M 28 HIS P 58 HIS Q 32 HIS ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN X 35 ASN Z 77 ASN c 19 HIS ** e 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 HIS ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 91450 Z= 0.281 Angle : 0.641 10.764 132175 Z= 0.328 Chirality : 0.041 0.279 16263 Planarity : 0.005 0.054 10021 Dihedral : 22.269 179.662 35278 Min Nonbonded Distance : 1.064 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.91 % Favored : 91.07 % Rotamer: Outliers : 8.07 % Allowed : 24.36 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -2.51 (0.10), residues: 5824 helix: -0.76 (0.12), residues: 1726 sheet: -1.47 (0.16), residues: 975 loop : -2.30 (0.10), residues: 3123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 204 HIS 0.012 0.001 HIS E 171 PHE 0.027 0.002 PHE J 135 TYR 0.024 0.002 TYR K 149 ARG 0.010 0.000 ARG f 95 *********************** 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 1380 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 968 time to evaluate : 5.405 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 123 LYS cc_start: 0.5546 (pttt) cc_final: 0.5137 (mttp) REVERT: C 46 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8558 (mt) REVERT: C 89 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8262 (mmtm) REVERT: C 102 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7204 (tpt-90) REVERT: D 20 LYS cc_start: 0.2926 (OUTLIER) cc_final: 0.2649 (mtmm) REVERT: D 59 SER cc_start: 0.8995 (p) cc_final: 0.7869 (t) REVERT: D 63 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8189 (mptt) REVERT: D 78 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7094 (mt-10) REVERT: D 87 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8632 (pp) REVERT: D 99 ASN cc_start: 0.9107 (t0) cc_final: 0.8699 (t0) REVERT: F 104 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.8978 (m) REVERT: F 149 SER cc_start: 0.8508 (p) cc_final: 0.8152 (m) REVERT: H 197 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7571 (ptmm) REVERT: H 210 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7885 (tm-30) REVERT: I 13 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: I 105 ASN cc_start: 0.8433 (t0) cc_final: 0.8071 (t0) REVERT: I 140 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7788 (mtt90) REVERT: I 152 ASP cc_start: 0.8017 (t0) cc_final: 0.7512 (t0) REVERT: I 155 GLN cc_start: 0.7718 (mt0) cc_final: 0.6993 (mm110) REVERT: I 192 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8953 (mp) REVERT: I 223 LYS cc_start: 0.7352 (mptt) cc_final: 0.7064 (tmtt) REVERT: J 57 ARG cc_start: 0.6265 (mtm110) cc_final: 0.6003 (mtm110) REVERT: J 106 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5561 (mmm160) REVERT: J 115 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5396 (ttmt) REVERT: J 162 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7241 (mm110) REVERT: K 62 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8807 (t) REVERT: K 92 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7650 (tmm160) REVERT: K 141 ARG cc_start: 0.7149 (ptp90) cc_final: 0.6766 (ptt90) REVERT: K 181 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: L 154 GLN cc_start: 0.8565 (tp40) cc_final: 0.8325 (tp-100) REVERT: M 3 MET cc_start: 0.8537 (ptp) cc_final: 0.8181 (ptp) REVERT: M 61 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7977 (mt0) REVERT: M 70 TYR cc_start: 0.8207 (m-10) cc_final: 0.7975 (m-80) REVERT: N 31 GLU cc_start: 0.3744 (OUTLIER) cc_final: 0.2105 (pm20) REVERT: N 113 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8106 (tp) REVERT: N 121 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7633 (mm-40) REVERT: O 35 ILE cc_start: 0.8638 (pt) cc_final: 0.8171 (mm) REVERT: P 4 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8373 (ptp) REVERT: P 29 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7943 (p) REVERT: Q 66 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7593 (ptp-170) REVERT: Q 80 ASP cc_start: 0.8224 (t0) cc_final: 0.7987 (t0) REVERT: Q 98 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8214 (mmm160) REVERT: R 22 LEU cc_start: 0.8427 (pp) cc_final: 0.7979 (tt) REVERT: R 41 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7668 (mm-40) REVERT: R 61 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8195 (ptp90) REVERT: R 66 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7639 (mt-10) REVERT: R 71 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: R 93 MET cc_start: 0.7825 (tpp) cc_final: 0.7104 (mmp) REVERT: R 106 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: S 16 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8859 (tmtp) REVERT: S 29 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7838 (p0) REVERT: S 113 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9062 (tt) REVERT: T 36 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8130 (tm-30) REVERT: T 80 ARG cc_start: 0.7575 (ttm170) cc_final: 0.7261 (mmp80) REVERT: T 91 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7752 (tp) REVERT: T 93 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.5753 (pm20) REVERT: U 28 PHE cc_start: 0.8420 (m-80) cc_final: 0.8113 (m-10) REVERT: U 40 TYR cc_start: 0.8957 (t80) cc_final: 0.8709 (t80) REVERT: U 142 ARG cc_start: 0.7280 (mmm160) cc_final: 0.5756 (ttp80) REVERT: V 35 ASP cc_start: 0.8541 (p0) cc_final: 0.8216 (p0) REVERT: V 50 GLU cc_start: 0.6891 (tp30) cc_final: 0.6677 (tp30) REVERT: V 85 ASN cc_start: 0.9005 (m-40) cc_final: 0.8568 (m-40) REVERT: W 21 ARG cc_start: 0.8513 (ttm170) cc_final: 0.7455 (ttp-170) REVERT: W 33 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7732 (mm-30) REVERT: W 61 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8451 (mt) REVERT: X 21 ASN cc_start: 0.8536 (t0) cc_final: 0.7908 (t0) REVERT: X 33 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: X 41 LYS cc_start: 0.8787 (ptmm) cc_final: 0.8263 (ptpt) REVERT: X 82 ASN cc_start: 0.7739 (t0) cc_final: 0.7420 (t0) REVERT: Y 4 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7581 (mtt) REVERT: Z 1 MET cc_start: 0.2693 (OUTLIER) cc_final: 0.2171 (ttt) REVERT: Z 90 CYS cc_start: 0.8181 (m) cc_final: 0.7919 (m) REVERT: Z 139 GLU cc_start: 0.7862 (pp20) cc_final: 0.7415 (pp20) REVERT: a 110 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7719 (ttt90) REVERT: c 42 LYS cc_start: 0.7803 (mttp) cc_final: 0.7550 (mptt) REVERT: c 81 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7908 (ttm-80) REVERT: c 84 HIS cc_start: 0.5076 (OUTLIER) cc_final: 0.4532 (m-70) REVERT: d 43 ILE cc_start: 0.9332 (mp) cc_final: 0.9082 (mt) REVERT: e 6 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7936 (tt) REVERT: e 16 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: g 116 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8303 (p0) REVERT: g 189 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7868 (mt) REVERT: g 249 CYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6883 (p) REVERT: g 257 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8613 (mmtp) REVERT: g 271 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8229 (mttp) REVERT: j 68 LYS cc_start: 0.8450 (tttp) cc_final: 0.7486 (mppt) REVERT: j 90 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7415 (p0) REVERT: j 99 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: k 17 LYS cc_start: 0.8525 (tptt) cc_final: 0.7988 (tppt) REVERT: k 63 LYS cc_start: 0.6234 (mptt) cc_final: 0.5904 (tppt) REVERT: k 147 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.4966 (p90) REVERT: k 148 ARG cc_start: 0.7218 (ptt180) cc_final: 0.5955 (ttt180) REVERT: k 158 LYS cc_start: 0.6672 (mttt) cc_final: 0.6145 (mtpt) REVERT: k 242 GLU cc_start: 0.5897 (mm-30) cc_final: 0.5331 (mt-10) REVERT: k 310 ASN cc_start: 0.5043 (m-40) cc_final: 0.4747 (m110) REVERT: k 335 GLU cc_start: -0.0061 (OUTLIER) cc_final: -0.0335 (mm-30) REVERT: k 345 MET cc_start: 0.3440 (ptp) cc_final: 0.3069 (ptp) REVERT: k 436 TYR cc_start: 0.2513 (OUTLIER) cc_final: 0.2149 (t80) REVERT: k 520 HIS cc_start: 0.4094 (OUTLIER) cc_final: 0.3750 (t-90) REVERT: k 524 MET cc_start: 0.3922 (OUTLIER) cc_final: 0.3624 (pmm) REVERT: k 551 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.5976 (tt) REVERT: l 20 MET cc_start: 0.7871 (tmm) cc_final: 0.7638 (ttp) REVERT: n 76 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7505 (mtp85) REVERT: n 79 ILE cc_start: 0.8944 (mm) cc_final: 0.8715 (mt) REVERT: n 112 ASN cc_start: 0.7152 (t0) cc_final: 0.6636 (t0) outliers start: 412 outliers final: 288 residues processed: 1269 average time/residue: 0.8103 time to fit residues: 1756.2942 Evaluate side-chains 1275 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 936 time to evaluate : 6.