Starting phenix.real_space_refine on Sun Mar 24 00:07:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssw_25415/03_2024/7ssw_25415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssw_25415/03_2024/7ssw_25415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssw_25415/03_2024/7ssw_25415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssw_25415/03_2024/7ssw_25415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssw_25415/03_2024/7ssw_25415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssw_25415/03_2024/7ssw_25415.pdb" } resolution = 3.8 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= 0.115 sd= 0.851 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: 5 Type Number sf(0) Gaussians P 4732 5.49 5 S 147 5.16 5 C 74114 2.51 5 N 27492 2.21 5 O 41111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 167": "OD1" <-> "OD2" Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ASP 43": "OD1" <-> "OD2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 16": "OE1" <-> "OE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 152": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 176": "OD1" <-> "OD2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "d GLU 197": "OE1" <-> "OE2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "e ASP 9": "OD1" <-> "OD2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 50": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ASP 112": "OD1" <-> "OD2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "e TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e ASP 173": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 38": "OD1" <-> "OD2" Residue "f ASP 46": "OD1" <-> "OD2" Residue "f ASP 55": "OD1" <-> "OD2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ASP 165": "OD1" <-> "OD2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "f GLU 172": "OE1" <-> "OE2" Residue "g PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g ASP 98": "OD1" <-> "OD2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 25": "OE1" <-> "OE2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 166": "OD1" <-> "OD2" Residue "a ASP 179": "OD1" <-> "OD2" Residue "a GLU 190": "OE1" <-> "OE2" Residue "i PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i ASP 95": "OD1" <-> "OD2" Residue "i GLU 107": "OE1" <-> "OE2" Residue "i GLU 140": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 90": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k ASP 12": "OD1" <-> "OD2" Residue "k ASP 56": "OD1" <-> "OD2" Residue "k PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 80": "OD1" <-> "OD2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "k GLU 121": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 144": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ASP 70": "OD1" <-> "OD2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 114": "OE1" <-> "OE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 80": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ASP 15": "OD1" <-> "OD2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p GLU 43": "OE1" <-> "OE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 67": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ASP 95": "OD1" <-> "OD2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s ASP 22": "OD1" <-> "OD2" Residue "s ASP 68": "OD1" <-> "OD2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ASP 37": "OD1" <-> "OD2" Residue "t GLU 42": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t ASP 79": "OD1" <-> "OD2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 7": "OE1" <-> "OE2" Residue "v GLU 11": "OE1" <-> "OE2" Residue "v GLU 55": "OE1" <-> "OE2" Residue "v GLU 69": "OE1" <-> "OE2" Residue "v TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 11": "OD1" <-> "OD2" Residue "w PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 66": "OE1" <-> "OE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 24": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 38": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "G TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 160": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 28": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 41": "OD1" <-> "OD2" Residue "R ASP 81": "OD1" <-> "OD2" Residue "S ASP 37": "OD1" <-> "OD2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "W TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Z ASP 12": "OD1" <-> "OD2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147596 Number of models: 1 Model: "" Number of chains: 56 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 102, 'rna2p_pyr': 63, 'rna3p_pur': 772, 'rna3p_pyr': 602} Link IDs: {'rna2p': 165, 'rna3p': 1373} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 233, 'rna2p_pyr': 110, 'rna3p_pur': 1441, 'rna3p_pyr': 1119} Link IDs: {'rna2p': 343, 'rna3p': 2559} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "i" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 436 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Time building chain proxies: 57.56, per 1000 atoms: 0.39 Number of scatterers: 147596 At special positions: 0 Unit cell: (269.635, 250.611, 243.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 147 16.00 P 4732 15.00 O 41111 8.00 N 27492 7.00 C 74114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.42 Conformation dependent library (CDL) restraints added in 8.7 seconds 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10812 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 81 sheets defined 30.0% alpha, 13.3% beta 927 base pairs and 2451 stacking pairs defined. Time for finding SS restraints: 45.23 Creating SS restraints... Processing helix chain 'b' and resid 29 through 33 Processing helix chain 'b' and resid 198 through 202 removed outlier: 3.943A pdb=" N LEU b 201 " --> pdb=" O GLU b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 212 removed outlier: 3.948A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP b 212 " --> pdb=" O GLY b 208 " (cutoff:3.500A) Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'c' and resid 61 through 70 removed outlier: 3.734A pdb=" N PHE c 68 " --> pdb=" O GLU c 64 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.950A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA c 102 " --> pdb=" O GLU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.861A pdb=" N VAL d 28 " --> pdb=" O ASN d 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS d 29 " --> pdb=" O GLU d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 109 removed outlier: 3.774A pdb=" N ARG d 102 " --> pdb=" O LYS d 98 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA d 104 " --> pdb=" O MET d 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU d 105 " --> pdb=" O TYR d 101 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER d 107 " --> pdb=" O GLY d 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE d 108 " --> pdb=" O ALA d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 115 Processing helix chain 'd' and resid 130 through 140 removed outlier: 4.098A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN d 136 " --> pdb=" O LYS d 132 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS d 139 " --> pdb=" O ALA d 135 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP d 140 " --> pdb=" O GLN d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 159 removed outlier: 3.641A pdb=" N LEU d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 181 Processing helix chain 'd' and resid 190 through 201 removed outlier: 3.987A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN d 195 " --> pdb=" O ASP d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 6 Processing helix chain 'e' and resid 9 through 17 removed outlier: 3.529A pdb=" N LYS e 14 " --> pdb=" O GLU e 10 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU e 15 " --> pdb=" O VAL e 11 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 27 Processing helix chain 'e' and resid 47 through 60 removed outlier: 3.625A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA e 58 " --> pdb=" O ALA e 54 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER e 60 " --> pdb=" O LEU e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 77 Processing helix chain 'e' and resid 94 through 104 removed outlier: 3.853A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 169 removed outlier: 3.569A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.505A pdb=" N GLN f 63 " --> pdb=" O ASP f 59 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA f 67 " --> pdb=" O GLN f 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG f 68 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 150 Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.611A pdb=" N ALA g 26 " --> pdb=" O LYS g 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 51 removed outlier: 3.595A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 60 Processing helix chain 'g' and resid 61 through 69 removed outlier: 3.584A pdb=" N ALA g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 101 removed outlier: 3.848A pdb=" N ASP g 101 " --> pdb=" O ARG g 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 13 removed outlier: 4.362A pdb=" N ARG a 9 " --> pdb=" O THR a 5 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG a 12 " --> pdb=" O MET a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 27 removed outlier: 3.780A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 58 removed outlier: 4.190A pdb=" N ASN a 58 " --> pdb=" O SER a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 199 removed outlier: 3.687A pdb=" N LYS a 186 " --> pdb=" O ALA a 182 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA a 191 " --> pdb=" O GLU a 187 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU a 192 " --> pdb=" O ASN a 188 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU a 196 " --> pdb=" O LEU a 192 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA a 199 " --> pdb=" O ALA a 195 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 30 removed outlier: 3.779A pdb=" N GLN i 29 " --> pdb=" O PRO i 25 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 33 through 35 No H-bonds generated for 'chain 'i' and resid 33 through 35' Processing helix chain 'i' and resid 36 through 43 removed outlier: 3.773A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 114 removed outlier: 4.356A pdb=" N LEU i 105 " --> pdb=" O SER i 101 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 133 removed outlier: 3.647A pdb=" N MET i 124 " --> pdb=" O ASP i 120 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR i 125 " --> pdb=" O ILE i 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG i 133 " --> pdb=" O GLU i 129 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 37 removed outlier: 4.227A pdb=" N THR j 30 " --> pdb=" O GLY j 26 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU j 32 " --> pdb=" O LEU j 28 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 94 removed outlier: 3.671A pdb=" N ALA j 94 " --> pdb=" O GLU j 90 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 109 removed outlier: 3.803A pdb=" N VAL j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE j 103 " --> pdb=" O ARG j 99 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA j 104 " --> pdb=" O VAL j 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 removed outlier: 3.703A pdb=" N ARG j 116 " --> pdb=" O GLY j 112 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA j 117 " --> pdb=" O PRO j 113 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 118 removed outlier: 3.524A pdb=" N LEU k 118 " --> pdb=" O LYS k 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 removed outlier: 4.086A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 73 Processing helix chain 'l' and resid 95 through 99 removed outlier: 3.528A pdb=" N ASN l 99 " --> pdb=" O LYS l 96 " (cutoff:3.500A) Processing helix chain 'l' and resid 130 through 138 Processing helix chain 'm' and resid 43 through 56 removed outlier: 3.569A pdb=" N ALA m 52 " --> pdb=" O ALA m 48 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 4.418A pdb=" N GLU m 115 " --> pdb=" O GLU m 111 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE m 117 " --> pdb=" O ALA m 113 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.536A pdb=" N ASN n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL n 29 " --> pdb=" O ALA n 25 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS n 31 " --> pdb=" O SER n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 42 Processing helix chain 'n' and resid 44 through 49 Processing helix chain 'n' and resid 60 through 67 removed outlier: 3.798A pdb=" N ARG n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 79 Processing helix chain 'o' and resid 3 through 22 removed outlier: 3.622A pdb=" N ALA o 11 " --> pdb=" O ARG o 7 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG o 16 " --> pdb=" O THR o 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 82 removed outlier: 3.637A pdb=" N VAL o 74 " --> pdb=" O ALA o 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY o 75 " --> pdb=" O ALA o 71 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS o 76 " --> pdb=" O ALA o 72 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 113 removed outlier: 3.953A pdb=" N ALA o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 10 removed outlier: 3.706A pdb=" N GLN p 9 " --> pdb=" O LYS p 5 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 100 removed outlier: 3.574A pdb=" N ARG p 100 " --> pdb=" O TYR p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 107 removed outlier: 3.774A pdb=" N ALA p 106 " --> pdb=" O THR p 103 " (cutoff:3.500A) Processing helix chain 'q' and resid 8 through 21 removed outlier: 3.942A pdb=" N HIS q 13 " --> pdb=" O ALA q 9 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU q 17 " --> pdb=" O HIS q 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS q 18 " --> pdb=" O LYS q 14 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 28 Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.932A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA q 41 " --> pdb=" O ALA q 37 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR q 44 " --> pdb=" O LYS q 40 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA q 45 " --> pdb=" O ALA q 41 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR q 46 " --> pdb=" O GLY q 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG q 47 " --> pdb=" O GLN q 43 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG q 49 " --> pdb=" O ALA q 45 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA q 66 " --> pdb=" O ALA q 62 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.621A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA q 98 " --> pdb=" O LEU q 94 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL q 99 " --> pdb=" O ALA q 95 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE q 100 " --> pdb=" O ASP q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 115 removed outlier: 3.748A pdb=" N GLU q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA q 114 " --> pdb=" O GLU q 110 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 22 removed outlier: 3.527A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP s 22 " --> pdb=" O ARG s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 removed outlier: 3.766A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR s 37 " --> pdb=" O LEU s 33 " (cutoff:3.500A) Processing helix chain 's' and resid 38 through 40 No H-bonds generated for 'chain 's' and resid 38 through 40' Processing helix chain 's' and resid 41 through 62 removed outlier: 3.762A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU s 52 " --> pdb=" O LYS s 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER s 53 " --> pdb=" O LYS s 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE s 55 " --> pdb=" O LEU s 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN s 61 " --> pdb=" O ASN s 57 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 7 removed outlier: 3.726A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) Processing helix chain 't' and resid 19 through 26 removed outlier: 4.200A pdb=" N GLU t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS t 26 " --> pdb=" O THR t 22 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 removed outlier: 3.546A pdb=" N GLN t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE t 51 " --> pdb=" O VAL t 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 65 through 67 No H-bonds generated for 'chain 'u' and resid 65 through 67' Processing helix chain 'v' and resid 13 through 23 removed outlier: 3.529A pdb=" N LEU v 20 " --> pdb=" O ALA v 16 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 45 through 51 Processing helix chain 'x' and resid 56 through 61 Processing helix chain 'x' and resid 62 through 