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 GLN Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain P residue 4 MET 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 22 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 104 GLN Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 29 ASN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 GLN Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 33 GLN Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 110 ARG Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 74 CYS Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 3 LEU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 4 GLN Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 120 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 84 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 262 LEU Chi-restraints excluded: chain k residue 266 ASP Chi-restraints excluded: chain k residue 278 VAL Chi-restraints excluded: chain k residue 289 LEU Chi-restraints excluded: chain k residue 294 SER Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 329 LEU Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 376 VAL Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 434 ASP Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 468 GLN Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 524 MET Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 534 VAL Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 64 ASN Chi-restraints excluded: chain n residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 606 optimal weight: 5.9990 chunk 413 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 621 optimal weight: 7.9990 chunk 503 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 371 optimal weight: 8.9990 chunk 653 optimal weight: 0.0050 chunk 183 optimal weight: 6.9990 overall best weight: 5.6002 ------------------------------------------------------------------------------- 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** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS M 50 GLN R 103 ASN U 87 GLN V 12 GLN X 35 ASN Z 46 HIS b 72 HIS c 49 HIS ** e 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 203 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 251 GLN ** k 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 520 HIS n 112 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 91450 Z= 0.391 Angle : 0.702 10.938 132175 Z= 0.357 Chirality : 0.044 0.289 16263 Planarity : 0.005 0.057 10021 Dihedral : 22.292 179.734 35270 Min Nonbonded Distance : 1.039 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.74 % Favored : 90.25 % Rotamer: Outliers : 8.96 % Allowed : 24.57 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: -0.75 (0.12), residues: 1715 sheet: -1.49 (0.16), residues: 967 loop : -2.34 (0.10), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 204 HIS 0.015 0.001 HIS E 171 PHE 0.021 0.002 PHE c 79 TYR 0.018 0.002 TYR U 77 ARG 0.010 0.001 ARG f 95 *********************** 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 1416 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 457 poor density : 959 time to evaluate : 5.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.5550 (pttt) cc_final: 0.5084 (mttp) REVERT: A 246 GLU cc_start: 0.7121 (mm-30) cc_final: 0.5729 (pm20) REVERT: C 42 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8219 (mtpt) REVERT: C 89 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8404 (mmtm) REVERT: D 20 LYS cc_start: 0.3021 (OUTLIER) cc_final: 0.2672 (mtmm) REVERT: D 59 SER cc_start: 0.9035 (p) cc_final: 0.7821 (t) REVERT: D 63 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8182 (mptt) REVERT: D 78 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: D 87 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8640 (pp) REVERT: D 99 ASN cc_start: 0.9109 (t0) cc_final: 0.8716 (t0) REVERT: E 150 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7948 (mmtp) REVERT: E 225 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: F 51 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8907 (tp) REVERT: F 57 ASN cc_start: 0.8716 (t0) cc_final: 0.8369 (t0) REVERT: F 149 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8086 (m) REVERT: G 108 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8046 (ptt-90) REVERT: H 74 LYS cc_start: 0.8473 (mttt) cc_final: 0.8272 (mttt) REVERT: H 197 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7864 (ptmm) REVERT: H 210 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7885 (tm-30) REVERT: I 21 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: I 105 ASN cc_start: 0.8609 (t0) cc_final: 0.8201 (t0) REVERT: I 140 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7787 (mtt90) REVERT: I 155 GLN cc_start: 0.7757 (mt0) cc_final: 0.6987 (mm-40) REVERT: I 223 LYS cc_start: 0.7353 (mptt) cc_final: 0.7069 (tmtt) REVERT: J 57 ARG cc_start: 0.6105 (mtm110) cc_final: 0.5857 (mtm110) REVERT: J 115 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5378 (ttmt) REVERT: J 162 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7371 (mm110) REVERT: K 62 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8786 (t) REVERT: K 92 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7832 (tmm160) REVERT: K 135 GLU cc_start: 0.8603 (mp0) cc_final: 0.8213 (mp0) REVERT: K 148 LYS cc_start: 0.7582 (pttm) cc_final: 0.6844 (pttt) REVERT: K 181 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: L 103 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: L 154 GLN cc_start: 0.8505 (tp40) cc_final: 0.8263 (tp-100) REVERT: L 169 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7152 (ttm-80) REVERT: M 5 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8047 (mttt) REVERT: M 61 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7988 (mt0) REVERT: M 70 TYR cc_start: 0.8245 (m-10) cc_final: 0.8013 (m-80) REVERT: N 31 GLU cc_start: 0.4134 (OUTLIER) cc_final: 0.2522 (pm20) REVERT: N 113 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8087 (tp) REVERT: O 35 ILE cc_start: 0.8677 (pt) cc_final: 0.8223 (mm) REVERT: P 4 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8536 (ptp) REVERT: Q 66 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7601 (ptp-170) REVERT: Q 80 ASP cc_start: 0.8281 (t0) cc_final: 0.8019 (t0) REVERT: Q 97 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8836 (tt) REVERT: Q 98 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8051 (mmm160) REVERT: R 15 PHE cc_start: 0.2570 (OUTLIER) cc_final: 0.2351 (m-10) REVERT: R 22 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7949 (tt) REVERT: R 41 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7691 (mm-40) REVERT: R 61 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8355 (ptp90) REVERT: R 71 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6731 (tt0) REVERT: R 106 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6750 (tp30) REVERT: S 29 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7941 (p0) REVERT: S 113 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9105 (tt) REVERT: T 36 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8142 (tm-30) REVERT: T 74 GLN cc_start: 0.8916 (tt0) cc_final: 0.8611 (tt0) REVERT: T 80 ARG cc_start: 0.7638 (ttm170) cc_final: 0.7312 (mmp80) REVERT: T 91 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7767 (tp) REVERT: T 93 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.5895 (pm20) REVERT: U 28 PHE cc_start: 0.8471 (m-80) cc_final: 0.8014 (m-10) REVERT: U 40 TYR cc_start: 0.9029 (t80) cc_final: 0.8771 (t80) REVERT: U 142 ARG cc_start: 0.7335 (mmm160) cc_final: 0.5736 (ttp80) REVERT: V 35 ASP cc_start: 0.8568 (p0) cc_final: 0.8252 (p0) REVERT: V 50 GLU cc_start: 0.6984 (tp30) cc_final: 0.6750 (tp30) REVERT: W 21 ARG cc_start: 0.8501 (ttm170) cc_final: 0.7377 (ttp-170) REVERT: W 33 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7755 (mm-30) REVERT: W 61 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8451 (mt) REVERT: X 21 ASN cc_start: 0.8607 (t0) cc_final: 0.7661 (t0) REVERT: X 33 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: X 41 LYS cc_start: 0.8794 (ptmm) cc_final: 0.8262 (ptpt) REVERT: X 82 ASN cc_start: 0.7736 (t0) cc_final: 0.7399 (t0) REVERT: Y 4 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7768 (mtt) REVERT: Y 80 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: Z 1 MET cc_start: 0.2816 (OUTLIER) cc_final: 0.2214 (ttt) REVERT: Z 90 CYS cc_start: 0.8196 (m) cc_final: 0.7926 (m) REVERT: Z 98 ASP cc_start: 0.8774 (p0) cc_final: 0.8571 (p0) REVERT: Z 139 GLU cc_start: 0.7869 (pp20) cc_final: 0.7482 (pp20) REVERT: a 11 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8966 (ptpt) REVERT: c 18 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8338 (ptpt) REVERT: c 42 LYS cc_start: 0.7721 (mttp) cc_final: 0.7503 (mptt) REVERT: c 81 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7855 (ttm-80) REVERT: c 84 HIS cc_start: 0.5236 (OUTLIER) cc_final: 0.4746 (m-70) REVERT: d 43 ILE cc_start: 0.9392 (mp) cc_final: 0.9140 (mt) REVERT: e 6 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8036 (tt) REVERT: e 16 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: f 95 ARG cc_start: 0.8174 (ptm-80) cc_final: 0.7374 (ptm-80) REVERT: g 12 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8433 (tmtt) REVERT: g 52 TYR cc_start: 0.7883 (t80) cc_final: 0.7639 (t80) REVERT: g 57 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7876 (ttm-80) REVERT: g 116 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8356 (p0) REVERT: g 189 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7870 (mt) REVERT: g 249 CYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7004 (p) REVERT: g 257 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8578 (mmtp) REVERT: g 271 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8147 (mttp) REVERT: j 44 ASN cc_start: 0.7915 (m110) cc_final: 0.7474 (m110) REVERT: j 68 LYS cc_start: 0.8469 (tttp) cc_final: 0.7544 (mptt) REVERT: j 90 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7464 (p0) REVERT: j 99 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: k 5 LEU cc_start: 0.6506 (mt) cc_final: 0.6279 (mp) REVERT: k 17 LYS cc_start: 0.8464 (tptt) cc_final: 0.7968 (tppt) REVERT: k 63 LYS cc_start: 0.6252 (mptt) cc_final: 0.5939 (tppt) REVERT: k 96 ARG cc_start: 0.5429 (ttt180) cc_final: 0.4512 (ptt-90) REVERT: k 147 PHE cc_start: 0.6279 (p90) cc_final: 0.5238 (p90) REVERT: k 148 ARG cc_start: 0.7267 (ptt180) cc_final: 0.5973 (ttt180) REVERT: k 158 LYS cc_start: 0.6772 (mttt) cc_final: 0.6196 (mtpt) REVERT: k 242 GLU cc_start: 0.5736 (mm-30) cc_final: 0.5234 (mt-10) REVERT: k 335 GLU cc_start: 0.0334 (OUTLIER) cc_final: -0.0673 (tm-30) REVERT: k 345 MET cc_start: 0.3586 (ptp) cc_final: 0.3287 (ptp) REVERT: k 436 TYR cc_start: 0.2669 (OUTLIER) cc_final: 0.2370 (t80) REVERT: k 520 HIS cc_start: 0.3342 (OUTLIER) cc_final: 0.2735 (t70) REVERT: k 524 MET cc_start: 0.3979 (OUTLIER) cc_final: 0.3683 (pmm) REVERT: k 551 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5808 (tt) REVERT: n 66 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7655 (ptpt) REVERT: n 79 ILE cc_start: 0.8939 (mm) cc_final: 0.8700 (mt) outliers start: 457 outliers final: 338 residues processed: 1297 average time/residue: 0.8068 time to fit residues: 1785.8234 Evaluate side-chains 1337 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 942 time to evaluate : 5.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 149 SER Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 21 GLU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 88 ASN 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 115 SER Chi-restraints excluded: chain K residue 128 LYS Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 GLN Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain P residue 4 MET 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 22 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 15 PHE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 29 ASN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 GLN Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 33 GLN Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 74 CYS Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 3 LEU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 4 GLN Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 120 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 199 THR Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 84 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 160 LEU Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 262 LEU Chi-restraints excluded: chain k residue 266 ASP Chi-restraints excluded: chain k residue 278 VAL Chi-restraints excluded: chain k residue 289 LEU Chi-restraints excluded: chain k residue 294 SER Chi-restraints excluded: chain k residue 313 LEU Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 329 LEU Chi-restraints excluded: chain k residue 333 VAL Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 376 VAL Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 387 THR Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 432 ILE Chi-restraints excluded: chain k residue 434 ASP Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 468 GLN Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 489 SER Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 524 MET Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain k residue 534 VAL Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 66 LYS 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: 7.9990 chunk 655 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 427 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 728 optimal weight: 6.9990 chunk 604 optimal weight: 0.7980 chunk 337 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 382 optimal weight: 0.3980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS H 97 ASN J 25 GLN ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 ASN M 28 HIS Q 103 ASN S 97 GLN V 12 GLN ** W 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 ASN X 47 ASN ** e 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 GLN k 203 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 468 GLN k 520 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 91450 Z= 0.154 Angle : 0.586 11.441 132175 Z= 0.299 Chirality : 0.037 0.263 16263 Planarity : 0.004 0.057 10021 Dihedral : 22.183 179.629 35264 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.59 % Favored : 92.39 % Rotamer: Outliers : 6.49 % Allowed : 27.57 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.11), residues: 5824 helix: -0.34 (0.13), residues: 1702 sheet: -1.32 (0.16), residues: 966 loop : -2.16 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 132 HIS 0.016 0.001 HIS k 520 PHE 0.017 0.001 PHE k 225 TYR 0.013 0.001 TYR N 37 ARG 0.010 0.000 ARG f 95 *********************** 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 1329 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 998 time to evaluate : 5.312 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 11 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6330 (p90) REVERT: A 123 LYS cc_start: 0.5651 (pttt) cc_final: 0.5196 (mttp) REVERT: A 246 GLU cc_start: 0.7135 (mm-30) cc_final: 0.5724 (pm20) REVERT: C 41 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8732 (ttm170) REVERT: C 42 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8218 (mtpt) REVERT: C 89 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8376 (mmtm) REVERT: D 59 SER cc_start: 0.9049 (p) cc_final: 0.7887 (t) REVERT: D 63 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8208 (mptt) REVERT: D 78 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: D 87 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8514 (pp) REVERT: E 150 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8237 (mmtp) REVERT: F 57 ASN cc_start: 0.8695 (t0) cc_final: 0.8353 (t0) REVERT: F 104 SER cc_start: 0.9374 (p) cc_final: 0.8982 (m) REVERT: F 149 SER cc_start: 0.8494 (p) cc_final: 0.8204 (m) REVERT: G 108 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7976 (ptt-90) REVERT: H 210 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7850 (tm-30) REVERT: I 105 ASN cc_start: 0.8420 (t0) cc_final: 0.8020 (t0) REVERT: I 140 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7780 (mtm-85) REVERT: I 155 GLN cc_start: 0.7334 (mt0) cc_final: 0.6857 (mm-40) REVERT: I 223 LYS cc_start: 0.7374 (mptt) cc_final: 0.7082 (tmtt) REVERT: J 57 ARG cc_start: 0.6053 (mtm110) cc_final: 0.5832 (mtm110) REVERT: J 115 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5423 (ttmt) REVERT: J 162 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7354 (mm110) REVERT: K 62 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8791 (t) REVERT: K 92 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7687 (tmm160) REVERT: K 148 LYS cc_start: 0.7530 (pttm) cc_final: 0.7176 (pttt) REVERT: L 154 GLN cc_start: 0.8496 (tp40) cc_final: 0.8251 (tp-100) REVERT: L 169 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7229 (ttm-80) REVERT: M 5 LYS cc_start: 0.8653 (ttmt) cc_final: 0.7966 (mttt) REVERT: M 49 MET cc_start: 0.8891 (tpp) cc_final: 0.8576 (tpp) REVERT: M 61 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7977 (mt0) REVERT: M 70 TYR cc_start: 0.8171 (m-10) cc_final: 0.7930 (m-80) REVERT: N 27 GLU cc_start: 0.3129 (OUTLIER) cc_final: 0.2742 (tt0) REVERT: N 31 GLU cc_start: 0.3830 (OUTLIER) cc_final: 0.2335 (pm20) REVERT: N 106 HIS cc_start: 0.9239 (OUTLIER) cc_final: 0.9029 (p90) REVERT: N 113 LEU cc_start: 0.8404 (tp) cc_final: 0.8163 (tp) REVERT: N 121 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7643 (mm-40) REVERT: O 35 ILE cc_start: 0.8573 (pt) cc_final: 0.8249 (mt) REVERT: P 29 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7840 (p) REVERT: Q 66 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7551 (ptp-170) REVERT: Q 80 ASP cc_start: 0.8211 (t0) cc_final: 0.7986 (t0) REVERT: Q 97 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8797 (tt) REVERT: Q 98 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8078 (mmm160) REVERT: R 22 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7934 (tt) REVERT: R 71 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6494 (tt0) REVERT: R 106 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: S 16 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8746 (tmtp) REVERT: T 18 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6963 (mm-30) REVERT: T 36 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8109 (tm-30) REVERT: T 80 ARG cc_start: 0.7581 (ttm170) cc_final: 0.7231 (mmp80) REVERT: T 91 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7458 (tp) REVERT: U 19 ASN cc_start: 0.8758 (m110) cc_final: 0.8368 (m110) REVERT: U 28 PHE cc_start: 0.8280 (m-80) cc_final: 0.7869 (m-10) REVERT: U 40 TYR cc_start: 0.8864 (t80) cc_final: 0.8647 (t80) REVERT: U 142 ARG cc_start: 0.7290 (mmm160) cc_final: 0.5763 (ttp80) REVERT: V 35 ASP cc_start: 0.8516 (p0) cc_final: 0.8149 (p0) REVERT: V 85 ASN cc_start: 0.8961 (m110) cc_final: 0.8500 (m-40) REVERT: W 19 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6933 (mmt180) REVERT: W 21 ARG cc_start: 0.8484 (ttm170) cc_final: 0.7626 (ttp-170) REVERT: W 33 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7686 (mm-30) REVERT: X 16 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8646 (mtmt) REVERT: X 21 ASN cc_start: 0.8484 (t0) cc_final: 0.7634 (t0) REVERT: X 41 LYS cc_start: 0.8686 (ptmm) cc_final: 0.8260 (ptpt) REVERT: X 66 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7492 (t70) REVERT: X 82 ASN cc_start: 0.7734 (t0) cc_final: 0.7411 (t0) REVERT: Z 1 MET cc_start: 0.2296 (ttp) cc_final: 0.1988 (ttt) REVERT: Z 63 ASN cc_start: 0.8775 (p0) cc_final: 0.8369 (p0) REVERT: Z 98 ASP cc_start: 0.8703 (p0) cc_final: 0.8491 (p0) REVERT: Z 139 GLU cc_start: 0.7895 (pp20) cc_final: 0.7507 (pp20) REVERT: a 11 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8926 (ptpt) REVERT: a 23 MET cc_start: 0.8425 (pmm) cc_final: 0.8156 (pmm) REVERT: c 42 LYS cc_start: 0.7747 (mttp) cc_final: 0.7259 (mmtm) REVERT: c 84 HIS cc_start: 0.5078 (OUTLIER) cc_final: 0.4504 (m-70) REVERT: d 43 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9115 (mt) REVERT: g 5 MET cc_start: 0.6865 (mmm) cc_final: 0.6646 (mmm) REVERT: g 12 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8396 (tmtt) REVERT: g 57 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7750 (ttm-80) REVERT: g 116 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8297 (p0) REVERT: g 145 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6855 (pt0) REVERT: g 189 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7907 (mt) REVERT: g 257 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8610 (mmtp) REVERT: g 271 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8155 (mttp) REVERT: j 68 LYS cc_start: 0.8465 (tttp) cc_final: 0.7451 (mppt) REVERT: j 90 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7491 (p0) REVERT: j 99 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: k 17 LYS cc_start: 0.8384 (tptt) cc_final: 0.7951 (tppt) REVERT: k 63 LYS cc_start: 0.6322 (mptt) cc_final: 0.6021 (tppt) REVERT: k 147 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.4767 (p90) REVERT: k 148 ARG cc_start: 0.7079 (ptt180) cc_final: 0.5870 (ttt180) REVERT: k 158 LYS cc_start: 0.6785 (mttt) cc_final: 0.6284 (mtpt) REVERT: k 242 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5609 (mt-10) REVERT: k 251 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.5678 (tp-100) REVERT: k 310 ASN cc_start: 0.4870 (m-40) cc_final: 0.4452 (m-40) REVERT: k 335 GLU cc_start: 0.0473 (OUTLIER) cc_final: -0.0416 (tm-30) REVERT: k 345 MET cc_start: 0.3400 (ptp) cc_final: 0.3174 (ptp) REVERT: k 446 MET cc_start: 0.3591 (mtt) cc_final: 0.2874 (mmt) REVERT: k 520 HIS cc_start: 0.3840 (OUTLIER) cc_final: 0.3543 (t70) REVERT: k 524 MET cc_start: 0.4165 (OUTLIER) cc_final: 0.3836 (pmm) REVERT: k 551 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.5983 (tt) REVERT: l 20 MET cc_start: 0.7892 (tmm) cc_final: 0.7615 (ttp) REVERT: n 50 PHE cc_start: 0.7973 (m-80) cc_final: 0.7619 (m-80) REVERT: n 76 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7452 (mtp85) outliers start: 331 outliers final: 224 residues processed: 1241 average time/residue: 0.8033 time to fit residues: 1692.5040 Evaluate side-chains 1223 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 958 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 HIS Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 138 ASN Chi-restraints excluded: chain K residue 155 ASN Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 27 GLU Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 104 GLN Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 76 GLN Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 4 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 120 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 57 ARG Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain k residue 106 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 251 GLN Chi-restraints excluded: chain k residue 266 ASP Chi-restraints excluded: chain k residue 289 LEU Chi-restraints excluded: chain k residue 313 LEU Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 370 THR Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 468 GLN Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 524 MET Chi-restraints excluded: chain k residue 534 VAL Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain n residue 44 LEU 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: 3.9990 chunk 82 optimal weight: 20.0000 chunk 415 optimal weight: 0.0980 chunk 532 optimal weight: 10.0000 chunk 412 optimal weight: 7.9990 chunk 613 optimal weight: 9.9990 chunk 406 optimal weight: 6.9990 chunk 725 optimal weight: 20.0000 chunk 454 optimal weight: 2.9990 chunk 442 optimal weight: 9.9990 chunk 335 optimal weight: 3.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN G 8 HIS I 155 GLN ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN K 138 ASN K 181 GLN M 28 HIS M 50 GLN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 203 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 468 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 91450 Z= 0.270 Angle : 0.624 12.021 132175 Z= 0.318 Chirality : 0.040 0.270 16263 Planarity : 0.005 0.055 10021 Dihedral : 22.126 179.757 35217 Min Nonbonded Distance : 1.056 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.00 % Favored : 90.99 % Rotamer: Outliers : 7.15 % Allowed : 27.32 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 5824 helix: -0.32 (0.12), residues: 1710 sheet: -1.33 (0.16), residues: 971 loop : -2.17 (0.10), residues: 3143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 204 HIS 0.012 0.001 HIS E 171 PHE 0.022 0.001 PHE J 135 TYR 0.024 0.001 TYR K 113 ARG 0.012 0.000 ARG f 95 *********************** 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 1323 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 958 time to evaluate : 5.420 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 123 LYS cc_start: 0.5628 (pttt) cc_final: 0.5158 (mttp) REVERT: A 246 GLU cc_start: 0.7114 (mm-30) cc_final: 0.5652 (pm20) REVERT: C 41 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8766 (ttm170) REVERT: C 46 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8507 (mt) REVERT: C 89 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8409 (mmtm) REVERT: C 208 GLU cc_start: 0.6815 (pt0) cc_final: 0.5808 (mm-30) REVERT: D 59 SER cc_start: 0.9054 (p) cc_final: 0.7886 (t) REVERT: D 63 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8171 (mptt) REVERT: D 78 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: D 87 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8575 (pp) REVERT: E 150 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8077 (mmtp) REVERT: F 57 ASN cc_start: 0.8689 (t0) cc_final: 0.8342 (t0) REVERT: F 104 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.9001 (m) REVERT: F 149 SER cc_start: 0.8534 (p) cc_final: 0.8187 (m) REVERT: G 95 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8376 (p) REVERT: G 108 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7942 (ptt-90) REVERT: H 197 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7497 (ptmm) REVERT: H 210 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7902 (tm-30) REVERT: I 105 ASN cc_start: 0.8444 (t0) cc_final: 0.7946 (t0) REVERT: I 140 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7828 (mtm-85) REVERT: I 155 GLN cc_start: 0.7350 (mt0) cc_final: 0.6851 (mm-40) REVERT: I 223 LYS cc_start: 0.7403 (mptt) cc_final: 0.7099 (tmtt) REVERT: J 115 LYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5431 (ttmt) REVERT: J 162 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7484 (mm110) REVERT: K 62 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8800 (t) REVERT: K 92 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7776 (tmm160) REVERT: K 148 LYS cc_start: 0.7476 (pttm) cc_final: 0.7088 (pttt) REVERT: L 10 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8722 (ptp-170) REVERT: L 103 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: L 154 GLN cc_start: 0.8476 (tp40) cc_final: 0.8228 (tp-100) REVERT: L 169 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7172 (ttm-80) REVERT: M 5 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8143 (mtmm) REVERT: M 61 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7974 (mt0) REVERT: M 70 TYR cc_start: 0.8204 (m-10) cc_final: 0.7971 (m-80) REVERT: N 31 GLU cc_start: 0.3891 (OUTLIER) cc_final: 0.2342 (pm20) REVERT: N 113 LEU cc_start: 0.8412 (tp) cc_final: 0.8141 (tp) REVERT: O 35 ILE cc_start: 0.8592 (pt) cc_final: 0.8269 (mt) REVERT: P 29 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7967 (p) REVERT: Q 66 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7600 (ptp-170) REVERT: Q 80 ASP cc_start: 0.8254 (t0) cc_final: 0.8018 (t0) REVERT: Q 97 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8812 (tt) REVERT: Q 98 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8122 (mmm160) REVERT: R 22 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7961 (tt) REVERT: R 106 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6687 (tp30) REVERT: S 16 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8792 (tmtp) REVERT: S 113 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9053 (tt) REVERT: T 18 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7016 (mm-30) REVERT: T 36 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8163 (tm-30) REVERT: T 80 ARG cc_start: 0.7602 (ttm170) cc_final: 0.7265 (mmp80) REVERT: T 91 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7564 (tp) REVERT: U 28 PHE cc_start: 0.8383 (m-80) cc_final: 0.7947 (m-10) REVERT: U 40 TYR cc_start: 0.8924 (t80) cc_final: 0.8692 (t80) REVERT: U 54 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8751 (ptpp) REVERT: V 35 ASP cc_start: 0.8505 (p0) cc_final: 0.8178 (p0) REVERT: V 85 ASN cc_start: 0.9045 (m110) cc_final: 0.8508 (m-40) REVERT: W 21 ARG cc_start: 0.8537 (ttm170) cc_final: 0.7393 (ttp-170) REVERT: W 33 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7727 (mm-30) REVERT: X 21 ASN cc_start: 0.8556 (t0) cc_final: 0.7598 (t0) REVERT: X 41 LYS cc_start: 0.8746 (ptmm) cc_final: 0.8242 (ptpt) REVERT: X 47 ASN cc_start: 0.8926 (p0) cc_final: 0.8596 (p0) REVERT: X 82 ASN cc_start: 0.7775 (t0) cc_final: 0.7480 (t0) REVERT: Y 36 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7591 (mmp-170) REVERT: Y 80 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: Z 1 MET cc_start: 0.2752 (ttp) cc_final: 0.2286 (ttt) REVERT: Z 98 ASP cc_start: 0.8694 (p0) cc_final: 0.8451 (p0) REVERT: Z 139 GLU cc_start: 0.7846 (pp20) cc_final: 0.7503 (pp20) REVERT: a 11 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8949 (ptpt) REVERT: c 42 LYS cc_start: 0.7696 (mttp) cc_final: 0.7291 (mmtm) REVERT: c 84 HIS cc_start: 0.5222 (OUTLIER) cc_final: 0.4754 (m-70) REVERT: d 43 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9151 (mt) REVERT: e 6 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7948 (tt) REVERT: e 16 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: f 95 ARG cc_start: 0.8063 (ptm-80) cc_final: 0.7267 (ptm-80) REVERT: g 12 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8413 (tmtt) REVERT: g 116 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8349 (p0) REVERT: g 189 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7815 (mt) REVERT: g 257 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8576 (mmtp) REVERT: j 68 LYS cc_start: 0.8517 (tttp) cc_final: 0.7492 (mppt) REVERT: j 99 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: k 5 LEU cc_start: 0.6396 (mt) cc_final: 0.6184 (mp) REVERT: k 17 LYS cc_start: 0.8415 (tptt) cc_final: 0.7962 (tppt) REVERT: k 63 LYS cc_start: 0.6411 (mptt) cc_final: 0.5972 (tppt) REVERT: k 147 PHE cc_start: 0.6178 (p90) cc_final: 0.5229 (p90) REVERT: k 148 ARG cc_start: 0.7140 (ptt180) cc_final: 0.5910 (ttt180) REVERT: k 158 LYS cc_start: 0.6771 (mttt) cc_final: 0.6229 (mtpt) REVERT: k 242 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5760 (mt-10) REVERT: k 251 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.5698 (tp-100) REVERT: k 335 GLU cc_start: 0.0409 (OUTLIER) cc_final: -0.0476 (tm-30) REVERT: k 345 MET cc_start: 0.3430 (ptp) cc_final: 0.3138 (ptp) REVERT: k 446 MET cc_start: 0.3283 (mtt) cc_final: 0.2637 (mmt) REVERT: k 520 HIS cc_start: 0.4247 (OUTLIER) cc_final: 0.3759 (t-90) REVERT: k 551 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.5971 (tt) REVERT: l 20 MET cc_start: 0.7944 (tmm) cc_final: 0.7691 (ttp) REVERT: n 66 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7663 (ptpt) REVERT: n 76 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7497 (mtp85) outliers start: 365 outliers final: 262 residues processed: 1231 average time/residue: 0.8144 time to fit residues: 1704.1901 Evaluate side-chains 1250 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 945 time to evaluate : 5.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 128 LYS Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 138 ASN Chi-restraints excluded: chain K residue 155 ASN Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain M residue 28 HIS Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 104 GLN Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 50 PHE Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 36 ARG Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 4 GLN Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 16 GLN Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 120 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 35 SER Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 SER 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 116 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 106 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 160 LEU Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 251 GLN Chi-restraints excluded: chain k residue 262 LEU Chi-restraints excluded: chain k residue 266 ASP Chi-restraints excluded: chain k residue 278 VAL Chi-restraints excluded: chain k residue 289 LEU Chi-restraints excluded: chain k residue 294 SER Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 376 VAL Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 434 ASP Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 468 GLN Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 534 VAL Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain k residue 598 ASP Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 64 ASN Chi-restraints excluded: chain n residue 66 LYS 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: 10.0000 chunk 289 optimal weight: 0.0370 chunk 433 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 461 optimal weight: 0.7980 chunk 494 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 570 optimal weight: 0.8980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS R 79 HIS ** W 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 203 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 91450 Z= 0.141 Angle : 0.571 15.343 132175 Z= 0.291 Chirality : 0.036 0.262 16263 Planarity : 0.004 0.054 10021 Dihedral : 22.082 179.956 35210 Min Nonbonded Distance : 1.174 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.07 % Favored : 92.91 % Rotamer: Outliers : 5.45 % Allowed : 29.39 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 5824 helix: -0.09 (0.13), residues: 1718 sheet: -1.19 (0.16), residues: 971 loop : -2.04 (0.10), residues: 3135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 7 HIS 0.020 0.001 HIS M 28 PHE 0.021 0.001 PHE k 225 TYR 0.015 0.001 TYR g 228 ARG 0.013 0.000 ARG J 106 *********************** 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 1270 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 992 time to evaluate : 5.392 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 11 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6339 (p90) REVERT: A 123 LYS cc_start: 0.5695 (pttt) cc_final: 0.5347 (mttp) REVERT: A 246 GLU cc_start: 0.7125 (mm-30) cc_final: 0.5648 (pm20) REVERT: C 89 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8096 (mmtm) REVERT: C 208 GLU cc_start: 0.6721 (pt0) cc_final: 0.5800 (mm-30) REVERT: D 59 SER cc_start: 0.9058 (p) cc_final: 0.7915 (t) REVERT: D 63 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8178 (mptt) REVERT: D 78 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: D 87 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8389 (pp) REVERT: E 150 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8420 (mmtp) REVERT: E 245 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: F 57 ASN cc_start: 0.8638 (t0) cc_final: 0.8282 (t0) REVERT: F 104 SER cc_start: 0.9387 (p) cc_final: 0.8993 (m) REVERT: F 149 SER cc_start: 0.8444 (p) cc_final: 0.8192 (m) REVERT: G 95 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8317 (p) REVERT: G 108 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7868 (ptt-90) REVERT: H 210 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7862 (tm-30) REVERT: I 105 ASN cc_start: 0.8365 (t0) cc_final: 0.7805 (t0) REVERT: I 140 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7698 (mtt90) REVERT: I 155 GLN cc_start: 0.7353 (mt0) cc_final: 0.6820 (mm-40) REVERT: I 223 LYS cc_start: 0.7432 (mptt) cc_final: 0.7047 (tmtt) REVERT: J 115 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5475 (ttpt) REVERT: J 162 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7384 (mm110) REVERT: K 62 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8789 (t) REVERT: K 92 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7694 (tmm160) REVERT: K 148 LYS cc_start: 0.7576 (pttm) cc_final: 0.7233 (pttt) REVERT: K 157 LYS cc_start: 0.8572 (tptt) cc_final: 0.8208 (tptt) REVERT: K 191 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: L 169 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7309 (ttm-80) REVERT: M 5 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8129 (mtmm) REVERT: M 61 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7970 (mt0) REVERT: N 31 GLU cc_start: 0.3750 (OUTLIER) cc_final: 0.2322 (pm20) REVERT: N 113 LEU cc_start: 0.8414 (tp) cc_final: 0.8152 (tp) REVERT: O 35 ILE cc_start: 0.8471 (pt) cc_final: 0.8130 (mt) REVERT: P 29 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7808 (p) REVERT: P 56 ASP cc_start: 0.8586 (m-30) cc_final: 0.8210 (m-30) REVERT: Q 80 ASP cc_start: 0.8250 (t0) cc_final: 0.8029 (t0) REVERT: Q 97 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8816 (tt) REVERT: Q 98 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7994 (mmm160) REVERT: R 22 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7891 (tt) REVERT: R 111 MET cc_start: 0.8733 (mtt) cc_final: 0.8314 (mtt) REVERT: S 129 SER cc_start: 0.8998 (p) cc_final: 0.8717 (m) REVERT: T 18 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7044 (mm-30) REVERT: T 80 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7218 (mmp80) REVERT: T 91 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7445 (tp) REVERT: U 19 ASN cc_start: 0.8734 (m110) cc_final: 0.8355 (m110) REVERT: U 28 PHE cc_start: 0.8276 (m-80) cc_final: 0.7908 (m-10) REVERT: U 40 TYR cc_start: 0.8832 (t80) cc_final: 0.8630 (t80) REVERT: V 13 GLU cc_start: 0.7701 (pm20) cc_final: 0.7348 (pm20) REVERT: V 35 ASP cc_start: 0.8414 (p0) cc_final: 0.8155 (p0) REVERT: V 85 ASN cc_start: 0.8939 (m110) cc_final: 0.8496 (m-40) REVERT: W 19 ARG cc_start: 0.6707 (mmt180) cc_final: 0.6303 (mmm160) REVERT: W 21 ARG cc_start: 0.8555 (ttm170) cc_final: 0.7613 (ttp-170) REVERT: W 33 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7628 (mm-30) REVERT: W 41 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7712 (ttp-110) REVERT: X 16 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8605 (mtmt) REVERT: X 41 LYS cc_start: 0.8695 (ptmm) cc_final: 0.8233 (ptpt) REVERT: X 47 ASN cc_start: 0.8909 (p0) cc_final: 0.8661 (p0) REVERT: X 66 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7477 (t70) REVERT: X 82 ASN cc_start: 0.7746 (t0) cc_final: 0.7480 (t0) REVERT: Z 1 MET cc_start: 0.2123 (ttp) cc_final: 0.1849 (ttt) REVERT: Z 61 GLN cc_start: 0.8336 (mt0) cc_final: 0.8091 (mt0) REVERT: Z 63 ASN cc_start: 0.8689 (p0) cc_final: 0.8294 (p0) REVERT: Z 98 ASP cc_start: 0.8610 (p0) cc_final: 0.8374 (p0) REVERT: Z 139 GLU cc_start: 0.7829 (pp20) cc_final: 0.7484 (pp20) REVERT: a 11 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8951 (ptpt) REVERT: c 42 LYS cc_start: 0.7648 (mttp) cc_final: 0.7267 (mmtm) REVERT: c 84 HIS cc_start: 0.5148 (OUTLIER) cc_final: 0.4661 (m-70) REVERT: d 43 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9119 (mt) REVERT: f 95 ARG cc_start: 0.8022 (ptm-80) cc_final: 0.7221 (ptm-80) REVERT: g 12 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8353 (ptpp) REVERT: g 116 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8286 (p0) REVERT: g 189 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7988 (mt) REVERT: g 257 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8480 (mmtp) REVERT: g 271 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8132 (mttp) REVERT: j 68 LYS cc_start: 0.8459 (tttp) cc_final: 0.7360 (mppt) REVERT: j 82 ARG cc_start: 0.6512 (mtt180) cc_final: 0.5979 (mtt180) REVERT: j 99 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: k 17 LYS cc_start: 0.8281 (tptt) cc_final: 0.7851 (tppt) REVERT: k 63 LYS cc_start: 0.6085 (mptt) cc_final: 0.5754 (tppt) REVERT: k 147 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.4739 (p90) REVERT: k 148 ARG cc_start: 0.6970 (ptt180) cc_final: 0.5828 (ttt180) REVERT: k 158 LYS cc_start: 0.6817 (mttt) cc_final: 0.6286 (mtpt) REVERT: k 242 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5888 (mt-10) REVERT: k 251 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.5684 (tp-100) REVERT: k 310 ASN cc_start: 0.4898 (m-40) cc_final: 0.4493 (m110) REVERT: k 335 GLU cc_start: 0.0594 (OUTLIER) cc_final: -0.0271 (tm-30) REVERT: k 345 MET cc_start: 0.3389 (ptp) cc_final: 0.3168 (ptp) REVERT: k 446 MET cc_start: 0.3642 (mtt) cc_final: 0.2921 (mmt) REVERT: k 520 HIS cc_start: 0.3343 (OUTLIER) cc_final: 0.2545 (t-90) REVERT: k 551 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6036 (tt) REVERT: l 20 MET cc_start: 0.7858 (tmm) cc_final: 0.7629 (ttp) REVERT: n 50 PHE cc_start: 0.7942 (m-80) cc_final: 0.7721 (m-80) REVERT: n 76 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7375 (mtp85) outliers start: 278 outliers final: 211 residues processed: 1198 average time/residue: 0.8927 time to fit residues: 1850.7173 Evaluate side-chains 1204 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 960 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 HIS Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 138 ASN Chi-restraints excluded: chain K residue 155 ASN Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain M residue 28 HIS Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 62 VAL 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 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 104 GLN Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 76 GLN Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 93 SER Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 120 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 35 SER Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 160 LEU Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 251 GLN Chi-restraints excluded: chain k residue 266 ASP Chi-restraints excluded: chain k residue 289 LEU Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 420 SER Chi-restraints excluded: chain k residue 426 GLN Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 534 VAL Chi-restraints excluded: chain k residue 538 ILE Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain k residue 598 ASP Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 99 LEU Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 660 optimal weight: 10.0000 chunk 695 optimal weight: 10.0000 chunk 634 optimal weight: 9.9990 chunk 676 optimal weight: 20.0000 chunk 407 optimal weight: 3.9990 chunk 294 optimal weight: 0.0020 chunk 531 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 611 optimal weight: 5.9990 chunk 639 optimal weight: 10.0000 chunk 673 optimal weight: 3.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 ASN M 28 HIS M 50 GLN ** O 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 HIS ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 203 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 520 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 91450 Z= 0.235 Angle : 0.599 14.314 132175 Z= 0.303 Chirality : 0.038 0.267 16263 Planarity : 0.004 0.051 10021 Dihedral : 22.022 179.930 35193 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.57 % Favored : 91.41 % Rotamer: Outliers : 5.55 % Allowed : 29.49 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.11), residues: 5824 helix: -0.10 (0.13), residues: 1719 sheet: -1.15 (0.16), residues: 963 loop : -2.05 (0.10), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 7 HIS 0.010 0.001 HIS E 171 PHE 0.017 0.001 PHE J 135 TYR 0.019 0.001 TYR D 133 ARG 0.011 0.000 ARG J 106 *********************** 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 1232 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 949 time to evaluate : 5.878 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 123 LYS cc_start: 0.5678 (pttt) cc_final: 0.5264 (mttp) REVERT: A 246 GLU cc_start: 0.7137 (mm-30) cc_final: 0.5679 (pm20) REVERT: C 89 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8176 (mmtm) REVERT: C 136 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8036 (mt-10) REVERT: C 208 GLU cc_start: 0.6693 (pt0) cc_final: 0.5774 (mm-30) REVERT: D 59 SER cc_start: 0.9067 (p) cc_final: 0.7916 (t) REVERT: D 63 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8198 (mptt) REVERT: D 78 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6865 (mt-10) REVERT: D 87 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8444 (pp) REVERT: E 150 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8108 (mmtp) REVERT: E 245 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: F 57 ASN cc_start: 0.8687 (t0) cc_final: 0.8345 (t0) REVERT: F 104 SER cc_start: 0.9404 (p) cc_final: 0.9011 (m) REVERT: F 109 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8974 (mp) REVERT: F 149 SER cc_start: 0.8482 (p) cc_final: 0.8172 (m) REVERT: G 108 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8007 (ptt-90) REVERT: H 96 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8161 (ppt170) REVERT: H 210 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7860 (tm-30) REVERT: I 105 ASN cc_start: 0.8478 (t0) cc_final: 0.8021 (t0) REVERT: I 155 GLN cc_start: 0.7455 (mt0) cc_final: 0.6793 (mm-40) REVERT: I 223 LYS cc_start: 0.7437 (mptt) cc_final: 0.7059 (tmtt) REVERT: J 31 GLU cc_start: 0.5276 (mt-10) cc_final: 0.4998 (mt-10) REVERT: J 115 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5441 (ttpt) REVERT: J 162 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7436 (mm110) REVERT: K 62 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8827 (t) REVERT: K 92 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7740 (tmm160) REVERT: K 148 LYS cc_start: 0.7639 (pttm) cc_final: 0.7290 (pttt) REVERT: K 191 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: L 169 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7268 (ttm-80) REVERT: M 5 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8167 (mtmt) REVERT: M 50 GLN cc_start: 0.8898 (tt0) cc_final: 0.8640 (tt0) REVERT: M 61 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7956 (mt0) REVERT: N 31 GLU cc_start: 0.3879 (OUTLIER) cc_final: 0.2430 (pm20) REVERT: N 113 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8113 (tp) REVERT: O 35 ILE cc_start: 0.8530 (pt) cc_final: 0.8199 (mt) REVERT: P 29 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7865 (p) REVERT: P 56 ASP cc_start: 0.8656 (m-30) cc_final: 0.8342 (m-30) REVERT: Q 66 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7574 (ptp-170) REVERT: Q 80 ASP cc_start: 0.8285 (t0) cc_final: 0.8052 (t0) REVERT: Q 97 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8834 (tt) REVERT: Q 98 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8146 (mmm160) REVERT: R 22 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7932 (tt) REVERT: S 16 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8683 (tmtp) REVERT: S 129 SER cc_start: 0.9022 (p) cc_final: 0.8728 (m) REVERT: T 18 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7059 (mm-30) REVERT: T 36 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8180 (tm-30) REVERT: U 19 ASN cc_start: 0.8755 (m110) cc_final: 0.8370 (m110) REVERT: U 28 PHE cc_start: 0.8340 (m-80) cc_final: 0.7908 (m-10) REVERT: U 40 TYR cc_start: 0.8897 (t80) cc_final: 0.8681 (t80) REVERT: V 35 ASP cc_start: 0.8444 (p0) cc_final: 0.8087 (p0) REVERT: V 85 ASN cc_start: 0.8981 (m110) cc_final: 0.8500 (m-40) REVERT: W 19 ARG cc_start: 0.6536 (mmt180) cc_final: 0.6318 (mmm160) REVERT: W 21 ARG cc_start: 0.8577 (ttm170) cc_final: 0.7346 (ttp-170) REVERT: W 33 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7674 (mm-30) REVERT: X 16 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8678 (mtmt) REVERT: X 21 ASN cc_start: 0.8519 (t0) cc_final: 0.7650 (t0) REVERT: X 41 LYS cc_start: 0.8725 (ptmm) cc_final: 0.8227 (ptpt) REVERT: X 66 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7551 (t70) REVERT: X 82 ASN cc_start: 0.7825 (t0) cc_final: 0.7545 (t0) REVERT: Y 80 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: Z 1 MET cc_start: 0.2367 (ttp) cc_final: 0.1964 (ttt) REVERT: Z 61 GLN cc_start: 0.8369 (mt0) cc_final: 0.8133 (mt0) REVERT: Z 139 GLU cc_start: 0.7835 (pp20) cc_final: 0.7487 (pp20) REVERT: a 11 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8903 (ptpt) REVERT: c 42 LYS cc_start: 0.7648 (mttp) cc_final: 0.7307 (mmtm) REVERT: c 84 HIS cc_start: 0.5459 (OUTLIER) cc_final: 0.4936 (m-70) REVERT: d 43 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9156 (mt) REVERT: f 95 ARG cc_start: 0.8042 (ptm-80) cc_final: 0.7223 (ptm-80) REVERT: g 12 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8362 (ptpp) REVERT: g 116 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8338 (p0) REVERT: g 189 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7828 (mt) REVERT: g 257 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8534 (mmtp) REVERT: g 271 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: j 68 LYS cc_start: 0.8497 (tttp) cc_final: 0.7403 (mppt) REVERT: j 99 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: k 17 LYS cc_start: 0.8388 (tptt) cc_final: 0.7968 (tppt) REVERT: k 63 LYS cc_start: 0.6376 (mptt) cc_final: 0.5914 (tppt) REVERT: k 147 PHE cc_start: 0.6096 (p90) cc_final: 0.4980 (p90) REVERT: k 148 ARG cc_start: 0.7031 (ptt180) cc_final: 0.5894 (ttt180) REVERT: k 158 LYS cc_start: 0.6780 (mttt) cc_final: 0.6245 (mtpt) REVERT: k 251 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.5721 (tp-100) REVERT: k 335 GLU cc_start: 0.0649 (OUTLIER) cc_final: -0.0250 (tm-30) REVERT: k 345 MET cc_start: 0.3342 (ptp) cc_final: 0.3129 (ptp) REVERT: k 446 MET cc_start: 0.3644 (mtt) cc_final: 0.2917 (mmt) REVERT: k 520 HIS cc_start: 0.2904 (OUTLIER) cc_final: 0.2173 (t70) REVERT: k 551 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.5955 (tt) REVERT: l 20 MET cc_start: 0.7876 (tmm) cc_final: 0.7596 (ttp) outliers start: 283 outliers final: 221 residues processed: 1159 average time/residue: 0.8015 time to fit residues: 1586.7210 Evaluate side-chains 1190 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 935 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 128 LYS Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 155 ASN Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 62 VAL 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 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 15 PHE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 120 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 35 SER Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 251 GLN Chi-restraints excluded: chain k residue 266 ASP Chi-restraints excluded: chain k residue 289 LEU Chi-restraints excluded: chain k residue 294 SER Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 420 SER Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 489 SER Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 534 VAL Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 552 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain n residue 44 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: 9.9990 chunk 715 optimal weight: 10.0000 chunk 436 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 497 optimal weight: 3.9990 chunk 750 optimal weight: 0.4980 chunk 690 optimal weight: 20.0000 chunk 597 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 461 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS M 77 GLN S 97 GLN W 18 HIS W 92 HIS X 47 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 203 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 91450 Z= 0.235 Angle : 0.605 14.320 132175 Z= 0.306 Chirality : 0.038 0.265 16263 Planarity : 0.004 0.068 10021 Dihedral : 22.023 179.848 35186 Min Nonbonded Distance : 1.088 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.48 % Favored : 91.50 % Rotamer: Outliers : 5.58 % Allowed : 29.57 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.11), residues: 5824 helix: -0.10 (0.13), residues: 1715 sheet: -1.07 (0.17), residues: 951 loop : -2.03 (0.10), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 7 HIS 0.010 0.001 HIS E 171 PHE 0.024 0.001 PHE k 225 TYR 0.016 0.001 TYR D 133 ARG 0.010 0.000 ARG k 469 ********************** 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 1235 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 950 time to evaluate : 5.503 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 123 LYS cc_start: 0.5719 (pttt) cc_final: 0.5293 (mttp) REVERT: A 246 GLU cc_start: 0.7138 (mm-30) cc_final: 0.5680 (pm20) REVERT: C 89 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8177 (mmtm) REVERT: C 136 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 208 GLU cc_start: 0.6739 (pt0) cc_final: 0.5793 (mm-30) REVERT: D 59 SER cc_start: 0.9077 (p) cc_final: 0.7926 (t) REVERT: D 63 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8174 (mptt) REVERT: D 78 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: D 87 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8418 (pp) REVERT: E 150 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8096 (mmtp) REVERT: E 245 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: F 57 ASN cc_start: 0.8699 (t0) cc_final: 0.8389 (t0) REVERT: F 104 SER cc_start: 0.9396 (p) cc_final: 0.9013 (m) REVERT: F 109 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8970 (mp) REVERT: F 149 SER cc_start: 0.8465 (p) cc_final: 0.8153 (m) REVERT: G 108 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7911 (ptt-90) REVERT: H 96 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.6685 (ptt180) REVERT: H 197 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7477 (ptmm) REVERT: H 210 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7883 (tm-30) REVERT: I 105 ASN cc_start: 0.8421 (t0) cc_final: 0.7954 (t0) REVERT: I 155 GLN cc_start: 0.7392 (mt0) cc_final: 0.6765 (mm-40) REVERT: I 223 LYS cc_start: 0.7412 (mptt) cc_final: 0.7033 (tmtt) REVERT: J 31 GLU cc_start: 0.5305 (mt-10) cc_final: 0.4979 (mt-10) REVERT: J 115 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5391 (ttpt) REVERT: J 120 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7887 (mmt90) REVERT: J 162 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7429 (mm110) REVERT: K 62 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8840 (t) REVERT: K 92 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7757 (tmm160) REVERT: K 148 LYS cc_start: 0.7605 (pttm) cc_final: 0.7262 (pttt) REVERT: K 191 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6975 (mm-30) REVERT: L 169 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7257 (ttm-80) REVERT: M 5 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8162 (mtmt) REVERT: M 61 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7949 (mt0) REVERT: M 70 TYR cc_start: 0.8151 (m-80) cc_final: 0.7863 (m-80) REVERT: N 31 GLU cc_start: 0.3899 (OUTLIER) cc_final: 0.2459 (pm20) REVERT: N 113 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8137 (tp) REVERT: O 35 ILE cc_start: 0.8526 (pt) cc_final: 0.8194 (mt) REVERT: P 29 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7874 (p) REVERT: P 56 ASP cc_start: 0.8651 (m-30) cc_final: 0.8399 (m-30) REVERT: Q 66 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7569 (ptp-170) REVERT: Q 80 ASP cc_start: 0.8297 (t0) cc_final: 0.8068 (t0) REVERT: Q 97 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8843 (tt) REVERT: Q 98 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8128 (mmm160) REVERT: R 22 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8009 (tt) REVERT: S 129 SER cc_start: 0.9022 (p) cc_final: 0.8703 (m) REVERT: T 18 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7044 (mm-30) REVERT: T 36 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8181 (tm-30) REVERT: U 19 ASN cc_start: 0.8761 (m110) cc_final: 0.8377 (m110) REVERT: U 28 PHE cc_start: 0.8345 (m-80) cc_final: 0.7906 (m-10) REVERT: U 40 TYR cc_start: 0.8917 (t80) cc_final: 0.8690 (t80) REVERT: V 35 ASP cc_start: 0.8502 (p0) cc_final: 0.8186 (p0) REVERT: V 85 ASN cc_start: 0.9033 (m110) cc_final: 0.8519 (m-40) REVERT: W 21 ARG cc_start: 0.8508 (ttm170) cc_final: 0.7322 (ttp-170) REVERT: W 33 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7673 (mm-30) REVERT: X 16 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8677 (mtmt) REVERT: X 21 ASN cc_start: 0.8524 (t0) cc_final: 0.7668 (t0) REVERT: X 41 LYS cc_start: 0.8720 (ptmm) cc_final: 0.8304 (ptpt) REVERT: X 66 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7569 (t70) REVERT: X 82 ASN cc_start: 0.7787 (t0) cc_final: 0.7517 (t0) REVERT: Y 80 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: Z 1 MET cc_start: 0.2556 (ttp) cc_final: 0.2118 (ttt) REVERT: Z 61 GLN cc_start: 0.8422 (mt0) cc_final: 0.8197 (mt0) REVERT: Z 98 ASP cc_start: 0.8658 (p0) cc_final: 0.8405 (p0) REVERT: Z 139 GLU cc_start: 0.7879 (pp20) cc_final: 0.7536 (pp20) REVERT: a 11 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8945 (ptpt) REVERT: c 42 LYS cc_start: 0.7633 (mttp) cc_final: 0.7295 (mmtm) REVERT: d 36 ASP cc_start: 0.8272 (p0) cc_final: 0.8009 (p0) REVERT: d 43 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9158 (mt) REVERT: f 95 ARG cc_start: 0.8059 (ptm-80) cc_final: 0.7251 (ptm-80) REVERT: g 12 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8366 (ptpp) REVERT: g 116 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8339 (p0) REVERT: g 145 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: g 189 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7811 (mt) REVERT: g 257 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8491 (mmtp) REVERT: g 271 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8140 (mttp) REVERT: j 68 LYS cc_start: 0.8489 (tttp) cc_final: 0.7381 (mppt) REVERT: j 99 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: k 17 LYS cc_start: 0.8398 (tptt) cc_final: 0.7981 (tppt) REVERT: k 63 LYS cc_start: 0.6418 (mptt) cc_final: 0.5921 (tppt) REVERT: k 147 PHE cc_start: 0.6130 (p90) cc_final: 0.5155 (p90) REVERT: k 148 ARG cc_start: 0.7040 (ptt180) cc_final: 0.5891 (ttt180) REVERT: k 158 LYS cc_start: 0.6824 (mttt) cc_final: 0.6297 (mtpt) REVERT: k 171 GLN cc_start: 0.4091 (OUTLIER) cc_final: 0.2954 (tp-100) REVERT: k 335 GLU cc_start: 0.0652 (OUTLIER) cc_final: -0.0325 (tp30) REVERT: k 446 MET cc_start: 0.3594 (mtt) cc_final: 0.2895 (mmt) REVERT: k 520 HIS cc_start: 0.3675 (OUTLIER) cc_final: 0.3047 (t-90) REVERT: k 524 MET cc_start: 0.4122 (pmm) cc_final: 0.3831 (pmm) REVERT: k 551 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.5955 (tt) REVERT: l 20 MET cc_start: 0.7880 (tmm) cc_final: 0.7593 (ttp) REVERT: n 66 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7638 (ptpt) outliers start: 285 outliers final: 229 residues processed: 1161 average time/residue: 0.8177 time to fit residues: 1626.4135 Evaluate side-chains 1202 residues out of total 5103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 937 time to evaluate : 5.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 140 ARG Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 128 LYS Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 155 ASN Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain M residue 28 HIS Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain O residue 13 ASP Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 75 ASN 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 29 THR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 105 LYS Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 116 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 66 ASP Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 50 ILE Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 11 LYS Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 35 VAL Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain e residue 18 SER Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 120 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 35 SER Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 257 LYS Chi-restraints excluded: chain g residue 271 LYS Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 31 ASP Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 THR Chi-restraints excluded: chain j residue 83 ASP Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 171 GLN Chi-restraints excluded: chain k residue 237 ILE Chi-restraints excluded: chain k residue 266 ASP Chi-restraints excluded: chain k residue 289 LEU Chi-restraints excluded: chain k residue 294 SER Chi-restraints excluded: chain k residue 335 GLU Chi-restraints excluded: chain k residue 338 ASN Chi-restraints excluded: chain k residue 385 LYS Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 420 SER Chi-restraints excluded: chain k residue 429 HIS Chi-restraints excluded: chain k residue 436 TYR Chi-restraints excluded: chain k residue 459 VAL Chi-restraints excluded: chain k residue 470 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 476 LEU Chi-restraints excluded: chain k residue 484 LEU Chi-restraints excluded: chain k residue 520 HIS Chi-restraints excluded: chain k residue 534 VAL Chi-restraints excluded: chain k residue 551 LEU Chi-restraints excluded: chain k residue 571 ASN Chi-restraints excluded: chain k residue 573 TYR Chi-restraints excluded: chain k residue 598 ASP Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 66 LYS 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: 6.9990 chunk 636 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 550 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 598 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 614 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN M 28 HIS M 50 GLN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 HIS ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 203 GLN ** k 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 520 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.085743 restraints weight = 170599.557| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.76 r_work: 0.2903 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 91450 Z= 0.345 Angle : 0.681 14.240 132175 Z= 0.344 Chirality : 0.042 0.265 16263 Planarity : 0.005 0.069 10021 Dihedral : 22.080 179.598 35182 Min Nonbonded Distance : 1.034 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.48 % Favored : 90.50 % Rotamer: Outliers : 5.84 % Allowed : 29.41 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.11), residues: 5824 helix: -0.31 (0.12), residues: 1723 sheet: -1.09 (0.16), residues: 946 loop : -2.13 (0.10), residues: 3155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 204 HIS 0.015 0.001 HIS E 171 PHE 0.019 0.002 PHE c 79 TYR 0.032 0.002 TYR T 21 ARG 0.015 0.001 ARG W 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26711.74 seconds wall clock time: 464 minutes 20.03 seconds (27860.03 seconds total)