73 removed outlier: 3.539A pdb=" N ARG x 71 " --> pdb=" O LEU x 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 23 removed outlier: 3.776A pdb=" N LEU y 14 " --> pdb=" O SER y 10 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN y 20 " --> pdb=" O THR y 16 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU y 22 " --> pdb=" O LEU y 18 " (cutoff:3.500A) Processing helix chain 'y' and resid 26 through 35 removed outlier: 3.988A pdb=" N ALA y 32 " --> pdb=" O LEU y 28 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 42 removed outlier: 3.915A pdb=" N LEU y 42 " --> pdb=" O GLN y 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 39 through 42' Processing helix chain 'y' and resid 43 through 59 removed outlier: 4.113A pdb=" N ASP y 49 " --> pdb=" O GLN y 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU y 56 " --> pdb=" O ARG y 52 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN y 58 " --> pdb=" O LYS y 54 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.501A pdb=" N LEU z 24 " --> pdb=" O LYS z 20 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY z 27 " --> pdb=" O LEU z 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 45 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.957A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 35 removed outlier: 3.982A pdb=" N ARG D 28 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D 30 " --> pdb=" O ASN D 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 42 removed outlier: 3.751A pdb=" N HIS E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 removed outlier: 3.949A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 62 removed outlier: 3.706A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.911A pdb=" N LEU G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA G 54 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.520A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 119 removed outlier: 4.243A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 127 removed outlier: 3.569A pdb=" N LYS G 127 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 139 Processing helix chain 'G' and resid 140 through 148 removed outlier: 4.042A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 170 through 177 removed outlier: 4.157A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 223 removed outlier: 3.737A pdb=" N ARG G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU G 222 " --> pdb=" O ALA G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 43 removed outlier: 3.649A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 removed outlier: 3.570A pdb=" N ILE H 76 " --> pdb=" O PRO H 72 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 77' Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.704A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 removed outlier: 3.670A pdb=" N LEU H 110 " --> pdb=" O LYS H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 110' Processing helix chain 'H' and resid 111 through 121 removed outlier: 3.739A pdb=" N SER H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 4.067A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN H 138 " --> pdb=" O LYS H 134 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU H 143 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 15 Processing helix chain 'I' and resid 48 through 65 removed outlier: 4.145A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS I 57 " --> pdb=" O GLN I 53 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS I 59 " --> pdb=" O ARG I 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 80 removed outlier: 3.709A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 94 removed outlier: 3.504A pdb=" N LEU I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.949A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 119 removed outlier: 3.741A pdb=" N ARG I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 160 removed outlier: 3.616A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.795A pdb=" N LEU I 190 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 204 removed outlier: 3.522A pdb=" N VAL I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 69 removed outlier: 3.617A pdb=" N GLN J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 67 " --> pdb=" O MET J 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 144 removed outlier: 3.668A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 153 Processing helix chain 'J' and resid 159 through 164 removed outlier: 3.608A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 159 through 164' Processing helix chain 'K' and resid 18 through 32 removed outlier: 4.297A pdb=" N GLU K 23 " --> pdb=" O PRO K 19 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.608A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.945A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.541A pdb=" N VAL L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 3.736A pdb=" N TYR L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 48 removed outlier: 3.543A pdb=" N THR L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 53 removed outlier: 3.657A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 66 removed outlier: 4.168A pdb=" N GLU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 108 removed outlier: 3.984A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 128 removed outlier: 4.007A pdb=" N ARG L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU L 119 " --> pdb=" O MET L 115 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 removed outlier: 3.530A pdb=" N LYS L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU L 138 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 18 removed outlier: 3.557A pdb=" N ARG M 12 " --> pdb=" O ASP M 8 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE M 13 " --> pdb=" O MET M 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY M 16 " --> pdb=" O ARG M 12 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 36 removed outlier: 3.827A pdb=" N VAL M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 98 removed outlier: 4.005A pdb=" N ALA M 96 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY M 97 " --> pdb=" O VAL M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.570A pdb=" N TYR N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 55 removed outlier: 3.863A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.956A pdb=" N ILE N 78 " --> pdb=" O GLN N 74 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG N 84 " --> pdb=" O HIS N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 99 removed outlier: 4.046A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU N 97 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG N 98 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 32 removed outlier: 3.580A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 85 removed outlier: 4.181A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 50 Processing helix chain 'P' and resid 58 through 67 Processing helix chain 'P' and resid 68 through 71 Processing helix chain 'P' and resid 93 through 103 removed outlier: 3.779A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 removed outlier: 3.593A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 118 removed outlier: 3.714A pdb=" N GLY Q 117 " --> pdb=" O SER Q 114 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL Q 118 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 114 through 118' Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 27 through 37 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.515A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 62 No H-bonds generated for 'chain 'R' and resid 60 through 62' Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.562A pdb=" N ARG R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 91 removed outlier: 3.621A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 14 removed outlier: 3.583A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG S 12 " --> pdb=" O ARG S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 50 removed outlier: 3.793A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS S 46 " --> pdb=" O ASN S 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 88 removed outlier: 3.799A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 14 removed outlier: 3.992A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL T 11 " --> pdb=" O THR T 7 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 42 removed outlier: 3.787A pdb=" N ALA T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR T 32 " --> pdb=" O VAL T 28 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN T 36 " --> pdb=" O THR T 32 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N HIS T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 73 removed outlier: 3.817A pdb=" N SER T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU T 69 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 84 removed outlier: 4.194A pdb=" N ILE T 81 " --> pdb=" O TYR T 77 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG T 83 " --> pdb=" O GLN T 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 removed outlier: 3.640A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS U 59 " --> pdb=" O ASP U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 75 Processing helix chain 'W' and resid 11 through 16 Processing helix chain 'W' and resid 24 through 29 removed outlier: 3.597A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 removed outlier: 4.001A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG W 60 " --> pdb=" O ARG W 56 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.701A pdb=" N LYS X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 3.777A pdb=" N ILE X 44 " --> pdb=" O PRO X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 74 removed outlier: 3.507A pdb=" N GLU X 72 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE X 73 " --> pdb=" O LEU X 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA X 74 " --> pdb=" O GLY X 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 69 through 74' Processing helix chain 'Y' and resid 4 through 6 No H-bonds generated for 'chain 'Y' and resid 4 through 6' Processing helix chain 'Y' and resid 7 through 19 removed outlier: 3.722A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER Y 13 " --> pdb=" O ARG Y 9 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA Y 16 " --> pdb=" O GLN Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 39 removed outlier: 4.434A pdb=" N MET Y 26 " --> pdb=" O SER Y 22 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG Y 28 " --> pdb=" O ARG Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 52 removed outlier: 4.119A pdb=" N GLU Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 60 removed outlier: 4.540A pdb=" N ILE Y 56 " --> pdb=" O GLU Y 52 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 86 removed outlier: 3.691A pdb=" N ALA Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA Y 80 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN Y 81 " --> pdb=" O ASN Y 77 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA Y 86 " --> pdb=" O ILE Y 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 22 removed outlier: 3.668A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 29 Processing helix chain 'Z' and resid 38 through 54 removed outlier: 3.946A pdb=" N LYS Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'b' and resid 100 through 104 removed outlier: 6.840A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 128 through 130 Processing sheet with id=AA4, first strand: chain 'b' and resid 162 through 166 removed outlier: 7.320A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG b 166 " --> pdb=" O TYR b 170 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR b 170 " --> pdb=" O ARG b 166 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG b 268 " --> pdb=" O MET b 180 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS b 182 " --> pdb=" O ILE b 266 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE b 266 " --> pdb=" O LYS b 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 5 through 15 removed outlier: 6.760A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET c 11 " --> pdb=" O VAL c 24 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL c 24 " --> pdb=" O MET c 11 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG c 13 " --> pdb=" O ILE c 22 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE c 22 " --> pdb=" O ARG c 13 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE c 27 " --> pdb=" O LEU c 187 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS c 190 " --> pdb=" O VAL c 177 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL c 177 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN c 173 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL c 109 " --> pdb=" O GLN c 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 77 through 82 removed outlier: 5.462A pdb=" N GLY c 78 " --> pdb=" O THR c 52 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR c 52 " --> pdb=" O GLY c 78 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR c 51 " --> pdb=" O ARG c 33 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 121 removed outlier: 6.877A pdb=" N ILE d 119 " --> pdb=" O MET d 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'd' and resid 148 through 149 removed outlier: 6.466A pdb=" N ILE d 148 " --> pdb=" O ARG d 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'e' and resid 88 through 91 removed outlier: 3.805A pdb=" N THR e 34 " --> pdb=" O THR e 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB4, first strand: chain 'f' and resid 16 through 19 removed outlier: 3.583A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 129 through 134 Processing sheet with id=AB6, first strand: chain 'f' and resid 96 through 98 removed outlier: 3.808A pdb=" N LYS f 98 " --> pdb=" O VAL f 101 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL f 101 " --> pdb=" O LYS f 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'g' and resid 4 through 5 removed outlier: 3.765A pdb=" N ILE g 4 " --> pdb=" O VAL g 37 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL g 37 " --> pdb=" O ILE g 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'g' and resid 77 through 81 removed outlier: 6.000A pdb=" N VAL g 78 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL g 147 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE g 80 " --> pdb=" O VAL g 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL g 130 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER g 131 " --> pdb=" O ARG g 116 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG g 116 " --> pdb=" O SER g 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 170 through 177 removed outlier: 3.714A pdb=" N ILE a 175 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 61 through 64 Processing sheet with id=AC2, first strand: chain 'i' and resid 9 through 10 removed outlier: 3.840A pdb=" N LEU i 10 " --> pdb=" O VAL i 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'i' and resid 99 through 100 Processing sheet with id=AC4, first strand: chain 'j' and resid 53 through 55 removed outlier: 6.296A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU j 140 " --> pdb=" O TRP j 15 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL j 17 " --> pdb=" O LEU j 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'j' and resid 23 through 24 removed outlier: 6.162A pdb=" N LYS j 23 " --> pdb=" O ALA j 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'j' and resid 74 through 77 Processing sheet with id=AC7, first strand: chain 'k' and resid 8 through 10 removed outlier: 4.887A pdb=" N CYS k 21 " --> pdb=" O THR k 42 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR k 42 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP k 56 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL k 63 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k' and resid 69 through 71 removed outlier: 3.525A pdb=" N SER k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG k 78 " --> pdb=" O GLU p 70 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA p 57 " --> pdb=" O ILE p 49 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE p 49 " --> pdb=" O ALA p 57 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR p 59 " --> pdb=" O ILE p 47 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL p 45 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE p 63 " --> pdb=" O GLU p 43 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU p 43 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AD1, first strand: chain 'l' and resid 109 through 110 Processing sheet with id=AD2, first strand: chain 'm' and resid 100 through 101 removed outlier: 3.675A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'm' and resid 39 through 42 removed outlier: 3.615A pdb=" N ILE m 96 " --> pdb=" O GLY m 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'm' and resid 63 through 65 Processing sheet with id=AD5, first strand: chain 'm' and resid 74 through 75 removed outlier: 3.846A pdb=" N GLU m 75 " --> pdb=" O ASN m 88 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN m 88 " --> pdb=" O GLU m 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'n' and resid 33 through 37 removed outlier: 3.631A pdb=" N ILE n 34 " --> pdb=" O ILE n 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE n 113 " --> pdb=" O ILE n 34 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR n 36 " --> pdb=" O ALA n 111 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'o' and resid 47 through 52 removed outlier: 4.009A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA o 37 " --> pdb=" O ALA o 51 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU o 26 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'p' and resid 29 through 32 Processing sheet with id=AD9, first strand: chain 'r' and resid 12 through 14 removed outlier: 3.516A pdb=" N HIS r 12 " --> pdb=" O PHE r 5 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL r 4 " --> pdb=" O MET r 40 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 19 through 22 removed outlier: 3.835A pdb=" N VAL r 20 " --> pdb=" O VAL r 96 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'r' and resid 72 through 77 Processing sheet with id=AE3, first strand: chain 's' and resid 4 through 10 removed outlier: 5.735A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG s 92 " --> pdb=" O PRO s 87 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP s 94 " --> pdb=" O ILE s 85 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE s 85 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE s 96 " --> pdb=" O LYS s 83 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS s 83 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS s 98 " --> pdb=" O SER s 81 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER s 81 " --> pdb=" O LYS s 98 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS s 73 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 't' and resid 11 through 14 removed outlier: 4.121A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS t 33 " --> pdb=" O ALA t 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU t 32 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AE6, first strand: chain 'u' and resid 11 through 12 removed outlier: 4.612A pdb=" N ILE u 71 " --> pdb=" O ASP u 80 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP u 80 " --> pdb=" O ILE u 71 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'u' and resid 24 through 27 removed outlier: 6.888A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AE9, first strand: chain 'v' and resid 28 through 31 removed outlier: 3.516A pdb=" N PHE v 91 " --> pdb=" O ILE v 29 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG v 93 " --> pdb=" O TYR v 31 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N HIS v 88 " --> pdb=" O VAL v 77 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL v 77 " --> pdb=" O HIS v 88 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP v 90 " --> pdb=" O GLN v 75 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE v 4 " --> pdb=" O VAL v 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.616A pdb=" N ILE w 32 " --> pdb=" O ALA w 57 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA w 57 " --> pdb=" O ILE w 32 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL w 34 " --> pdb=" O LEU w 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE w 56 " --> pdb=" O GLY w 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'w' and resid 42 through 45 removed outlier: 5.591A pdb=" N ALA w 43 " --> pdb=" O ILE w 76 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ILE w 78 " --> pdb=" O ALA w 43 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA w 45 " --> pdb=" O ILE w 78 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'x' and resid 32 through 33 Processing sheet with id=AF4, first strand: chain 'x' and resid 36 through 38 Processing sheet with id=AF5, first strand: chain 'z' and resid 34 through 38 removed outlier: 3.546A pdb=" N ILE z 6 " --> pdb=" O VAL z 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AF7, first strand: chain 'C' and resid 7 through 9 Processing sheet with id=AF8, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'E' and resid 22 through 23 Processing sheet with id=AG1, first strand: chain 'F' and resid 15 through 17 Processing sheet with id=AG2, first strand: chain 'G' and resid 89 through 91 removed outlier: 5.840A pdb=" N ILE G 66 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL G 91 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE G 68 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE G 161 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU G 160 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE G 185 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL G 162 " --> pdb=" O ILE G 185 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.527A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE H 63 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASN H 101 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA H 103 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE H 67 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 164 through 170 removed outlier: 3.578A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY H 196 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL H 199 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS H 203 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.615A pdb=" N ARG I 127 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL I 124 " --> pdb=" O ARG I 127 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET I 123 " --> pdb=" O SER I 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER I 143 " --> pdb=" O MET I 123 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL I 142 " --> pdb=" O GLY I 179 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 14 through 19 removed outlier: 7.169A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL J 17 " --> pdb=" O THR J 33 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR J 33 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR J 36 " --> pdb=" O GLY J 48 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY J 48 " --> pdb=" O THR J 36 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 22 through 23 Processing sheet with id=AG8, first strand: chain 'J' and resid 84 through 85 Processing sheet with id=AG9, first strand: chain 'K' and resid 2 through 4 Processing sheet with id=AH1, first strand: chain 'K' and resid 41 through 46 removed outlier: 5.543A pdb=" N ASP K 41 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU K 61 " --> pdb=" O ASP K 41 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 72 through 74 Processing sheet with id=AH3, first strand: chain 'M' and resid 23 through 27 removed outlier: 3.721A pdb=" N VAL M 24 " --> pdb=" O LEU M 60 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.554A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE M 100 " --> pdb=" O VAL M 128 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.520A pdb=" N TYR N 5 " --> pdb=" O ILE N 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA N 15 " --> pdb=" O LYS N 67 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS N 67 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG N 17 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 70 through 73 removed outlier: 3.615A pdb=" N ARG O 72 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU O 10 " --> pdb=" O ARG O 72 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 65 through 67 Processing sheet with id=AH8, first strand: chain 'P' and resid 17 through 18 removed outlier: 3.797A pdb=" N GLY P 18 " --> pdb=" O ASN P 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU P 81 " --> pdb=" O ARG P 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'P' and resid 40 through 44 removed outlier: 3.542A pdb=" N ASN P 28 " --> pdb=" O SER P 25 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 28 through 31 removed outlier: 3.637A pdb=" N LYS Q 29 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE Q 81 " --> pdb=" O LYS Q 29 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY Q 31 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 34 through 39 removed outlier: 4.833A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG Q 49 " --> pdb=" O THR Q 39 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'U' and resid 3 through 4 removed outlier: 3.598A pdb=" N ILE U 4 " --> pdb=" O THR U 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'U' and resid 6 through 9 Processing sheet with id=AI5, first strand: chain 'U' and resid 37 through 39 Processing sheet with id=AI6, first strand: chain 'V' and resid 7 through 10 removed outlier: 6.952A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG V 61 " --> pdb=" O THR V 73 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AI8, first strand: chain 'V' and resid 23 through 26 Processing sheet with id=AI9, first strand: chain 'X' and resid 49 through 51 1117 hydrogen bonds defined for protein. 3099 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2243 hydrogen bonds 3732 hydrogen bond angles 0 basepair planarities 927 basepair parallelities 2451 stacking parallelities Total time for adding SS restraints: 189.63 Time building geometry restraints manager: 66.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 23740 1.33 - 1.46: 67714 1.46 - 1.58: 59215 1.58 - 1.70: 9463 1.70 - 1.82: 266 Bond restraints: 160398 Sorted by residual: bond pdb=" C VAL K 18 " pdb=" N PRO K 19 " ideal model delta sigma weight residual 1.334 1.429 -0.095 1.51e-02 4.39e+03 3.98e+01 bond pdb=" O3' C 6 13 " pdb=" P A 6 14 " ideal model delta sigma weight residual 1.607 1.701 -0.094 1.50e-02 4.44e+03 3.95e+01 bond pdb=" P A 6 14 " pdb=" OP1 A 6 14 " ideal model delta sigma weight residual 1.485 1.597 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CA LEU W 66 " pdb=" C LEU W 66 " ideal model delta sigma weight residual 1.522 1.447 0.075 1.37e-02 5.33e+03 3.02e+01 bond pdb=" C LEU n 38 " pdb=" N PRO n 39 " ideal model delta sigma weight residual 1.337 1.389 -0.052 1.11e-02 8.12e+03 2.21e+01 ... (remaining 160393 not shown) Histogram of bond angle deviations from ideal: 75.40 - 88.75: 1 88.75 - 102.10: 6122 102.10 - 115.45: 128409 115.45 - 128.80: 101019 128.80 - 142.15: 4485 Bond angle restraints: 240036 Sorted by residual: angle pdb=" O3' C 6 13 " pdb=" P A 6 14 " pdb=" O5' A 6 14 " ideal model delta sigma weight residual 104.00 75.40 28.60 1.50e+00 4.44e-01 3.63e+02 angle pdb=" C3' C 31158 " pdb=" C2' C 31158 " pdb=" O2' C 31158 " ideal model delta sigma weight residual 110.70 131.01 -20.31 1.50e+00 4.44e-01 1.83e+02 angle pdb=" O2' C 31158 " pdb=" C2' C 31158 " pdb=" C1' C 31158 " ideal model delta sigma weight residual 108.40 125.89 -17.49 1.50e+00 4.44e-01 1.36e+02 angle pdb=" O3' C 6 13 " pdb=" P A 6 14 " pdb=" OP1 A 6 14 " ideal model delta sigma weight residual 108.00 142.15 -34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C2' G 11828 " pdb=" C1' G 11828 " pdb=" N9 G 11828 " ideal model delta sigma weight residual 112.00 124.94 -12.94 1.50e+00 4.44e-01 7.44e+01 ... (remaining 240031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 90767 35.55 - 71.10: 10742 71.10 - 106.64: 1279 106.64 - 142.19: 16 142.19 - 177.74: 25 Dihedral angle restraints: 102829 sinusoidal: 86070 harmonic: 16759 Sorted by residual: dihedral pdb=" C5' A 4 13 " pdb=" C4' A 4 13 " pdb=" C3' A 4 13 " pdb=" O3' A 4 13 " ideal model delta sinusoidal sigma weight residual 82.00 -43.51 125.51 1 8.00e+00 1.56e-02 2.37e+02 dihedral pdb=" CA ASN Z 8 " pdb=" C ASN Z 8 " pdb=" N GLU Z 9 " pdb=" CA GLU Z 9 " ideal model delta harmonic sigma weight residual 180.00 109.82 70.18 0 5.00e+00 4.00e-02 1.97e+02 dihedral pdb=" CA GLY d 82 " pdb=" C GLY d 82 " pdb=" N VAL d 83 " pdb=" CA VAL d 83 " ideal model delta harmonic sigma weight residual -180.00 -121.64 -58.36 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 102826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.957: 30696 0.957 - 1.915: 0 1.915 - 2.872: 1 2.872 - 3.829: 0 3.829 - 4.786: 2 Chirality restraints: 30699 Sorted by residual: chirality pdb=" C4' A 4 13 " pdb=" C5' A 4 13 " pdb=" O4' A 4 13 " pdb=" C3' A 4 13 " both_signs ideal model delta sigma weight residual False -2.50 2.29 -4.79 2.00e-01 2.50e+01 5.73e+02 chirality pdb=" C2' C 1 889 " pdb=" C3' C 1 889 " pdb=" O2' C 1 889 " pdb=" C1' C 1 889 " both_signs ideal model delta sigma weight residual False -2.52 1.90 -4.42 2.00e-01 2.50e+01 4.88e+02 chirality pdb=" C2' C 31158 " pdb=" C3' C 31158 " pdb=" O2' C 31158 " pdb=" C1' C 31158 " both_signs ideal model delta sigma weight residual False -2.75 -0.21 -2.54 2.00e-01 2.50e+01 1.62e+02 ... (remaining 30696 not shown) Planarity restraints: 12823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 11828 " -0.247 2.00e-02 2.50e+03 1.04e-01 3.26e+02 pdb=" N9 G 11828 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G 11828 " 0.122 2.00e-02 2.50e+03 pdb=" N7 G 11828 " 0.108 2.00e-02 2.50e+03 pdb=" C5 G 11828 " 0.043 2.00e-02 2.50e+03 pdb=" C6 G 11828 " -0.049 2.00e-02 2.50e+03 pdb=" O6 G 11828 " -0.158 2.00e-02 2.50e+03 pdb=" N1 G 11828 " -0.040 2.00e-02 2.50e+03 pdb=" C2 G 11828 " 0.022 2.00e-02 2.50e+03 pdb=" N2 G 11828 " 0.063 2.00e-02 2.50e+03 pdb=" N3 G 11828 " 0.054 2.00e-02 2.50e+03 pdb=" C4 G 11828 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11969 " -0.189 2.00e-02 2.50e+03 8.44e-02 1.96e+02 pdb=" N9 A 11969 " 0.009 2.00e-02 2.50e+03 pdb=" C8 A 11969 " 0.077 2.00e-02 2.50e+03 pdb=" N7 A 11969 " 0.074 2.00e-02 2.50e+03 pdb=" C5 A 11969 " 0.041 2.00e-02 2.50e+03 pdb=" C6 A 11969 " -0.026 2.00e-02 2.50e+03 pdb=" N6 A 11969 " -0.142 2.00e-02 2.50e+03 pdb=" N1 A 11969 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 11969 " 0.040 2.00e-02 2.50e+03 pdb=" N3 A 11969 " 0.061 2.00e-02 2.50e+03 pdb=" C4 A 11969 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12109 " 0.156 2.00e-02 2.50e+03 8.53e-02 1.64e+02 pdb=" N1 U 12109 " -0.007 2.00e-02 2.50e+03 pdb=" C2 U 12109 " -0.030 2.00e-02 2.50e+03 pdb=" O2 U 12109 " -0.059 2.00e-02 2.50e+03 pdb=" N3 U 12109 " -0.026 2.00e-02 2.50e+03 pdb=" C4 U 12109 " -0.025 2.00e-02 2.50e+03 pdb=" O4 U 12109 " 0.150 2.00e-02 2.50e+03 pdb=" C5 U 12109 " -0.084 2.00e-02 2.50e+03 pdb=" C6 U 12109 " -0.076 2.00e-02 2.50e+03 ... (remaining 12820 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 5 2.20 - 2.88: 45252 2.88 - 3.55: 209361 3.55 - 4.23: 440645 4.23 - 4.90: 592051 Nonbonded interactions: 1287314 Sorted by model distance: nonbonded pdb=" OG1 THR G 71 " pdb=" OE2 GLU G 168 " model vdw 1.525 2.440 nonbonded pdb=" O3' C 6 13 " pdb=" C5' A 6 14 " model vdw 1.790 2.752 nonbonded pdb=" N VAL G 162 " pdb=" O PHE G 183 " model vdw 2.174 2.520 nonbonded pdb=" O LEU G 160 " pdb=" N PHE G 183 " model vdw 2.194 2.520 nonbonded pdb=" N7 A 6 21 " pdb=" O2 U 6 47 " model vdw 2.197 3.120 ... (remaining 1287309 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 22.870 Check model and map are aligned: 1.590 Set scattering table: 1.000 Process input model: 459.390 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 494.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 160398 Z= 0.505 Angle : 1.034 34.146 240036 Z= 0.647 Chirality : 0.090 4.786 30699 Planarity : 0.012 0.104 12823 Dihedral : 23.224 177.739 92017 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.44 % Favored : 85.18 % Rotamer: Outliers : 0.87 % Allowed : 12.99 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.55 % 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: -5.23 (0.08), residues: 5783 helix: -4.19 (0.08), residues: 1382 sheet: -2.89 (0.16), residues: 810 loop : -3.49 (0.08), residues: 3591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP b 212 HIS 0.014 0.003 HIS T 45 PHE 0.039 0.003 PHE Z 36 TYR 0.025 0.003 TYR e 142 ARG 0.024 0.001 ARG X 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1559 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1517 time to evaluate : 6.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7029 (mm) cc_final: 0.6696 (mm) REVERT: b 38 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7183 (mmmt) REVERT: b 113 ASP cc_start: 0.8797 (t70) cc_final: 0.8431 (t0) REVERT: b 247 TRP cc_start: 0.7662 (m-90) cc_final: 0.6955 (m-90) REVERT: c 55 LYS cc_start: 0.8001 (tppt) cc_final: 0.7506 (ttpt) REVERT: c 124 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8074 (mtp180) REVERT: c 168 GLU cc_start: 0.6768 (tt0) cc_final: 0.6513 (mt-10) REVERT: d 100 MET cc_start: 0.8282 (mtp) cc_final: 0.8002 (mtp) REVERT: d 200 LEU cc_start: 0.6962 (mm) cc_final: 0.6619 (mm) REVERT: e 6 TYR cc_start: 0.8268 (t80) cc_final: 0.7986 (t80) REVERT: e 14 LYS cc_start: 0.8478 (tttt) cc_final: 0.7679 (pttt) REVERT: e 16 MET cc_start: 0.2607 (tpt) cc_final: 0.1795 (mmm) REVERT: e 36 ASN cc_start: 0.7261 (t0) cc_final: 0.5785 (t0) REVERT: e 97 GLU cc_start: 0.8531 (tp30) cc_final: 0.8153 (tp30) REVERT: e 147 ARG cc_start: 0.7123 (mmp80) cc_final: 0.6551 (mmp80) REVERT: e 152 ASP cc_start: 0.5377 (p0) cc_final: 0.4909 (m-30) REVERT: f 18 ILE cc_start: 0.6474 (mm) cc_final: 0.6145 (mp) REVERT: a 21 TYR cc_start: 0.4068 (m-10) cc_final: 0.3720 (m-10) REVERT: k 17 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7535 (ttm-80) REVERT: k 118 LEU cc_start: 0.8231 (mt) cc_final: 0.7825 (mp) REVERT: l 29 LYS cc_start: 0.8610 (pptt) cc_final: 0.8303 (pttm) REVERT: l 127 VAL cc_start: 0.8169 (t) cc_final: 0.7895 (t) REVERT: m 95 LEU cc_start: 0.7964 (mt) cc_final: 0.7609 (mt) REVERT: m 117 PHE cc_start: 0.7526 (m-10) cc_final: 0.6103 (m-80) REVERT: n 2 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7143 (ptm-80) REVERT: n 43 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7457 (mm-30) REVERT: n 54 LEU cc_start: 0.8602 (tp) cc_final: 0.8377 (tt) REVERT: n 90 ARG cc_start: 0.7565 (mmt90) cc_final: 0.7331 (mmt-90) REVERT: o 112 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8519 (mt-10) REVERT: p 95 LYS cc_start: 0.7683 (mmtp) cc_final: 0.7436 (mmtp) REVERT: q 91 ARG cc_start: 0.6644 (mmp80) cc_final: 0.6293 (mmp80) REVERT: q 108 LEU cc_start: 0.8449 (mt) cc_final: 0.8185 (mt) REVERT: s 11 ARG cc_start: 0.7371 (tpp-160) cc_final: 0.6965 (tpp-160) REVERT: t 4 GLU cc_start: 0.8037 (tt0) cc_final: 0.7820 (tt0) REVERT: t 9 LYS cc_start: 0.8326 (mttt) cc_final: 0.7655 (tmmt) REVERT: t 52 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7678 (mp0) REVERT: t 88 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8395 (mttm) REVERT: u 25 LYS cc_start: 0.6397 (tppt) cc_final: 0.5958 (mtmm) REVERT: v 7 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6037 (tm-30) REVERT: v 8 VAL cc_start: 0.5779 (m) cc_final: 0.5111 (t) REVERT: v 31 TYR cc_start: 0.6526 (p90) cc_final: 0.6110 (p90) REVERT: v 76 ASP cc_start: 0.7289 (m-30) cc_final: 0.6298 (m-30) REVERT: w 20 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8252 (mmtt) REVERT: w 71 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8568 (mmtm) REVERT: y 24 GLU cc_start: 0.8031 (mp0) cc_final: 0.7782 (mp0) REVERT: y 45 GLN cc_start: 0.8388 (mm110) cc_final: 0.8111 (mm-40) REVERT: C 31 GLU cc_start: 0.7975 (tp30) cc_final: 0.7774 (tp30) REVERT: E 34 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7633 (ptmt) REVERT: G 99 MET cc_start: 0.6397 (mmm) cc_final: 0.5934 (mmm) REVERT: G 135 MET cc_start: 0.7785 (ppp) cc_final: 0.7549 (ppp) REVERT: G 173 LYS cc_start: 0.6453 (mmtm) cc_final: 0.5336 (ttpp) REVERT: H 141 MET cc_start: -0.1084 (mmm) cc_final: -0.1560 (mmm) REVERT: H 178 ARG cc_start: 0.4145 (ttt180) cc_final: 0.2467 (ttp-170) REVERT: I 13 ARG cc_start: 0.7950 (tpm170) cc_final: 0.7509 (tpp80) REVERT: I 28 ASP cc_start: 0.7853 (t70) cc_final: 0.7619 (t70) REVERT: I 72 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7866 (mtt180) REVERT: J 18 ASN cc_start: 0.8283 (t0) cc_final: 0.8016 (t0) REVERT: J 51 LYS cc_start: 0.8246 (pttp) cc_final: 0.7740 (ptmt) REVERT: K 88 MET cc_start: 0.5410 (tmm) cc_final: 0.5156 (tmm) REVERT: L 52 ARG cc_start: 0.8389 (ttt180) cc_final: 0.8134 (ttm170) REVERT: L 138 GLU cc_start: 0.9305 (tp30) cc_final: 0.8902 (tp30) REVERT: M 26 MET cc_start: 0.8070 (pmm) cc_final: 0.7597 (pmm) REVERT: M 51 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7898 (tm-30) REVERT: M 57 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6883 (pm20) REVERT: M 87 ARG cc_start: 0.7131 (mtp-110) cc_final: 0.6641 (mtp-110) REVERT: M 95 MET cc_start: 0.7186 (mtp) cc_final: 0.6804 (mmm) REVERT: N 12 LYS cc_start: 0.6841 (ttmt) cc_final: 0.6328 (tmtt) REVERT: N 108 ARG cc_start: 0.6875 (mmt90) cc_final: 0.6537 (mmt90) REVERT: O 62 ARG cc_start: 0.7399 (mpt-90) cc_final: 0.6977 (mtt-85) REVERT: O 97 ASP cc_start: 0.7297 (m-30) cc_final: 0.6819 (m-30) REVERT: P 28 ASN cc_start: 0.7320 (t0) cc_final: 0.6766 (m110) REVERT: Q 8 ARG cc_start: 0.8289 (mtm180) cc_final: 0.7553 (ttp-110) REVERT: Q 9 LYS cc_start: 0.8926 (tptp) cc_final: 0.8619 (tppp) REVERT: Q 82 ARG cc_start: 0.3928 (ptt90) cc_final: 0.2322 (ptt90) REVERT: T 57 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.6905 (ttp-170) REVERT: T 58 MET cc_start: 0.8302 (mtt) cc_final: 0.8083 (mtt) REVERT: V 25 GLU cc_start: 0.7349 (pm20) cc_final: 0.7098 (pm20) REVERT: X 31 ARG cc_start: 0.5215 (mmt90) cc_final: 0.4926 (ptm160) REVERT: X 33 TRP cc_start: 0.6711 (m100) cc_final: 0.6266 (m-10) REVERT: Y 60 GLN cc_start: 0.8334 (mt0) cc_final: 0.8082 (pm20) REVERT: Z 6 ARG cc_start: 0.5708 (tmm-80) cc_final: 0.5240 (ttm-80) REVERT: Z 19 LYS cc_start: 0.8172 (mttt) cc_final: 0.7204 (mmtm) outliers start: 42 outliers final: 15 residues processed: 1549 average time/residue: 1.5476 time to fit residues: 4028.2305 Evaluate side-chains 1257 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1242 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain Q residue 89 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 875 optimal weight: 9.9990 chunk 785 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 530 optimal weight: 0.9990 chunk 419 optimal weight: 10.0000 chunk 812 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 494 optimal weight: 4.9990 chunk 604 optimal weight: 3.9990 chunk 941 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN b 24 HIS b 238 ASN b 242 HIS c 36 GLN d 9 GLN ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN f 63 GLN f 72 ASN f 103 ASN f 114 HIS g 43 ASN i 5 GLN ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 ASN l 35 HIS l 38 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN n 11 ASN n 31 HIS o 38 GLN p 55 HIS p 65 ASN q 36 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 HIS s 15 GLN t 59 ASN u 73 ASN u 98 ASN v 44 HIS ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 42 HIS w 46 ASN y 15 ASN y 36 GLN D 16 HIS ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN E 25 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN H 7 ASN H 31 ASN H 139 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN I 70 GLN I 88 ASN I 139 ASN J 11 GLN J 72 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN J 131 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN L 141 HIS M 75 GLN N 31 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS P 100 ASN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN V 8 GLN W 51 GLN W 53 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 160398 Z= 0.277 Angle : 0.791 14.381 240036 Z= 0.405 Chirality : 0.044 0.379 30699 Planarity : 0.006 0.095 12823 Dihedral : 23.877 171.574 80479 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.73 % Favored : 85.99 % Rotamer: Outliers : 4.89 % Allowed : 21.64 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.54 (0.09), residues: 5783 helix: -2.96 (0.10), residues: 1514 sheet: -2.65 (0.16), residues: 818 loop : -3.28 (0.09), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP p 30 HIS 0.008 0.001 HIS T 45 PHE 0.023 0.002 PHE S 20 TYR 0.024 0.002 TYR E 63 ARG 0.029 0.001 ARG I 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1316 time to evaluate : 6.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7115 (mm) REVERT: b 74 PRO cc_start: 0.7180 (Cg_exo) cc_final: 0.6753 (Cg_endo) REVERT: b 113 ASP cc_start: 0.8809 (t70) cc_final: 0.8411 (t0) REVERT: b 247 TRP cc_start: 0.7711 (m-90) cc_final: 0.7055 (m-90) REVERT: b 266 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8442 (mm) REVERT: c 55 LYS cc_start: 0.7928 (tppt) cc_final: 0.7560 (tttt) REVERT: e 14 LYS cc_start: 0.8516 (tttt) cc_final: 0.7756 (pttt) REVERT: e 16 MET cc_start: 0.2749 (tpt) cc_final: 0.1910 (mmm) REVERT: e 37 MET cc_start: 0.5525 (tpt) cc_final: 0.5235 (tpt) REVERT: e 97 GLU cc_start: 0.8446 (tp30) cc_final: 0.8180 (tp30) REVERT: e 98 PHE cc_start: 0.8461 (t80) cc_final: 0.8166 (t80) REVERT: e 101 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7672 (tpt-90) REVERT: j 140 LEU cc_start: 0.7817 (tp) cc_final: 0.7534 (tp) REVERT: k 17 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7244 (ttm170) REVERT: k 39 ILE cc_start: 0.8499 (tt) cc_final: 0.8244 (tt) REVERT: k 118 LEU cc_start: 0.8148 (mt) cc_final: 0.7823 (mp) REVERT: m 84 LYS cc_start: 0.7770 (tmtt) cc_final: 0.7487 (tttt) REVERT: n 2 ARG cc_start: 0.7530 (mmm-85) cc_final: 0.7053 (ptm160) REVERT: n 45 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7396 (ttp-170) REVERT: n 90 ARG cc_start: 0.7628 (mmt90) cc_final: 0.7395 (tmt-80) REVERT: p 74 GLN cc_start: 0.8304 (mp10) cc_final: 0.8085 (mp10) REVERT: p 95 LYS cc_start: 0.7739 (mmtp) cc_final: 0.7510 (mmtp) REVERT: p 100 ARG cc_start: 0.7419 (mmm160) cc_final: 0.7127 (mmm160) REVERT: q 4 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8480 (ttpt) REVERT: q 108 LEU cc_start: 0.8602 (mt) cc_final: 0.8264 (mt) REVERT: r 82 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6643 (t-90) REVERT: r 84 ARG cc_start: 0.7574 (ptp-110) cc_final: 0.6542 (ptp-110) REVERT: s 67 ASP cc_start: 0.8436 (m-30) cc_final: 0.7969 (p0) REVERT: t 1 MET cc_start: 0.4599 (ptt) cc_final: 0.4251 (ptt) REVERT: t 9 LYS cc_start: 0.8140 (mttt) cc_final: 0.7512 (tmmt) REVERT: t 15 HIS cc_start: 0.6137 (OUTLIER) cc_final: 0.5897 (t-170) REVERT: t 37 ASP cc_start: 0.7998 (t0) cc_final: 0.7746 (t0) REVERT: t 52 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7673 (mp0) REVERT: t 76 ARG cc_start: 0.7686 (tpt-90) cc_final: 0.7471 (mmm160) REVERT: u 42 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6806 (mmtt) REVERT: v 9 ARG cc_start: 0.6960 (mtm110) cc_final: 0.6514 (mtp180) REVERT: v 76 ASP cc_start: 0.7639 (m-30) cc_final: 0.7377 (m-30) REVERT: w 20 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8379 (mmtt) REVERT: w 21 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.7817 (mmm-85) REVERT: x 49 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.5476 (mtm-85) REVERT: y 23 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6541 (mmm160) REVERT: z 52 PHE cc_start: 0.7987 (p90) cc_final: 0.7068 (p90) REVERT: B 8 THR cc_start: 0.8471 (m) cc_final: 0.8261 (m) REVERT: D 35 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7692 (mtm-85) REVERT: F 34 LYS cc_start: 0.8247 (tptt) cc_final: 0.8034 (tppt) REVERT: G 99 MET cc_start: 0.6869 (mmm) cc_final: 0.6113 (mmm) REVERT: G 135 MET cc_start: 0.7894 (ppp) cc_final: 0.7635 (ppp) REVERT: H 178 ARG cc_start: 0.3958 (ttt180) cc_final: 0.2038 (ttp80) REVERT: I 72 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7825 (mtt180) REVERT: I 131 ILE cc_start: 0.8884 (mt) cc_final: 0.8604 (mt) REVERT: J 18 ASN cc_start: 0.8223 (t0) cc_final: 0.7929 (t0) REVERT: J 51 LYS cc_start: 0.8213 (pttp) cc_final: 0.7708 (ptmt) REVERT: J 163 ILE cc_start: 0.8084 (mm) cc_final: 0.7783 (tp) REVERT: K 68 GLN cc_start: 0.8017 (mp10) cc_final: 0.7655 (pp30) REVERT: L 101 ARG cc_start: 0.7927 (tpt-90) cc_final: 0.7579 (tpt170) REVERT: L 105 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8210 (mm-30) REVERT: L 138 GLU cc_start: 0.9306 (tp30) cc_final: 0.8774 (tp30) REVERT: M 51 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7841 (tm-30) REVERT: M 57 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7000 (pm20) REVERT: M 87 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.6998 (mtp-110) REVERT: M 88 LYS cc_start: 0.7336 (tttt) cc_final: 0.6753 (ptmt) REVERT: M 124 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6702 (mp) REVERT: N 12 LYS cc_start: 0.6655 (ttmt) cc_final: 0.6198 (tmtt) REVERT: N 108 ARG cc_start: 0.6742 (mmt90) cc_final: 0.6464 (mmt90) REVERT: O 7 ARG cc_start: 0.1112 (tpp80) cc_final: -0.1018 (tpp80) REVERT: O 16 ARG cc_start: 0.5793 (mmp-170) cc_final: 0.5402 (mmp-170) REVERT: O 68 ARG cc_start: 0.6437 (mtt180) cc_final: 0.5747 (mtt180) REVERT: O 97 ASP cc_start: 0.7165 (m-30) cc_final: 0.6621 (m-30) REVERT: P 28 ASN cc_start: 0.7218 (t0) cc_final: 0.6722 (m110) REVERT: P 43 TRP cc_start: 0.8239 (p-90) cc_final: 0.7511 (p-90) REVERT: P 79 LYS cc_start: 0.7762 (ptmt) cc_final: 0.7289 (pttp) REVERT: P 100 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7357 (m110) REVERT: Q 4 ASN cc_start: 0.7610 (m110) cc_final: 0.7409 (m110) REVERT: Q 8 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7567 (ttm110) REVERT: Q 9 LYS cc_start: 0.9036 (tptp) cc_final: 0.8763 (tppp) REVERT: Q 82 ARG cc_start: 0.4237 (ptt90) cc_final: 0.3480 (ptt180) REVERT: T 25 GLU cc_start: 0.8214 (pt0) cc_final: 0.7916 (pt0) REVERT: T 57 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.6550 (ttp-110) REVERT: U 51 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7214 (ttp80) REVERT: V 25 GLU cc_start: 0.7293 (pm20) cc_final: 0.7074 (pm20) REVERT: V 57 VAL cc_start: 0.7408 (t) cc_final: 0.6886 (t) REVERT: W 52 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7156 (ptp-170) REVERT: X 31 ARG cc_start: 0.5275 (mmt90) cc_final: 0.4946 (ptm160) REVERT: X 33 TRP cc_start: 0.6497 (m100) cc_final: 0.5885 (m-10) REVERT: X 65 MET cc_start: 0.6622 (mmt) cc_final: 0.6210 (mmt) REVERT: Y 54 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6637 (tm-30) REVERT: Z 20 ARG cc_start: 0.8341 (mtt180) cc_final: 0.8128 (mtt180) REVERT: Z 37 TYR cc_start: 0.5666 (t80) cc_final: 0.5464 (t80) outliers start: 235 outliers final: 155 residues processed: 1435 average time/residue: 1.4676 time to fit residues: 3580.8680 Evaluate side-chains 1368 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1203 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 78 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 15 GLN Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 42 LYS Chi-restraints excluded: chain u residue 71 ILE Chi-restraints excluded: chain u residue 99 SER Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 55 GLU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 75 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 49 ARG Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 46 MET Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 100 ASN Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Z residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 523 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 783 optimal weight: 0.9980 chunk 641 optimal weight: 7.9990 chunk 259 optimal weight: 40.0000 chunk 943 optimal weight: 20.0000 chunk 1019 optimal weight: 8.9990 chunk 840 optimal weight: 10.0000 chunk 935 optimal weight: 0.2980 chunk 321 optimal weight: 10.0000 chunk 756 optimal weight: 4.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN a 168 ASN ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS o 43 ASN q 58 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 46 ASN y 25 GLN B 5 ASN B 40 HIS F 33 HIS ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS S 59 GLN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 160398 Z= 0.208 Angle : 0.673 15.160 240036 Z= 0.347 Chirality : 0.038 0.370 30699 Planarity : 0.005 0.059 12823 Dihedral : 23.889 178.412 80473 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.54 % Favored : 86.27 % Rotamer: Outliers : 6.06 % Allowed : 23.72 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.12 (0.10), residues: 5783 helix: -2.40 (0.11), residues: 1523 sheet: -2.56 (0.16), residues: 816 loop : -3.07 (0.09), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP q 60 HIS 0.025 0.001 HIS K 55 PHE 0.035 0.002 PHE v 26 TYR 0.022 0.002 TYR e 142 ARG 0.014 0.001 ARG P 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1273 time to evaluate : 6.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7018 (mm) REVERT: b 113 ASP cc_start: 0.8782 (t70) cc_final: 0.8386 (t0) REVERT: b 247 TRP cc_start: 0.7740 (m-90) cc_final: 0.7068 (m-90) REVERT: c 55 LYS cc_start: 0.7807 (tppt) cc_final: 0.7531 (tttt) REVERT: d 144 GLU cc_start: 0.6787 (tp30) cc_final: 0.6429 (tp30) REVERT: e 14 LYS cc_start: 0.8514 (tttt) cc_final: 0.7854 (ptpp) REVERT: e 16 MET cc_start: 0.2980 (tpt) cc_final: 0.2233 (mmm) REVERT: e 36 ASN cc_start: 0.6431 (t0) cc_final: 0.6099 (t0) REVERT: e 37 MET cc_start: 0.5260 (tpt) cc_final: 0.4840 (tpt) REVERT: e 98 PHE cc_start: 0.8475 (t80) cc_final: 0.8142 (t80) REVERT: e 100 GLU cc_start: 0.6339 (tt0) cc_final: 0.5901 (mt-10) REVERT: e 140 ILE cc_start: 0.6608 (mp) cc_final: 0.6373 (mt) REVERT: e 151 LEU cc_start: 0.7644 (mp) cc_final: 0.7426 (mp) REVERT: f 100 ASN cc_start: 0.9145 (p0) cc_final: 0.8697 (p0) REVERT: f 131 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.6785 (m) REVERT: f 166 GLU cc_start: 0.7112 (tt0) cc_final: 0.6840 (tt0) REVERT: a 218 MET cc_start: 0.1310 (ttt) cc_final: 0.0956 (tmm) REVERT: i 71 LYS cc_start: 0.6640 (mmmt) cc_final: 0.6421 (mmmt) REVERT: k 118 LEU cc_start: 0.8123 (mt) cc_final: 0.7791 (mp) REVERT: l 36 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6818 (mtmm) REVERT: m 41 LEU cc_start: 0.8593 (mm) cc_final: 0.8374 (mm) REVERT: m 84 LYS cc_start: 0.7738 (tmtt) cc_final: 0.7402 (tttt) REVERT: m 128 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6085 (t) REVERT: n 2 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7012 (ptm160) REVERT: n 45 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7314 (ttp-170) REVERT: n 90 ARG cc_start: 0.7562 (mmt90) cc_final: 0.7285 (mmm-85) REVERT: o 29 HIS cc_start: 0.7880 (t-170) cc_final: 0.7608 (t-170) REVERT: q 108 LEU cc_start: 0.8562 (mt) cc_final: 0.8202 (mt) REVERT: r 37 GLU cc_start: 0.8039 (mp0) cc_final: 0.7817 (pm20) REVERT: r 82 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6668 (t-90) REVERT: r 84 ARG cc_start: 0.7571 (ptp-110) cc_final: 0.6554 (ptp-110) REVERT: s 67 ASP cc_start: 0.8353 (m-30) cc_final: 0.7984 (p0) REVERT: t 1 MET cc_start: 0.4515 (ptt) cc_final: 0.4258 (ptt) REVERT: t 9 LYS cc_start: 0.8080 (mttt) cc_final: 0.7512 (tmmt) REVERT: t 15 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5846 (t-170) REVERT: t 76 ARG cc_start: 0.7694 (tpt-90) cc_final: 0.7286 (mmm160) REVERT: u 42 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6743 (mmtt) REVERT: v 7 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6163 (tm-30) REVERT: v 75 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5901 (tt0) REVERT: v 76 ASP cc_start: 0.7608 (m-30) cc_final: 0.7357 (m-30) REVERT: w 20 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8356 (mmtt) REVERT: w 21 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.7697 (mmm-85) REVERT: x 5 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: x 25 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7043 (mttm) REVERT: x 49 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.5548 (mtm-85) REVERT: y 60 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8431 (tttt) REVERT: z 52 PHE cc_start: 0.7604 (p90) cc_final: 0.7092 (p90) REVERT: z 55 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7860 (tptt) REVERT: D 1 MET cc_start: 0.6973 (tmm) cc_final: 0.6700 (ppp) REVERT: D 19 ARG cc_start: 0.7620 (mtp180) cc_final: 0.7267 (mtp85) REVERT: D 35 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7659 (mtm-85) REVERT: G 27 LYS cc_start: 0.6577 (mptt) cc_final: 0.6296 (mptt) REVERT: G 58 LYS cc_start: 0.7511 (ptpt) cc_final: 0.7241 (pttm) REVERT: G 135 MET cc_start: 0.7898 (ppp) cc_final: 0.7612 (ppp) REVERT: I 186 GLU cc_start: 0.4071 (OUTLIER) cc_final: 0.3683 (tm-30) REVERT: J 18 ASN cc_start: 0.8245 (t0) cc_final: 0.7938 (t0) REVERT: J 51 LYS cc_start: 0.8111 (pttp) cc_final: 0.7589 (ptmt) REVERT: J 63 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: J 121 ASN cc_start: 0.6467 (t0) cc_final: 0.6255 (t0) REVERT: J 163 ILE cc_start: 0.8043 (mm) cc_final: 0.7700 (tp) REVERT: K 68 GLN cc_start: 0.8026 (mp10) cc_final: 0.7516 (pp30) REVERT: K 75 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6421 (pp20) REVERT: L 52 ARG cc_start: 0.8432 (ttm170) cc_final: 0.8185 (ttt180) REVERT: L 138 GLU cc_start: 0.9203 (tp30) cc_final: 0.8727 (tp30) REVERT: M 57 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6940 (pm20) REVERT: M 86 LYS cc_start: 0.7205 (mppt) cc_final: 0.6800 (mppt) REVERT: M 87 ARG cc_start: 0.7465 (mtp-110) cc_final: 0.7053 (mtp-110) REVERT: M 95 MET cc_start: 0.6835 (mmm) cc_final: 0.6614 (mmm) REVERT: M 124 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6487 (mp) REVERT: N 12 LYS cc_start: 0.6687 (ttmt) cc_final: 0.6192 (tmtt) REVERT: N 108 ARG cc_start: 0.6765 (mmt90) cc_final: 0.6502 (mmt90) REVERT: O 7 ARG cc_start: 0.1163 (tpp80) cc_final: -0.1030 (tpp80) REVERT: O 16 ARG cc_start: 0.5799 (mmp-170) cc_final: 0.5400 (mmp-170) REVERT: O 68 ARG cc_start: 0.6442 (mtt180) cc_final: 0.3469 (ptt-90) REVERT: O 72 ARG cc_start: 0.6408 (mmt-90) cc_final: 0.6131 (tpp-160) REVERT: O 97 ASP cc_start: 0.7141 (m-30) cc_final: 0.6655 (m-30) REVERT: P 28 ASN cc_start: 0.7248 (t0) cc_final: 0.6653 (m110) REVERT: P 43 TRP cc_start: 0.8161 (p-90) cc_final: 0.7410 (p-90) REVERT: P 63 GLN cc_start: 0.7713 (tt0) cc_final: 0.7258 (tp40) REVERT: Q 4 ASN cc_start: 0.7445 (m110) cc_final: 0.7209 (m110) REVERT: Q 8 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7536 (ttm110) REVERT: Q 82 ARG cc_start: 0.4100 (ptt90) cc_final: 0.3502 (ptt180) REVERT: T 25 GLU cc_start: 0.8171 (pt0) cc_final: 0.7854 (pt0) REVERT: T 57 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.6536 (ttp-110) REVERT: V 25 GLU cc_start: 0.7209 (pm20) cc_final: 0.6984 (pm20) REVERT: V 57 VAL cc_start: 0.7378 (t) cc_final: 0.6986 (t) REVERT: W 52 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7137 (ptp-170) REVERT: X 31 ARG cc_start: 0.5325 (mmt90) cc_final: 0.4976 (ptm160) REVERT: X 33 TRP cc_start: 0.6444 (m100) cc_final: 0.5862 (m-10) REVERT: X 65 MET cc_start: 0.6614 (mmt) cc_final: 0.6229 (mmt) REVERT: Y 24 ARG cc_start: 0.8541 (ttm170) cc_final: 0.8076 (mtm180) REVERT: Y 54 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6521 (tm-30) REVERT: Z 19 LYS cc_start: 0.8083 (mttt) cc_final: 0.7138 (mmtm) outliers start: 291 outliers final: 190 residues processed: 1433 average time/residue: 1.3379 time to fit residues: 3228.4429 Evaluate side-chains 1407 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1204 time to evaluate : 6.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 51 GLU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 80 GLN Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain f residue 176 LYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 36 LYS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 42 LYS Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 55 GLU Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 75 GLN Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 49 ARG Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 19 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 45 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 932 optimal weight: 20.0000 chunk 709 optimal weight: 9.9990 chunk 489 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 chunk 450 optimal weight: 10.0000 chunk 633 optimal weight: 9.9990 chunk 946 optimal weight: 0.0000 chunk 1002 optimal weight: 7.9990 chunk 494 optimal weight: 3.9990 chunk 897 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 ASN f 103 ASN ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN k 29 HIS ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS n 107 ASN o 38 GLN p 14 GLN q 36 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN v 75 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS K 94 HIS ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 160398 Z= 0.290 Angle : 0.751 16.321 240036 Z= 0.381 Chirality : 0.041 0.299 30699 Planarity : 0.006 0.096 12823 Dihedral : 24.071 177.187 80471 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.42 % Favored : 84.37 % Rotamer: Outliers : 7.18 % Allowed : 25.39 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.92 (0.10), residues: 5783 helix: -2.09 (0.12), residues: 1515 sheet: -2.54 (0.16), residues: 831 loop : -2.99 (0.10), residues: 3437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP q 60 HIS 0.011 0.002 HIS K 55 PHE 0.019 0.002 PHE Z 36 TYR 0.024 0.002 TYR q 75 ARG 0.017 0.001 ARG d 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1235 time to evaluate : 6.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7013 (mm) REVERT: b 113 ASP cc_start: 0.8858 (t70) cc_final: 0.8469 (t0) REVERT: b 247 TRP cc_start: 0.7810 (m-90) cc_final: 0.7132 (m-90) REVERT: c 55 LYS cc_start: 0.7897 (tppt) cc_final: 0.7471 (ttpt) REVERT: e 14 LYS cc_start: 0.8552 (tttt) cc_final: 0.7849 (ptpp) REVERT: e 16 MET cc_start: 0.3070 (tpt) cc_final: 0.2259 (mmm) REVERT: e 25 MET cc_start: 0.9082 (mmm) cc_final: 0.8623 (mpp) REVERT: e 37 MET cc_start: 0.5560 (tpt) cc_final: 0.5193 (tpt) REVERT: e 98 PHE cc_start: 0.8484 (t80) cc_final: 0.8118 (t80) REVERT: e 100 GLU cc_start: 0.6410 (tt0) cc_final: 0.5890 (mt-10) REVERT: e 140 ILE cc_start: 0.6879 (mp) cc_final: 0.6664 (mt) REVERT: f 123 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: f 166 GLU cc_start: 0.7128 (tt0) cc_final: 0.6748 (tt0) REVERT: i 71 LYS cc_start: 0.6653 (mmmt) cc_final: 0.6368 (mmmt) REVERT: i 108 ILE cc_start: -0.0428 (OUTLIER) cc_final: -0.0788 (mm) REVERT: j 140 LEU cc_start: 0.7924 (tp) cc_final: 0.7690 (tp) REVERT: k 95 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6927 (mm) REVERT: k 118 LEU cc_start: 0.8027 (mt) cc_final: 0.7715 (mp) REVERT: m 75 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: m 84 LYS cc_start: 0.7603 (tmtt) cc_final: 0.6795 (tptm) REVERT: m 128 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6145 (t) REVERT: n 2 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7116 (mtp-110) REVERT: n 42 LYS cc_start: 0.8216 (tppt) cc_final: 0.7483 (tptm) REVERT: n 45 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7232 (ttp-170) REVERT: n 86 ARG cc_start: 0.7260 (mtm180) cc_final: 0.7046 (mtm180) REVERT: n 90 ARG cc_start: 0.7599 (mmt90) cc_final: 0.7313 (mmm-85) REVERT: o 29 HIS cc_start: 0.7946 (t-170) cc_final: 0.7672 (t-170) REVERT: p 108 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7850 (mtm180) REVERT: q 60 TRP cc_start: 0.9202 (m-10) cc_final: 0.8971 (m-10) REVERT: q 71 ASN cc_start: 0.8088 (m-40) cc_final: 0.7311 (m-40) REVERT: q 108 LEU cc_start: 0.8582 (mt) cc_final: 0.8273 (mt) REVERT: r 82 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6691 (t-90) REVERT: r 84 ARG cc_start: 0.7594 (ptp-110) cc_final: 0.6541 (ptp-110) REVERT: s 31 GLN cc_start: 0.7397 (tm-30) cc_final: 0.7173 (tm-30) REVERT: s 67 ASP cc_start: 0.8450 (m-30) cc_final: 0.8094 (p0) REVERT: t 9 LYS cc_start: 0.8106 (mttt) cc_final: 0.7548 (tmmt) REVERT: t 44 LYS cc_start: 0.7855 (tttp) cc_final: 0.7635 (tttp) REVERT: t 76 ARG cc_start: 0.7732 (tpt-90) cc_final: 0.7330 (mmm160) REVERT: v 79 ARG cc_start: 0.7407 (mmm160) cc_final: 0.7184 (mmm160) REVERT: w 20 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8445 (mmtt) REVERT: w 21 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.7482 (mmm-85) REVERT: w 60 ASP cc_start: 0.7080 (m-30) cc_final: 0.6791 (m-30) REVERT: x 5 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6405 (tm-30) REVERT: x 40 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8265 (tm-30) REVERT: x 61 LYS cc_start: 0.6970 (mttp) cc_final: 0.6760 (mmtp) REVERT: y 60 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8462 (ttpp) REVERT: z 52 PHE cc_start: 0.7783 (p90) cc_final: 0.6938 (p90) REVERT: B 8 THR cc_start: 0.8449 (m) cc_final: 0.8205 (m) REVERT: B 39 ARG cc_start: 0.8313 (tpt170) cc_final: 0.8094 (tpt170) REVERT: D 1 MET cc_start: 0.7240 (tmm) cc_final: 0.6975 (ppp) REVERT: G 27 LYS cc_start: 0.6497 (mptt) cc_final: 0.6231 (mptt) REVERT: G 48 MET cc_start: 0.6890 (mtt) cc_final: 0.6138 (tmm) REVERT: G 135 MET cc_start: 0.7987 (ppp) cc_final: 0.7691 (ppp) REVERT: G 152 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7020 (p0) REVERT: H 178 ARG cc_start: 0.3814 (ttt180) cc_final: 0.3182 (tpp-160) REVERT: I 186 GLU cc_start: 0.4147 (OUTLIER) cc_final: 0.3744 (tm-30) REVERT: J 18 ASN cc_start: 0.8247 (t0) cc_final: 0.7966 (t0) REVERT: J 51 LYS cc_start: 0.8164 (pttp) cc_final: 0.7821 (ptmt) REVERT: J 63 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: J 121 ASN cc_start: 0.6619 (t0) cc_final: 0.6411 (t0) REVERT: J 163 ILE cc_start: 0.8059 (mm) cc_final: 0.7718 (tp) REVERT: M 51 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7755 (tm-30) REVERT: M 57 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6986 (pm20) REVERT: M 87 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7034 (mtp-110) REVERT: M 88 LYS cc_start: 0.7549 (tttt) cc_final: 0.7042 (ptmt) REVERT: N 108 ARG cc_start: 0.6803 (mmt90) cc_final: 0.6525 (mmt90) REVERT: O 7 ARG cc_start: 0.1205 (tpp80) cc_final: -0.0940 (tpp80) REVERT: O 16 ARG cc_start: 0.5935 (mmp-170) cc_final: 0.5560 (mmp-170) REVERT: O 68 ARG cc_start: 0.6722 (mtt180) cc_final: 0.3610 (ptt-90) REVERT: O 97 ASP cc_start: 0.6946 (m-30) cc_final: 0.6558 (m-30) REVERT: P 28 ASN cc_start: 0.7439 (t0) cc_final: 0.6712 (m110) REVERT: P 43 TRP cc_start: 0.8248 (p-90) cc_final: 0.7519 (p-90) REVERT: P 63 GLN cc_start: 0.7778 (tt0) cc_final: 0.7235 (tp40) REVERT: Q 8 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7603 (ttm110) REVERT: Q 61 GLU cc_start: 0.7286 (tm-30) cc_final: 0.7035 (tm-30) REVERT: Q 82 ARG cc_start: 0.4185 (ptt90) cc_final: 0.3721 (ptt180) REVERT: R 28 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7540 (tpp-160) REVERT: T 25 GLU cc_start: 0.8229 (pt0) cc_final: 0.7924 (pt0) REVERT: T 57 ARG cc_start: 0.7549 (ttp-170) cc_final: 0.6554 (ttp-110) REVERT: V 25 GLU cc_start: 0.7187 (pm20) cc_final: 0.6948 (pm20) REVERT: V 42 LYS cc_start: 0.7982 (tttt) cc_final: 0.7771 (tttm) REVERT: V 57 VAL cc_start: 0.7485 (t) cc_final: 0.7260 (t) REVERT: W 52 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7408 (ptp-170) REVERT: X 31 ARG cc_start: 0.5434 (mmt90) cc_final: 0.5019 (ptm160) REVERT: X 33 TRP cc_start: 0.6502 (m100) cc_final: 0.5916 (m100) REVERT: X 43 MET cc_start: 0.6321 (mtp) cc_final: 0.5813 (ttp) REVERT: X 65 MET cc_start: 0.6627 (mmt) cc_final: 0.6322 (mmt) REVERT: Y 24 ARG cc_start: 0.8719 (ttm170) cc_final: 0.8277 (mtm110) REVERT: Y 39 GLU cc_start: 0.8081 (mp0) cc_final: 0.7871 (mp0) REVERT: Y 54 GLN cc_start: 0.6899 (tm-30) cc_final: 0.6482 (tm-30) REVERT: Z 19 LYS cc_start: 0.8119 (mttt) cc_final: 0.7222 (mmtm) outliers start: 345 outliers final: 256 residues processed: 1427 average time/residue: 1.3485 time to fit residues: 3260.9388 Evaluate side-chains 1450 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1183 time to evaluate : 6.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 51 GLU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 123 GLU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain f residue 176 LYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 45 GLU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 19 HIS Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 41 TYR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 42 ILE Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain Z residue 62 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 834 optimal weight: 10.0000 chunk 569 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 746 optimal weight: 20.0000 chunk 413 optimal weight: 10.0000 chunk 855 optimal weight: 1.9990 chunk 692 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 511 optimal weight: 5.9990 chunk 899 optimal weight: 0.0060 chunk 252 optimal weight: 10.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 89 ASN ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 GLN i 33 ASN j 67 ASN k 3 GLN k 5 GLN k 29 HIS ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS n 81 ASN n 107 ASN o 38 GLN q 19 GLN q 36 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 160398 Z= 0.214 Angle : 0.672 18.343 240036 Z= 0.344 Chirality : 0.037 0.327 30699 Planarity : 0.005 0.099 12823 Dihedral : 24.072 175.551 80471 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.47 % Favored : 86.34 % Rotamer: Outliers : 6.93 % Allowed : 26.68 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.66 (0.10), residues: 5783 helix: -1.80 (0.12), residues: 1533 sheet: -2.32 (0.17), residues: 834 loop : -2.88 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP m 92 HIS 0.021 0.001 HIS K 55 PHE 0.038 0.002 PHE v 26 TYR 0.021 0.002 TYR e 142 ARG 0.015 0.001 ARG t 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1222 time to evaluate : 6.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7124 (mm) REVERT: b 113 ASP cc_start: 0.8818 (t70) cc_final: 0.8410 (t0) REVERT: b 247 TRP cc_start: 0.7760 (m-90) cc_final: 0.7120 (m-90) REVERT: d 144 GLU cc_start: 0.6745 (tp30) cc_final: 0.6392 (tp30) REVERT: e 14 LYS cc_start: 0.8537 (tttt) cc_final: 0.7850 (ptpp) REVERT: e 16 MET cc_start: 0.2997 (tpt) cc_final: 0.2240 (mmm) REVERT: e 36 ASN cc_start: 0.7003 (OUTLIER) cc_final: 0.6302 (m-40) REVERT: e 98 PHE cc_start: 0.8455 (t80) cc_final: 0.8077 (t80) REVERT: e 101 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7198 (tpt90) REVERT: e 139 GLU cc_start: 0.5445 (mm-30) cc_final: 0.5198 (mm-30) REVERT: f 100 ASN cc_start: 0.9137 (p0) cc_final: 0.8617 (p0) REVERT: f 123 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: f 166 GLU cc_start: 0.7066 (tt0) cc_final: 0.6688 (tt0) REVERT: i 71 LYS cc_start: 0.6598 (mmmt) cc_final: 0.6297 (mmmt) REVERT: k 44 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8162 (mmtm) REVERT: k 118 LEU cc_start: 0.8007 (mt) cc_final: 0.7706 (mp) REVERT: l 48 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.7073 (mtm-85) REVERT: m 41 LEU cc_start: 0.8554 (mm) cc_final: 0.8337 (mm) REVERT: m 75 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: m 84 LYS cc_start: 0.7626 (tmtt) cc_final: 0.7091 (tttt) REVERT: m 128 THR cc_start: 0.6820 (OUTLIER) cc_final: 0.6140 (t) REVERT: n 45 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.7104 (ttm170) REVERT: n 86 ARG cc_start: 0.7245 (mtm180) cc_final: 0.6997 (mtm180) REVERT: n 90 ARG cc_start: 0.7546 (mmt90) cc_final: 0.7234 (mmm-85) REVERT: o 29 HIS cc_start: 0.7954 (t-170) cc_final: 0.7701 (t-170) REVERT: o 34 HIS cc_start: 0.5320 (OUTLIER) cc_final: 0.5020 (m170) REVERT: o 111 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7941 (ptp-170) REVERT: q 108 LEU cc_start: 0.8644 (mt) cc_final: 0.8242 (mt) REVERT: r 62 GLU cc_start: 0.5148 (OUTLIER) cc_final: 0.4480 (pp20) REVERT: r 84 ARG cc_start: 0.7606 (ptp-110) cc_final: 0.7141 (ptp-110) REVERT: s 31 GLN cc_start: 0.7300 (tm-30) cc_final: 0.7057 (tm-30) REVERT: s 67 ASP cc_start: 0.8318 (m-30) cc_final: 0.8062 (p0) REVERT: t 9 LYS cc_start: 0.8019 (mttt) cc_final: 0.7489 (tmmt) REVERT: t 15 HIS cc_start: 0.5867 (OUTLIER) cc_final: 0.5615 (t-90) REVERT: t 76 ARG cc_start: 0.7744 (tpt-90) cc_final: 0.7338 (mmm160) REVERT: t 77 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7563 (ttm170) REVERT: u 42 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6723 (mmtt) REVERT: v 79 ARG cc_start: 0.7464 (mmm160) cc_final: 0.7229 (mmm160) REVERT: w 20 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8397 (mmtt) REVERT: w 21 ARG cc_start: 0.8165 (mmt-90) cc_final: 0.7528 (mmm-85) REVERT: w 60 ASP cc_start: 0.7169 (m-30) cc_final: 0.6791 (m-30) REVERT: x 5 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6347 (tm-30) REVERT: x 25 LYS cc_start: 0.7583 (mmtt) cc_final: 0.6976 (mttm) REVERT: x 40 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8331 (tm-30) REVERT: x 49 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.5932 (mtm-85) REVERT: x 61 LYS cc_start: 0.6883 (mttp) cc_final: 0.6457 (mttp) REVERT: y 30 MET cc_start: 0.5724 (ptm) cc_final: 0.5448 (ppp) REVERT: y 60 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8512 (tttt) REVERT: z 46 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7687 (ttm) REVERT: z 55 LYS cc_start: 0.8190 (tmtt) cc_final: 0.7873 (tptt) REVERT: B 8 THR cc_start: 0.8393 (m) cc_final: 0.8183 (m) REVERT: D 19 ARG cc_start: 0.7496 (mtp180) cc_final: 0.7239 (mmm-85) REVERT: G 44 LYS cc_start: 0.7064 (pttm) cc_final: 0.6286 (pttm) REVERT: G 48 MET cc_start: 0.6859 (mtt) cc_final: 0.6285 (tmm) REVERT: G 135 MET cc_start: 0.7988 (ppp) cc_final: 0.7678 (ppp) REVERT: H 79 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7556 (tptp) REVERT: H 178 ARG cc_start: 0.3708 (ttt180) cc_final: 0.1777 (ttp80) REVERT: I 72 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7779 (mtt180) REVERT: I 186 GLU cc_start: 0.4097 (OUTLIER) cc_final: 0.3713 (tm-30) REVERT: J 18 ASN cc_start: 0.8206 (t0) cc_final: 0.7942 (t0) REVERT: J 51 LYS cc_start: 0.8137 (pttp) cc_final: 0.7815 (ptmt) REVERT: J 63 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8018 (mmm) REVERT: J 110 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8455 (mtm) REVERT: J 163 ILE cc_start: 0.8051 (mm) cc_final: 0.7697 (tp) REVERT: K 68 GLN cc_start: 0.7935 (mp10) cc_final: 0.7494 (pp30) REVERT: L 138 GLU cc_start: 0.9175 (tp30) cc_final: 0.8762 (tp30) REVERT: M 57 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6626 (pp20) REVERT: M 86 LYS cc_start: 0.7543 (mppt) cc_final: 0.7031 (mppt) REVERT: M 88 LYS cc_start: 0.7711 (tttt) cc_final: 0.7298 (ptmt) REVERT: M 124 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6389 (mp) REVERT: N 12 LYS cc_start: 0.6705 (ttmt) cc_final: 0.6186 (tmtt) REVERT: N 87 MET cc_start: 0.5761 (mmm) cc_final: 0.5485 (mmm) REVERT: N 108 ARG cc_start: 0.6734 (mmt90) cc_final: 0.6462 (mmt90) REVERT: O 7 ARG cc_start: 0.1164 (tpp80) cc_final: -0.0933 (tpp80) REVERT: O 16 ARG cc_start: 0.5868 (mmp-170) cc_final: 0.5477 (mmp-170) REVERT: O 68 ARG cc_start: 0.6628 (mtt180) cc_final: 0.3579 (ptt-90) REVERT: O 97 ASP cc_start: 0.6898 (m-30) cc_final: 0.6539 (m-30) REVERT: P 43 TRP cc_start: 0.8237 (p-90) cc_final: 0.7464 (p-90) REVERT: P 63 GLN cc_start: 0.7622 (tt0) cc_final: 0.7127 (tp40) REVERT: P 75 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6107 (tt0) REVERT: Q 8 ARG cc_start: 0.8294 (mtm180) cc_final: 0.7491 (ttm110) REVERT: Q 82 ARG cc_start: 0.4182 (ptt90) cc_final: 0.3950 (ptt180) REVERT: R 28 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7508 (tpp-160) REVERT: S 19 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.5036 (m-80) REVERT: S 88 MET cc_start: 0.0175 (OUTLIER) cc_final: -0.0112 (ttm) REVERT: T 25 GLU cc_start: 0.8207 (pt0) cc_final: 0.7904 (pt0) REVERT: T 57 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.6551 (ttp-110) REVERT: U 56 ARG cc_start: 0.8149 (mmp-170) cc_final: 0.7699 (mmp80) REVERT: V 25 GLU cc_start: 0.7155 (pm20) cc_final: 0.6897 (pm20) REVERT: V 42 LYS cc_start: 0.7871 (tttt) cc_final: 0.7589 (tttm) REVERT: V 57 VAL cc_start: 0.7421 (t) cc_final: 0.7068 (t) REVERT: V 74 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6648 (pp) REVERT: W 52 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7281 (ptp-170) REVERT: X 31 ARG cc_start: 0.5397 (mmt90) cc_final: 0.5102 (ptm160) REVERT: X 65 MET cc_start: 0.6647 (mmt) cc_final: 0.6368 (mmt) REVERT: Y 19 HIS cc_start: 0.8323 (t-90) cc_final: 0.7953 (t-90) REVERT: Y 54 GLN cc_start: 0.6865 (tm-30) cc_final: 0.6430 (tm-30) REVERT: Z 19 LYS cc_start: 0.8148 (mttt) cc_final: 0.7244 (mmtm) REVERT: Z 46 ARG cc_start: 0.9289 (tpp-160) cc_final: 0.8964 (tpp-160) outliers start: 333 outliers final: 244 residues processed: 1410 average time/residue: 1.3524 time to fit residues: 3230.6854 Evaluate side-chains 1437 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1171 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 51 GLU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 36 ASN Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 123 GLU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 45 GLU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 42 LYS Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 49 ARG Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 19 HIS Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 46 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 28 ARG Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain Z residue 62 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 337 optimal weight: 9.9990 chunk 902 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 588 optimal weight: 30.0000 chunk 247 optimal weight: 10.0000 chunk 1003 optimal weight: 0.1980 chunk 832 optimal weight: 7.9990 chunk 464 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 526 optimal weight: 8.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN k 29 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 107 ASN o 38 GLN ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN E 27 ASN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS N 125 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 160398 Z= 0.247 Angle : 0.705 18.587 240036 Z= 0.357 Chirality : 0.038 0.287 30699 Planarity : 0.005 0.085 12823 Dihedral : 24.118 174.054 80471 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.18 % Favored : 84.66 % Rotamer: Outliers : 7.56 % Allowed : 27.01 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.61 (0.10), residues: 5783 helix: -1.67 (0.12), residues: 1528 sheet: -2.37 (0.16), residues: 860 loop : -2.87 (0.10), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP q 60 HIS 0.010 0.001 HIS E 30 PHE 0.020 0.002 PHE z 52 TYR 0.026 0.002 TYR q 75 ARG 0.013 0.001 ARG p 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1540 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 1177 time to evaluate : 6.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7195 (mm) REVERT: b 113 ASP cc_start: 0.8837 (t70) cc_final: 0.8420 (t0) REVERT: b 162 GLN cc_start: 0.7921 (tt0) cc_final: 0.7709 (mt0) REVERT: b 180 MET cc_start: 0.7207 (ptp) cc_final: 0.6907 (ptp) REVERT: b 247 TRP cc_start: 0.7807 (m-90) cc_final: 0.7143 (m-90) REVERT: d 144 GLU cc_start: 0.6784 (tp30) cc_final: 0.6434 (tp30) REVERT: e 14 LYS cc_start: 0.8576 (tttt) cc_final: 0.7759 (ptpp) REVERT: e 16 MET cc_start: 0.2955 (tpt) cc_final: 0.2158 (mmm) REVERT: e 37 MET cc_start: 0.5116 (tpt) cc_final: 0.4725 (tpt) REVERT: e 98 PHE cc_start: 0.8469 (t80) cc_final: 0.8149 (t80) REVERT: f 166 GLU cc_start: 0.7079 (tt0) cc_final: 0.6673 (tt0) REVERT: i 71 LYS cc_start: 0.6628 (mmmt) cc_final: 0.6297 (mmmt) REVERT: i 108 ILE cc_start: -0.0287 (OUTLIER) cc_final: -0.0672 (mm) REVERT: k 116 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7151 (tp) REVERT: l 48 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7117 (mtm-85) REVERT: m 75 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: m 84 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7270 (tttt) REVERT: m 128 THR cc_start: 0.6826 (OUTLIER) cc_final: 0.6137 (t) REVERT: n 2 ARG cc_start: 0.7588 (mmm160) cc_final: 0.6865 (mtp-110) REVERT: n 45 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7179 (ttp-170) REVERT: n 90 ARG cc_start: 0.7551 (mmt90) cc_final: 0.7252 (mmm-85) REVERT: o 29 HIS cc_start: 0.8000 (t-170) cc_final: 0.7718 (t-170) REVERT: o 111 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.7957 (ptp-170) REVERT: q 108 LEU cc_start: 0.8642 (mt) cc_final: 0.8206 (mt) REVERT: r 62 GLU cc_start: 0.5076 (OUTLIER) cc_final: 0.4377 (pp20) REVERT: r 84 ARG cc_start: 0.7558 (ptp-110) cc_final: 0.7144 (ptp-110) REVERT: s 31 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7126 (tm-30) REVERT: s 67 ASP cc_start: 0.8369 (m-30) cc_final: 0.8096 (p0) REVERT: t 9 LYS cc_start: 0.8101 (mttt) cc_final: 0.7549 (tmmt) REVERT: t 76 ARG cc_start: 0.7731 (tpt-90) cc_final: 0.7328 (mmm160) REVERT: u 42 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6861 (mmtt) REVERT: v 79 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7223 (mmm160) REVERT: w 20 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8400 (mmtt) REVERT: w 21 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.7617 (mmm-85) REVERT: x 5 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: x 25 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7143 (mttm) REVERT: x 31 ASN cc_start: 0.7240 (t0) cc_final: 0.6994 (p0) REVERT: x 40 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8432 (tm-30) REVERT: z 46 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7729 (ttm) REVERT: z 55 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7866 (tptt) REVERT: C 31 GLU cc_start: 0.7963 (tp30) cc_final: 0.7720 (tp30) REVERT: C 38 PHE cc_start: 0.5969 (t80) cc_final: 0.5728 (t80) REVERT: D 14 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7344 (ttm170) REVERT: D 35 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7851 (mtm-85) REVERT: F 35 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6652 (mt0) REVERT: G 44 LYS cc_start: 0.7139 (pttm) cc_final: 0.6338 (pttm) REVERT: G 48 MET cc_start: 0.6882 (mtt) cc_final: 0.6365 (tmm) REVERT: G 135 MET cc_start: 0.8018 (ppp) cc_final: 0.7704 (ppp) REVERT: G 152 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7395 (p0) REVERT: H 17 TRP cc_start: 0.6987 (t-100) cc_final: 0.6287 (t-100) REVERT: H 79 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7515 (tptp) REVERT: H 178 ARG cc_start: 0.3649 (ttt180) cc_final: 0.3115 (tpp-160) REVERT: I 13 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7166 (tpp80) REVERT: I 62 ARG cc_start: 0.5672 (mtm110) cc_final: 0.5423 (mtm110) REVERT: I 72 ARG cc_start: 0.8306 (mtt180) cc_final: 0.7819 (mtt180) REVERT: I 186 GLU cc_start: 0.4259 (OUTLIER) cc_final: 0.3887 (tm-30) REVERT: J 18 ASN cc_start: 0.8217 (t0) cc_final: 0.7956 (t0) REVERT: J 22 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7443 (tppt) REVERT: J 51 LYS cc_start: 0.8166 (pttp) cc_final: 0.7834 (ptmt) REVERT: J 63 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8072 (mmm) REVERT: J 121 ASN cc_start: 0.6785 (t0) cc_final: 0.6530 (t0) REVERT: J 163 ILE cc_start: 0.8126 (mm) cc_final: 0.7783 (tp) REVERT: K 68 GLN cc_start: 0.7932 (mp10) cc_final: 0.7443 (pp30) REVERT: L 138 GLU cc_start: 0.9156 (tp30) cc_final: 0.8658 (tp30) REVERT: M 51 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7458 (tm-30) REVERT: M 57 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6782 (pm20) REVERT: M 86 LYS cc_start: 0.7702 (mppt) cc_final: 0.7413 (mmtm) REVERT: M 124 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6582 (mp) REVERT: N 12 LYS cc_start: 0.6717 (ttmt) cc_final: 0.6200 (tmtt) REVERT: N 87 MET cc_start: 0.5900 (mmm) cc_final: 0.5626 (mmm) REVERT: N 108 ARG cc_start: 0.6762 (mmt90) cc_final: 0.6480 (mmt90) REVERT: O 97 ASP cc_start: 0.6918 (m-30) cc_final: 0.6561 (m-30) REVERT: P 43 TRP cc_start: 0.8259 (p-90) cc_final: 0.7510 (p-90) REVERT: P 63 GLN cc_start: 0.7607 (tt0) cc_final: 0.6955 (tp40) REVERT: P 75 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6147 (tt0) REVERT: P 84 MET cc_start: 0.8022 (mmm) cc_final: 0.7671 (mmm) REVERT: Q 8 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7530 (ttm110) REVERT: Q 82 ARG cc_start: 0.4209 (ptt90) cc_final: 0.3891 (ptt180) REVERT: R 80 MET cc_start: 0.8283 (pmm) cc_final: 0.8064 (pmm) REVERT: S 19 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.4969 (m-80) REVERT: T 25 GLU cc_start: 0.8221 (pt0) cc_final: 0.7896 (pt0) REVERT: T 57 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.6568 (ttp-110) REVERT: T 63 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8391 (tpp-160) REVERT: V 25 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: V 42 LYS cc_start: 0.7884 (tttt) cc_final: 0.7641 (tttm) REVERT: V 74 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6638 (pp) REVERT: W 52 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7342 (ptp-170) REVERT: X 31 ARG cc_start: 0.5433 (mmt90) cc_final: 0.5094 (ptm160) REVERT: X 65 MET cc_start: 0.6625 (mmt) cc_final: 0.6366 (mmt) REVERT: Y 54 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6450 (tm-30) REVERT: Z 19 LYS cc_start: 0.8180 (mttt) cc_final: 0.7319 (mmtm) outliers start: 363 outliers final: 285 residues processed: 1388 average time/residue: 1.4818 time to fit residues: 3543.2177 Evaluate side-chains 1454 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1149 time to evaluate : 6.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 51 GLU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain f residue 176 LYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 45 GLU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 145 ASN Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 130 PHE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 42 LYS Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 19 HIS Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 46 MET Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 30 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain Z residue 62 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 967 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 571 optimal weight: 20.0000 chunk 732 optimal weight: 7.9990 chunk 567 optimal weight: 7.9990 chunk 844 optimal weight: 30.0000 chunk 560 optimal weight: 6.9990 chunk 999 optimal weight: 8.9990 chunk 625 optimal weight: 4.9990 chunk 609 optimal weight: 9.9990 chunk 461 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 128 ASN k 29 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 61 ASN ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN P 27 ASN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 160398 Z= 0.375 Angle : 0.870 17.530 240036 Z= 0.434 Chirality : 0.045 0.312 30699 Planarity : 0.006 0.116 12823 Dihedral : 24.489 171.739 80471 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 29.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 17.07 % Favored : 82.71 % Rotamer: Outliers : 8.06 % Allowed : 27.72 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.86 (0.10), residues: 5783 helix: -1.95 (0.12), residues: 1547 sheet: -2.57 (0.16), residues: 848 loop : -2.97 (0.10), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP q 60 HIS 0.038 0.002 HIS K 55 PHE 0.047 0.002 PHE v 26 TYR 0.043 0.003 TYR q 75 ARG 0.019 0.001 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1588 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 1201 time to evaluate : 6.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7128 (mm) REVERT: b 52 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7991 (t70) REVERT: b 113 ASP cc_start: 0.8924 (t70) cc_final: 0.8528 (t0) REVERT: b 131 MET cc_start: 0.8245 (mmm) cc_final: 0.7109 (mtt) REVERT: b 162 GLN cc_start: 0.7925 (tt0) cc_final: 0.7721 (mt0) REVERT: b 180 MET cc_start: 0.7178 (ptp) cc_final: 0.6969 (ptp) REVERT: b 247 TRP cc_start: 0.7809 (m-90) cc_final: 0.7125 (m-90) REVERT: c 55 LYS cc_start: 0.8087 (tppt) cc_final: 0.7554 (ttpt) REVERT: c 64 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7683 (mp0) REVERT: d 144 GLU cc_start: 0.6852 (tp30) cc_final: 0.6463 (tp30) REVERT: e 14 LYS cc_start: 0.8667 (tttt) cc_final: 0.7886 (ptpp) REVERT: e 16 MET cc_start: 0.2986 (tpt) cc_final: 0.2139 (tpt) REVERT: e 98 PHE cc_start: 0.8504 (t80) cc_final: 0.8132 (t80) REVERT: e 140 ILE cc_start: 0.7166 (mp) cc_final: 0.6904 (mt) REVERT: f 176 LYS cc_start: 0.5445 (OUTLIER) cc_final: 0.4966 (ptpt) REVERT: i 71 LYS cc_start: 0.6593 (mmmt) cc_final: 0.6280 (mmmt) REVERT: i 108 ILE cc_start: -0.0446 (OUTLIER) cc_final: -0.0829 (mm) REVERT: j 55 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7589 (pt) REVERT: j 64 VAL cc_start: 0.5981 (OUTLIER) cc_final: 0.5641 (m) REVERT: j 75 TYR cc_start: 0.6523 (m-80) cc_final: 0.6225 (m-80) REVERT: k 44 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8196 (mmtm) REVERT: m 75 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: m 84 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7009 (tttm) REVERT: n 2 ARG cc_start: 0.7605 (mmm160) cc_final: 0.6973 (mtp-110) REVERT: n 42 LYS cc_start: 0.8329 (tppt) cc_final: 0.7416 (tptm) REVERT: n 45 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7062 (ttp-170) REVERT: n 90 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7203 (mmm-85) REVERT: o 111 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.7985 (ptp-170) REVERT: p 54 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7286 (tp) REVERT: q 108 LEU cc_start: 0.8598 (mt) cc_final: 0.8328 (mt) REVERT: t 9 LYS cc_start: 0.8119 (mttt) cc_final: 0.7567 (tmmt) REVERT: t 15 HIS cc_start: 0.6224 (OUTLIER) cc_final: 0.5912 (t-90) REVERT: t 37 ASP cc_start: 0.8061 (t0) cc_final: 0.7803 (t0) REVERT: t 70 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6961 (t70) REVERT: u 81 ARG cc_start: 0.6381 (mpp80) cc_final: 0.5740 (mpp80) REVERT: w 20 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8407 (mmtt) REVERT: w 21 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.7640 (mmm-85) REVERT: w 64 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8266 (pttm) REVERT: x 5 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: x 61 LYS cc_start: 0.7071 (mttp) cc_final: 0.6804 (mmtp) REVERT: z 55 LYS cc_start: 0.8253 (tmtt) cc_final: 0.7918 (tptt) REVERT: B 52 LYS cc_start: 0.7779 (tptp) cc_final: 0.6444 (tptm) REVERT: C 38 PHE cc_start: 0.5958 (t80) cc_final: 0.5678 (t80) REVERT: D 19 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7214 (mtp85) REVERT: F 35 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: F 36 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7144 (ttt90) REVERT: G 48 MET cc_start: 0.6910 (mtt) cc_final: 0.6400 (tmm) REVERT: G 135 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7805 (ppp) REVERT: G 152 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7574 (p0) REVERT: H 79 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7533 (tptp) REVERT: H 178 ARG cc_start: 0.3642 (ttt180) cc_final: 0.2631 (tpp-160) REVERT: I 72 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8031 (ptp-170) REVERT: I 186 GLU cc_start: 0.4373 (OUTLIER) cc_final: 0.3921 (tm-30) REVERT: J 19 ARG cc_start: 0.6744 (ttt180) cc_final: 0.6466 (ttt180) REVERT: J 51 LYS cc_start: 0.8273 (pttp) cc_final: 0.7906 (ptmt) REVERT: J 63 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: J 121 ASN cc_start: 0.6855 (t0) cc_final: 0.6479 (t0) REVERT: J 163 ILE cc_start: 0.8185 (mm) cc_final: 0.7828 (tp) REVERT: K 58 HIS cc_start: 0.6970 (t70) cc_final: 0.6507 (t70) REVERT: K 68 GLN cc_start: 0.8021 (mp10) cc_final: 0.7595 (pp30) REVERT: L 138 GLU cc_start: 0.9232 (tp30) cc_final: 0.8756 (tp30) REVERT: M 51 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7681 (tm-30) REVERT: M 57 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6791 (pm20) REVERT: N 12 LYS cc_start: 0.6756 (ttmt) cc_final: 0.6295 (tmtt) REVERT: N 87 MET cc_start: 0.6227 (mmm) cc_final: 0.5988 (mmm) REVERT: N 108 ARG cc_start: 0.6815 (mmt90) cc_final: 0.6515 (mmt90) REVERT: O 97 ASP cc_start: 0.7015 (m-30) cc_final: 0.6678 (m-30) REVERT: P 43 TRP cc_start: 0.8323 (p-90) cc_final: 0.7646 (p-90) REVERT: P 52 ARG cc_start: 0.6233 (tpt170) cc_final: 0.5877 (tpt90) REVERT: P 63 GLN cc_start: 0.7793 (tt0) cc_final: 0.7074 (tp40) REVERT: Q 8 ARG cc_start: 0.8334 (mtm180) cc_final: 0.7513 (ttm110) REVERT: Q 61 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: Q 82 ARG cc_start: 0.4272 (ptt90) cc_final: 0.3978 (ptt180) REVERT: S 19 TYR cc_start: 0.6066 (OUTLIER) cc_final: 0.5105 (m-80) REVERT: S 40 ARG cc_start: 0.6081 (mmp80) cc_final: 0.5234 (ttp-170) REVERT: T 57 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.6597 (ttp-110) REVERT: U 12 LYS cc_start: 0.4865 (OUTLIER) cc_final: 0.3483 (mmmm) REVERT: U 56 ARG cc_start: 0.8134 (mmp-170) cc_final: 0.7699 (mmp80) REVERT: V 42 LYS cc_start: 0.7936 (tttt) cc_final: 0.7723 (tttm) REVERT: X 31 ARG cc_start: 0.5381 (mmt90) cc_final: 0.5060 (ptm160) REVERT: X 43 MET cc_start: 0.6528 (mtp) cc_final: 0.6254 (ptm) REVERT: X 65 MET cc_start: 0.6694 (mmt) cc_final: 0.6435 (mmt) REVERT: Y 54 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6461 (tm-30) REVERT: Z 19 LYS cc_start: 0.8097 (mttt) cc_final: 0.7282 (mmtm) outliers start: 387 outliers final: 302 residues processed: 1421 average time/residue: 1.3551 time to fit residues: 3275.3276 Evaluate side-chains 1485 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1162 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 176 ARG Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 51 GLU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 134 GLN Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 123 GLU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain f residue 176 LYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 45 GLU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 5 GLN Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 130 PHE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 19 HIS Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 41 TYR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain Z residue 62 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 618 optimal weight: 10.0000 chunk 399 optimal weight: 10.0000 chunk 596 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 635 optimal weight: 0.9990 chunk 680 optimal weight: 6.9990 chunk 494 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 785 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 29 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 ASN o 38 GLN q 36 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 160398 Z= 0.347 Angle : 0.825 17.278 240036 Z= 0.414 Chirality : 0.044 0.376 30699 Planarity : 0.006 0.090 12823 Dihedral : 24.555 172.264 80471 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 27.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 16.27 % Favored : 83.52 % Rotamer: Outliers : 7.54 % Allowed : 28.99 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.81 (0.10), residues: 5783 helix: -1.87 (0.12), residues: 1517 sheet: -2.55 (0.16), residues: 854 loop : -2.96 (0.10), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP q 60 HIS 0.009 0.002 HIS E 30 PHE 0.023 0.002 PHE c 118 TYR 0.028 0.002 TYR q 75 ARG 0.012 0.001 ARG a 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1181 time to evaluate : 6.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7211 (mm) REVERT: b 113 ASP cc_start: 0.8902 (t70) cc_final: 0.8488 (t0) REVERT: b 162 GLN cc_start: 0.7952 (tt0) cc_final: 0.7681 (mt0) REVERT: b 247 TRP cc_start: 0.7813 (m-90) cc_final: 0.7128 (m-90) REVERT: c 55 LYS cc_start: 0.8062 (tppt) cc_final: 0.7549 (ttpt) REVERT: c 64 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7651 (mp0) REVERT: e 16 MET cc_start: 0.2957 (tpt) cc_final: 0.2018 (tpt) REVERT: e 98 PHE cc_start: 0.8481 (t80) cc_final: 0.8116 (t80) REVERT: f 166 GLU cc_start: 0.6962 (tt0) cc_final: 0.6605 (tt0) REVERT: f 176 LYS cc_start: 0.5433 (OUTLIER) cc_final: 0.4814 (ptpt) REVERT: i 71 LYS cc_start: 0.6667 (mmmt) cc_final: 0.6292 (mmmt) REVERT: i 108 ILE cc_start: -0.0263 (OUTLIER) cc_final: -0.0616 (mm) REVERT: j 55 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7584 (pt) REVERT: j 75 TYR cc_start: 0.6571 (m-80) cc_final: 0.6273 (m-80) REVERT: k 1 MET cc_start: 0.4499 (ptt) cc_final: 0.3300 (ptt) REVERT: k 44 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8248 (mmtm) REVERT: m 75 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: m 84 LYS cc_start: 0.7698 (tmtt) cc_final: 0.7046 (tttm) REVERT: n 2 ARG cc_start: 0.7580 (mmm160) cc_final: 0.6901 (mtp-110) REVERT: n 45 ARG cc_start: 0.7838 (ttp-170) cc_final: 0.7020 (ttp-170) REVERT: n 90 ARG cc_start: 0.7548 (mmt90) cc_final: 0.7216 (mmm-85) REVERT: o 111 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7969 (ptp-170) REVERT: p 54 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7296 (tp) REVERT: q 60 TRP cc_start: 0.9122 (m-10) cc_final: 0.8864 (m-10) REVERT: q 108 LEU cc_start: 0.8575 (mt) cc_final: 0.8311 (mt) REVERT: s 31 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7512 (pp30) REVERT: t 9 LYS cc_start: 0.8111 (mttt) cc_final: 0.7554 (tmmt) REVERT: t 15 HIS cc_start: 0.6299 (OUTLIER) cc_final: 0.5952 (t-90) REVERT: t 37 ASP cc_start: 0.8048 (t0) cc_final: 0.7770 (t0) REVERT: t 70 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6957 (t70) REVERT: t 76 ARG cc_start: 0.7805 (tpt-90) cc_final: 0.7420 (mmm160) REVERT: u 81 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5646 (mpp80) REVERT: w 20 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8445 (mmtt) REVERT: w 21 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.7642 (mmm-85) REVERT: x 5 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6457 (tm-30) REVERT: x 61 LYS cc_start: 0.7071 (mttp) cc_final: 0.6657 (mttp) REVERT: z 53 MET cc_start: 0.7675 (mtt) cc_final: 0.7418 (mtt) REVERT: C 38 PHE cc_start: 0.5984 (t80) cc_final: 0.5701 (t80) REVERT: D 14 ARG cc_start: 0.7681 (ttm170) cc_final: 0.7426 (ttm170) REVERT: F 35 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7022 (mt0) REVERT: F 36 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7400 (ttt90) REVERT: G 48 MET cc_start: 0.6872 (mtt) cc_final: 0.6493 (tmm) REVERT: G 135 MET cc_start: 0.8042 (ppp) cc_final: 0.7752 (ppp) REVERT: G 142 LYS cc_start: 0.7461 (mmmt) cc_final: 0.7196 (mmtt) REVERT: G 152 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7506 (p0) REVERT: H 79 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7507 (tptp) REVERT: H 178 ARG cc_start: 0.3516 (ttt180) cc_final: 0.3187 (tpp-160) REVERT: I 96 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6779 (ttt180) REVERT: I 186 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.3584 (tm-30) REVERT: J 51 LYS cc_start: 0.8227 (pttp) cc_final: 0.7863 (ptmt) REVERT: J 63 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8094 (mmm) REVERT: J 121 ASN cc_start: 0.6861 (t0) cc_final: 0.6461 (t0) REVERT: J 144 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7516 (mp0) REVERT: J 163 ILE cc_start: 0.8166 (mm) cc_final: 0.7804 (tp) REVERT: K 58 HIS cc_start: 0.6873 (t70) cc_final: 0.6451 (t70) REVERT: K 68 GLN cc_start: 0.8055 (mp10) cc_final: 0.7575 (pp30) REVERT: L 138 GLU cc_start: 0.9254 (tp30) cc_final: 0.8738 (tp30) REVERT: M 51 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7746 (tm-30) REVERT: M 57 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6776 (pm20) REVERT: M 88 LYS cc_start: 0.7837 (tttt) cc_final: 0.7320 (ptmt) REVERT: N 12 LYS cc_start: 0.6727 (ttmt) cc_final: 0.6272 (tmtt) REVERT: N 59 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6575 (tmtt) REVERT: N 87 MET cc_start: 0.6174 (mmm) cc_final: 0.5954 (mmm) REVERT: N 108 ARG cc_start: 0.6786 (mmt90) cc_final: 0.6460 (mmt90) REVERT: P 43 TRP cc_start: 0.8315 (p-90) cc_final: 0.7601 (p-90) REVERT: P 63 GLN cc_start: 0.7730 (tt0) cc_final: 0.7019 (tp40) REVERT: Q 8 ARG cc_start: 0.8257 (mtm180) cc_final: 0.7419 (ttm110) REVERT: Q 82 ARG cc_start: 0.4285 (ptt90) cc_final: 0.3886 (ptt180) REVERT: S 19 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.5061 (m-80) REVERT: S 40 ARG cc_start: 0.6117 (mmp80) cc_final: 0.5204 (ttp-170) REVERT: T 25 GLU cc_start: 0.8296 (pt0) cc_final: 0.7971 (pt0) REVERT: T 57 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.6784 (ttp-170) REVERT: U 12 LYS cc_start: 0.4710 (OUTLIER) cc_final: 0.3356 (mmmm) REVERT: U 56 ARG cc_start: 0.8107 (mmp-170) cc_final: 0.7670 (mmp80) REVERT: W 52 ARG cc_start: 0.8272 (mtt90) cc_final: 0.7404 (ptp-170) REVERT: X 31 ARG cc_start: 0.5365 (mmt90) cc_final: 0.5028 (ptm160) REVERT: X 43 MET cc_start: 0.6492 (mtp) cc_final: 0.6283 (ptm) REVERT: X 65 MET cc_start: 0.6718 (mmt) cc_final: 0.6465 (mmt) REVERT: Y 17 ARG cc_start: 0.7952 (tpp80) cc_final: 0.7706 (tpp80) REVERT: Y 54 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6510 (tm-30) REVERT: Z 19 LYS cc_start: 0.8140 (mttt) cc_final: 0.7365 (mmtm) outliers start: 362 outliers final: 311 residues processed: 1389 average time/residue: 1.3475 time to fit residues: 3190.0966 Evaluate side-chains 1485 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1154 time to evaluate : 6.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain f residue 176 LYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 45 GLU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 21 TYR Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 5 GLN Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 130 PHE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 63 ARG Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 19 HIS Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 96 ARG Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 149 LYS Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain Z residue 62 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 909 optimal weight: 5.9990 chunk 957 optimal weight: 5.9990 chunk 873 optimal weight: 7.9990 chunk 931 optimal weight: 30.0000 chunk 560 optimal weight: 4.9990 chunk 405 optimal weight: 10.0000 chunk 731 optimal weight: 3.9990 chunk 285 optimal weight: 9.9990 chunk 841 optimal weight: 7.9990 chunk 880 optimal weight: 8.9990 chunk 928 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 29 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 160398 Z= 0.305 Angle : 0.795 17.597 240036 Z= 0.400 Chirality : 0.042 0.421 30699 Planarity : 0.006 0.084 12823 Dihedral : 24.575 172.501 80471 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.50 % Favored : 83.31 % Rotamer: Outliers : 7.54 % Allowed : 29.82 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.10), residues: 5783 helix: -1.88 (0.12), residues: 1530 sheet: -2.59 (0.16), residues: 870 loop : -2.91 (0.10), residues: 3383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP r 92 HIS 0.009 0.001 HIS X 68 PHE 0.031 0.002 PHE z 52 TYR 0.033 0.002 TYR W 50 ARG 0.016 0.001 ARG E 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1175 time to evaluate : 6.306 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 33 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7284 (mm) REVERT: b 96 LYS cc_start: 0.9072 (tptt) cc_final: 0.8713 (tppt) REVERT: b 113 ASP cc_start: 0.8870 (t70) cc_final: 0.8438 (t0) REVERT: b 131 MET cc_start: 0.8183 (mmm) cc_final: 0.6913 (mtt) REVERT: b 132 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7954 (ttp-110) REVERT: b 180 MET cc_start: 0.7130 (ptp) cc_final: 0.6446 (pmm) REVERT: b 247 TRP cc_start: 0.7781 (m-90) cc_final: 0.7106 (m-90) REVERT: c 11 MET cc_start: 0.5200 (ttm) cc_final: 0.2567 (mtm) REVERT: c 55 LYS cc_start: 0.8026 (tppt) cc_final: 0.7531 (ttpt) REVERT: c 64 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7708 (mp0) REVERT: d 144 GLU cc_start: 0.6844 (tp30) cc_final: 0.6488 (tp30) REVERT: e 16 MET cc_start: 0.2923 (tpt) cc_final: 0.2069 (tpt) REVERT: e 98 PHE cc_start: 0.8463 (t80) cc_final: 0.8088 (t80) REVERT: e 140 ILE cc_start: 0.7420 (mp) cc_final: 0.7219 (mt) REVERT: f 166 GLU cc_start: 0.7037 (tt0) cc_final: 0.6596 (tt0) REVERT: a 181 ASP cc_start: 0.7162 (t0) cc_final: 0.6881 (t0) REVERT: a 218 MET cc_start: 0.1187 (tmm) cc_final: 0.0878 (tmm) REVERT: i 71 LYS cc_start: 0.6713 (mmmt) cc_final: 0.6323 (mmmt) REVERT: i 108 ILE cc_start: -0.0305 (OUTLIER) cc_final: -0.0650 (mm) REVERT: j 55 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7593 (pt) REVERT: j 75 TYR cc_start: 0.6573 (m-80) cc_final: 0.6295 (m-80) REVERT: k 44 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8287 (mmtm) REVERT: k 116 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7186 (tp) REVERT: l 23 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8281 (tp) REVERT: m 75 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: m 84 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7035 (tttm) REVERT: n 2 ARG cc_start: 0.7599 (mmm160) cc_final: 0.6909 (mtp-110) REVERT: n 90 ARG cc_start: 0.7541 (mmt90) cc_final: 0.7208 (mmm-85) REVERT: o 111 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7946 (ptp-170) REVERT: q 60 TRP cc_start: 0.9092 (m-10) cc_final: 0.8810 (m-10) REVERT: q 108 LEU cc_start: 0.8534 (mt) cc_final: 0.8271 (mt) REVERT: r 31 GLU cc_start: 0.8117 (pt0) cc_final: 0.7820 (pm20) REVERT: s 31 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7462 (pp30) REVERT: s 88 ARG cc_start: 0.7208 (mmp-170) cc_final: 0.6465 (mmp-170) REVERT: t 9 LYS cc_start: 0.8094 (mttt) cc_final: 0.7549 (tmmt) REVERT: t 15 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.5909 (t-90) REVERT: t 37 ASP cc_start: 0.8040 (t0) cc_final: 0.7743 (t0) REVERT: t 70 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6930 (t70) REVERT: t 76 ARG cc_start: 0.7802 (tpt-90) cc_final: 0.7420 (mmm160) REVERT: u 81 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5684 (mpp80) REVERT: w 20 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8486 (mmtt) REVERT: w 21 ARG cc_start: 0.8322 (mmt-90) cc_final: 0.7742 (mmm-85) REVERT: x 5 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: x 31 ASN cc_start: 0.7282 (t0) cc_final: 0.6987 (p0) REVERT: x 61 LYS cc_start: 0.7078 (mttp) cc_final: 0.6752 (mttp) REVERT: y 8 GLU cc_start: 0.5203 (mm-30) cc_final: 0.4873 (mp0) REVERT: z 55 LYS cc_start: 0.8277 (tmtt) cc_final: 0.7970 (tptt) REVERT: C 38 PHE cc_start: 0.5974 (t80) cc_final: 0.5595 (t80) REVERT: D 14 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7406 (ttm170) REVERT: F 35 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: G 48 MET cc_start: 0.6869 (mtt) cc_final: 0.6521 (tmm) REVERT: G 135 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7713 (ppp) REVERT: G 152 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7490 (p0) REVERT: H 17 TRP cc_start: 0.7015 (t-100) cc_final: 0.6339 (t-100) REVERT: H 79 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7491 (tptp) REVERT: H 178 ARG cc_start: 0.3634 (ttt180) cc_final: 0.3300 (tpp-160) REVERT: I 72 ARG cc_start: 0.8369 (mtt180) cc_final: 0.8167 (ptp-170) REVERT: I 186 GLU cc_start: 0.4015 (OUTLIER) cc_final: 0.3572 (tm-30) REVERT: J 51 LYS cc_start: 0.8222 (pttp) cc_final: 0.7854 (ptmt) REVERT: J 121 ASN cc_start: 0.6882 (t0) cc_final: 0.6581 (t0) REVERT: J 144 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7538 (mp0) REVERT: J 163 ILE cc_start: 0.8220 (mm) cc_final: 0.7872 (tp) REVERT: K 58 HIS cc_start: 0.6899 (t70) cc_final: 0.6484 (t70) REVERT: K 68 GLN cc_start: 0.8042 (mp10) cc_final: 0.7583 (pp30) REVERT: K 90 MET cc_start: 0.7713 (ppp) cc_final: 0.7284 (ppp) REVERT: L 138 GLU cc_start: 0.9231 (tp30) cc_final: 0.8714 (tp30) REVERT: M 51 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7766 (tm-30) REVERT: M 57 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6759 (pm20) REVERT: M 88 LYS cc_start: 0.7921 (tttt) cc_final: 0.7450 (ptmt) REVERT: N 12 LYS cc_start: 0.6705 (ttmt) cc_final: 0.6271 (tmtt) REVERT: N 59 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6648 (tmtt) REVERT: N 87 MET cc_start: 0.6228 (mmm) cc_final: 0.5998 (mmm) REVERT: N 108 ARG cc_start: 0.6788 (mmt90) cc_final: 0.6467 (mmt90) REVERT: O 97 ASP cc_start: 0.7099 (m-30) cc_final: 0.6793 (m-30) REVERT: P 43 TRP cc_start: 0.8304 (p-90) cc_final: 0.7598 (p-90) REVERT: P 63 GLN cc_start: 0.7728 (tt0) cc_final: 0.7051 (tp40) REVERT: Q 8 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7884 (ptp-170) REVERT: Q 82 ARG cc_start: 0.4249 (ptt90) cc_final: 0.3826 (ptt180) REVERT: S 19 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5021 (m-80) REVERT: S 40 ARG cc_start: 0.6095 (mmp80) cc_final: 0.5157 (ttp-170) REVERT: T 57 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.6789 (ttp-170) REVERT: U 12 LYS cc_start: 0.4610 (OUTLIER) cc_final: 0.3474 (mmmm) REVERT: U 56 ARG cc_start: 0.8136 (mmp-170) cc_final: 0.7695 (mmp80) REVERT: V 42 LYS cc_start: 0.7873 (tttt) cc_final: 0.7673 (tttm) REVERT: X 31 ARG cc_start: 0.5342 (mmt90) cc_final: 0.5050 (ptm160) REVERT: Y 17 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7699 (tpp80) REVERT: Y 54 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6529 (tm-30) REVERT: Z 19 LYS cc_start: 0.8169 (mttt) cc_final: 0.7399 (mmtm) outliers start: 362 outliers final: 313 residues processed: 1385 average time/residue: 1.3602 time to fit residues: 3208.2926 Evaluate side-chains 1482 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1150 time to evaluate : 5.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 197 THR Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 51 GLU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 45 GLU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 9 ARG Chi-restraints excluded: chain a residue 21 TYR Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 5 GLN Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 130 PHE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 49 GLU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 63 ARG Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 108 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 62 ASP Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 61 LEU Chi-restraints excluded: chain t residue 70 HIS Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 81 ARG Chi-restraints excluded: chain u residue 88 ASP Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 75 PHE Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 5 GLN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 19 HIS Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 149 LYS Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 205 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 115 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 60 TRP Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 30 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain Z residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 611 optimal weight: 9.9990 chunk 984 optimal weight: 5.9990 chunk 601 optimal weight: 4.9990 chunk 467 optimal weight: 0.0870 chunk 684 optimal weight: 0.9990 chunk 1033 optimal weight: 0.0970 chunk 950 optimal weight: 0.0050 chunk 822 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 635 optimal weight: 4.9990 chunk 504 optimal weight: 2.9990 overall best weight: 0.8374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 167 ASN ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 62 GLN e 80 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN j 58 ASN j 128 ASN j 132 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS p 9 GLN q 36 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 11 GLN s 61 ASN ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN E 27 ASN G 121 GLN H 122 GLN I 39 GLN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 134 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN P 118 ASN ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN V 30 HIS ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 ASN X 55 GLN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 160398 Z= 0.153 Angle : 0.651 26.250 240036 Z= 0.327 Chirality : 0.035 0.324 30699 Planarity : 0.005 0.110 12823 Dihedral : 24.245 178.403 80469 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.14 % Favored : 87.79 % Rotamer: Outliers : 4.54 % Allowed : 32.82 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.25 (0.10), residues: 5783 helix: -1.31 (0.13), residues: 1506 sheet: -2.24 (0.17), residues: 849 loop : -2.64 (0.10), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 42 HIS 0.008 0.001 HIS p 76 PHE 0.021 0.002 PHE X 40 TYR 0.022 0.002 TYR q 75 ARG 0.013 0.001 ARG D 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11566 Ramachandran restraints generated. 5783 Oldfield, 0 Emsley, 5783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1195 time to evaluate : 6.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 113 ASP cc_start: 0.8741 (t70) cc_final: 0.8287 (t0) REVERT: b 132 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7933 (ttp-110) REVERT: b 180 MET cc_start: 0.7067 (ptp) cc_final: 0.6649 (ptp) REVERT: b 247 TRP cc_start: 0.7541 (m-90) cc_final: 0.6954 (m-90) REVERT: c 55 LYS cc_start: 0.7772 (tppt) cc_final: 0.7334 (ttpt) REVERT: c 88 GLU cc_start: 0.6331 (pm20) cc_final: 0.5622 (pp20) REVERT: d 19 PHE cc_start: 0.8427 (m-80) cc_final: 0.8061 (m-80) REVERT: d 78 TRP cc_start: 0.8786 (m-10) cc_final: 0.8537 (m-10) REVERT: d 188 MET cc_start: 0.7231 (tpt) cc_final: 0.6303 (tpt) REVERT: e 16 MET cc_start: 0.2686 (tpt) cc_final: 0.2067 (tpt) REVERT: e 62 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: e 95 MET cc_start: 0.5050 (tmm) cc_final: 0.4589 (tmm) REVERT: e 98 PHE cc_start: 0.8371 (t80) cc_final: 0.8033 (t80) REVERT: f 84 LYS cc_start: 0.7290 (mttt) cc_final: 0.6683 (tptt) REVERT: f 100 ASN cc_start: 0.9240 (p0) cc_final: 0.8776 (p0) REVERT: f 166 GLU cc_start: 0.6785 (tt0) cc_final: 0.6474 (tt0) REVERT: j 75 TYR cc_start: 0.6224 (m-80) cc_final: 0.5978 (m-80) REVERT: k 116 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6943 (tp) REVERT: l 23 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8025 (tp) REVERT: m 75 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: m 92 TRP cc_start: 0.7066 (m-10) cc_final: 0.6842 (m-10) REVERT: n 45 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.6955 (ttm170) REVERT: q 108 LEU cc_start: 0.8602 (mt) cc_final: 0.8199 (mt) REVERT: r 62 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4157 (pp20) REVERT: s 31 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7339 (pp30) REVERT: s 67 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7847 (p0) REVERT: t 9 LYS cc_start: 0.8051 (mttt) cc_final: 0.7458 (tmmt) REVERT: t 15 HIS cc_start: 0.6069 (OUTLIER) cc_final: 0.5771 (t-90) REVERT: t 37 ASP cc_start: 0.7853 (t0) cc_final: 0.7622 (t0) REVERT: t 76 ARG cc_start: 0.7733 (tpt-90) cc_final: 0.7376 (mmm160) REVERT: u 81 ARG cc_start: 0.5819 (mpp80) cc_final: 0.5297 (mpp80) REVERT: w 20 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8372 (mmtt) REVERT: w 21 ARG cc_start: 0.8395 (mmt-90) cc_final: 0.7839 (mmm-85) REVERT: x 25 LYS cc_start: 0.7405 (mmtt) cc_final: 0.7023 (mttm) REVERT: y 8 GLU cc_start: 0.5004 (mm-30) cc_final: 0.4801 (mp0) REVERT: y 25 GLN cc_start: 0.6557 (tp-100) cc_final: 0.6323 (tp40) REVERT: z 55 LYS cc_start: 0.8137 (tmtt) cc_final: 0.7856 (tptt) REVERT: z 56 VAL cc_start: 0.7096 (m) cc_final: 0.6720 (m) REVERT: C 38 PHE cc_start: 0.5837 (t80) cc_final: 0.5453 (t80) REVERT: D 19 ARG cc_start: 0.7419 (mtp180) cc_final: 0.7032 (mtp85) REVERT: F 35 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6366 (mt0) REVERT: G 44 LYS cc_start: 0.7165 (pttm) cc_final: 0.6529 (pttm) REVERT: G 48 MET cc_start: 0.6752 (mtt) cc_final: 0.6454 (tmm) REVERT: G 135 MET cc_start: 0.7926 (ppp) cc_final: 0.7669 (ppp) REVERT: H 17 TRP cc_start: 0.7012 (t-100) cc_final: 0.6275 (t-100) REVERT: H 178 ARG cc_start: 0.3524 (ttt180) cc_final: 0.3057 (tpp-160) REVERT: I 72 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8060 (ptp-170) REVERT: I 186 GLU cc_start: 0.4248 (OUTLIER) cc_final: 0.3923 (tm-30) REVERT: J 13 LYS cc_start: 0.7214 (tptt) cc_final: 0.6720 (tptp) REVERT: J 51 LYS cc_start: 0.8140 (pttp) cc_final: 0.7700 (ptmt) REVERT: J 96 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6384 (tt0) REVERT: J 104 ILE cc_start: 0.9362 (mp) cc_final: 0.9149 (mp) REVERT: J 121 ASN cc_start: 0.6694 (t0) cc_final: 0.6450 (t0) REVERT: J 163 ILE cc_start: 0.8137 (mm) cc_final: 0.7708 (tp) REVERT: K 58 HIS cc_start: 0.6899 (t70) cc_final: 0.6451 (t70) REVERT: K 68 GLN cc_start: 0.8016 (mp10) cc_final: 0.7412 (pp30) REVERT: K 90 MET cc_start: 0.7741 (ppp) cc_final: 0.7440 (ppp) REVERT: L 115 MET cc_start: 0.6834 (mmt) cc_final: 0.6532 (mtp) REVERT: L 138 GLU cc_start: 0.9091 (tp30) cc_final: 0.8660 (tp30) REVERT: M 26 MET cc_start: 0.5987 (ptm) cc_final: 0.5640 (pmm) REVERT: M 95 MET cc_start: 0.5344 (mmt) cc_final: 0.4964 (mmt) REVERT: N 12 LYS cc_start: 0.6628 (ttmt) cc_final: 0.6188 (tmtt) REVERT: N 87 MET cc_start: 0.5964 (mmm) cc_final: 0.5521 (mmm) REVERT: N 108 ARG cc_start: 0.6691 (mmt90) cc_final: 0.6457 (mmt90) REVERT: O 97 ASP cc_start: 0.7121 (m-30) cc_final: 0.6854 (m-30) REVERT: P 28 ASN cc_start: 0.7467 (t0) cc_final: 0.7020 (m110) REVERT: P 43 TRP cc_start: 0.8105 (p-90) cc_final: 0.7346 (p-90) REVERT: P 63 GLN cc_start: 0.7668 (tt0) cc_final: 0.7332 (tp40) REVERT: P 86 LYS cc_start: 0.6532 (pttm) cc_final: 0.6274 (pttp) REVERT: Q 87 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7481 (tmmt) REVERT: S 19 TYR cc_start: 0.5790 (OUTLIER) cc_final: 0.4658 (m-80) REVERT: S 41 TRP cc_start: 0.6982 (m-90) cc_final: 0.6467 (m100) REVERT: T 25 GLU cc_start: 0.8153 (pt0) cc_final: 0.7869 (pt0) REVERT: T 57 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.6660 (ttp-170) REVERT: U 56 ARG cc_start: 0.8039 (mmp-170) cc_final: 0.7692 (mmp80) REVERT: X 31 ARG cc_start: 0.5272 (mmt90) cc_final: 0.4976 (ptm160) REVERT: Y 5 SER cc_start: 0.8872 (m) cc_final: 0.8428 (p) REVERT: Y 32 LYS cc_start: 0.7644 (mppt) cc_final: 0.7393 (mmtm) REVERT: Z 19 LYS cc_start: 0.8124 (mttt) cc_final: 0.7452 (mmtm) outliers start: 218 outliers final: 172 residues processed: 1325 average time/residue: 1.3522 time to fit residues: 3030.0962 Evaluate side-chains 1315 residues out of total 4802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1132 time to evaluate : 6.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 90 PHE Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 133 GLU Chi-restraints excluded: chain e residue 142 TYR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 29 ASN Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 112 VAL Chi-restraints excluded: chain f residue 176 LYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 45 GLU Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 212 VAL Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 52 ASP Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 100 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 90 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 130 PHE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 19 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 103 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 66 HIS Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 15 HIS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain v residue 5 ASN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 49 PHE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 52 ASN Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 68 HIS Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 653 optimal weight: 0.2980 chunk 876 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 758 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 228 optimal weight: 10.0000 chunk 823 optimal weight: 8.9990 chunk 344 optimal weight: 20.0000 chunk 846 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 128 ASN k 5 GLN k 29 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS ** o 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 61 ASN ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN I 39 GLN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 95 HIS S 3 GLN ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN W 51 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.163974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.140624 restraints weight = 379507.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.143352 restraints weight = 170326.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144251 restraints weight = 84970.654| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 160398 Z= 0.330 Angle : 0.807 21.861 240036 Z= 0.402 Chirality : 0.042 0.401 30699 Planarity : 0.006 0.122 12823 Dihedral : 24.440 173.397 80469 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.68 % Favored : 84.13 % Rotamer: Outliers : 5.00 % Allowed : 32.90 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.50 (0.10), residues: 5783 helix: -1.48 (0.13), residues: 1523 sheet: -2.45 (0.16), residues: 883 loop : -2.79 (0.10), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRP q 60 HIS 0.010 0.002 HIS X 51 PHE 0.029 0.002 PHE z 52 TYR 0.039 0.003 TYR I 74 ARG 0.018 0.001 ARG m 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43054.74 seconds wall clock time: 751 minutes 10.24 seconds (45070.24 seconds total)