Starting phenix.real_space_refine on Tue Mar 26 03:46:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss9_25405/03_2024/7ss9_25405.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss9_25405/03_2024/7ss9_25405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss9_25405/03_2024/7ss9_25405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss9_25405/03_2024/7ss9_25405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss9_25405/03_2024/7ss9_25405.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ss9_25405/03_2024/7ss9_25405.pdb" } resolution = 3.9 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= 0.114 sd= 0.809 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 156 5.16 5 C 75515 2.51 5 N 27871 2.21 5 O 41534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "8 ASP 442": "OD1" <-> "OD2" Residue "8 GLU 451": "OE1" <-> "OE2" Residue "8 ASP 471": "OD1" <-> "OD2" Residue "8 GLU 476": "OE1" <-> "OE2" Residue "8 PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 495": "NH1" <-> "NH2" Residue "8 GLU 502": "OE1" <-> "OE2" Residue "8 ARG 512": "NH1" <-> "NH2" Residue "8 GLU 535": "OE1" <-> "OE2" Residue "8 GLU 559": "OE1" <-> "OE2" Residue "8 ARG 577": "NH1" <-> "NH2" Residue "8 PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 585": "OD1" <-> "OD2" Residue "8 PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 622": "OE1" <-> "OE2" Residue "8 ASP 630": "OD1" <-> "OD2" Residue "8 ARG 637": "NH1" <-> "NH2" Residue "8 PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 671": "NH1" <-> "NH2" Residue "8 ARG 677": "NH1" <-> "NH2" Residue "8 TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 688": "OD1" <-> "OD2" Residue "b GLU 34": "OE1" <-> "OE2" Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b ASP 263": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 89": "OE1" <-> "OE2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "c ASP 200": "OD1" <-> "OD2" Residue "d GLU 2": "OE1" <-> "OE2" Residue "d GLU 16": "OE1" <-> "OE2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 91": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 116": "OD1" <-> "OD2" Residue "d PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 144": "OE1" <-> "OE2" Residue "d ASP 145": "OD1" <-> "OD2" 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 GLU 197": "OE1" <-> "OE2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 100": "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 ARG 132": "NH1" <-> "NH2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f ASP 113": "OD1" <-> "OD2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ASP 146": "OD1" <-> "OD2" Residue "f TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g ASP 17": "OD1" <-> "OD2" Residue "g PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 55": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 76": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 13": "OE1" <-> "OE2" Residue "a ASP 22": "OD1" <-> "OD2" 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 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 181": "OD1" <-> "OD2" Residue "a GLU 187": "OE1" <-> "OE2" Residue "i TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 115": "OD1" <-> "OD2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 49": "OD1" <-> "OD2" Residue "j TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k ASP 37": "OD1" <-> "OD2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k ASP 56": "OD1" <-> "OD2" Residue "k GLU 92": "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 GLU 51": "OE1" <-> "OE2" Residue "l TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ASP 81": "OD1" <-> "OD2" Residue "l GLU 86": "OE1" <-> "OE2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" 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 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 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 96": "NH1" <-> "NH2" 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 ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ASP 23": "OD1" <-> "OD2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" 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 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" 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 "s ASP 22": "OD1" <-> "OD2" Residue "s ASP 77": "OD1" <-> "OD2" 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 GLU 42": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 17": "OD1" <-> "OD2" Residue "u GLU 61": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u GLU 100": "OE1" <-> "OE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "v PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 25": "OE1" <-> "OE2" Residue "x PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 5": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" 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 ARG 51": "NH1" <-> "NH2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "E TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 40": "OD1" <-> "OD2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "K ASP 13": "OD1" <-> "OD2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "R ASP 10": "OD1" <-> "OD2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "S ASP 37": "OD1" <-> "OD2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T ASP 20": "OD1" <-> "OD2" Residue "T PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 48": "OD1" <-> "OD2" Residue "T ASP 67": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 69": "OD1" <-> "OD2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "X PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 14": "OE1" <-> "OE2" Residue "Y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 52": "OE1" <-> "OE2" Residue "Z PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 149808 Number of models: 1 Model: "" Number of chains: 57 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': 101, 'rna2p_pyr': 61, 'rna3p_pur': 773, 'rna3p_pyr': 604} Link IDs: {'rna2p': 162, 'rna3p': 1376} 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': 232, 'rna2p_pyr': 105, 'rna3p_pur': 1442, 'rna3p_pyr': 1124} Link IDs: {'rna2p': 337, 'rna3p': 2565} 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': 3, 'rna3p_pur': 60, 'rna3p_pyr': 52} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "8" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2213 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} 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: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} 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: 57.15, per 1000 atoms: 0.38 Number of scatterers: 149808 At special positions: 0 Unit cell: (270.462, 253.92, 243.167, 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 156 16.00 P 4732 15.00 O 41534 8.00 N 27871 7.00 C 75515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 14 " distance=2.03 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 27 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.33 Conformation dependent library (CDL) restraints added in 8.3 seconds 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11328 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 80 sheets defined 30.7% alpha, 14.6% beta 823 base pairs and 2455 stacking pairs defined. Time for finding SS restraints: 47.80 Creating SS restraints... Processing helix chain '8' and resid 426 through 429 Processing helix chain '8' and resid 430 through 438 removed outlier: 4.292A pdb=" N ALA 8 434 " --> pdb=" O LYS 8 430 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU 8 435 " --> pdb=" O MET 8 431 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY 8 436 " --> pdb=" O GLY 8 432 " (cutoff:3.500A) Processing helix chain '8' and resid 462 through 476 removed outlier: 3.641A pdb=" N LEU 8 466 " --> pdb=" O GLY 8 462 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP 8 467 " --> pdb=" O GLU 8 463 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE 8 468 " --> pdb=" O LEU 8 464 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL 8 470 " --> pdb=" O LEU 8 466 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG 8 472 " --> pdb=" O ILE 8 468 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET 8 473 " --> pdb=" O ILE 8 469 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG 8 475 " --> pdb=" O ASP 8 471 " (cutoff:3.500A) Processing helix chain '8' and resid 530 through 534 removed outlier: 4.182A pdb=" N TYR 8 534 " --> pdb=" O PRO 8 531 " (cutoff:3.500A) Processing helix chain '8' and resid 551 through 559 removed outlier: 3.664A pdb=" N GLU 8 559 " --> pdb=" O LYS 8 555 " (cutoff:3.500A) Processing helix chain '8' and resid 560 through 562 No H-bonds generated for 'chain '8' and resid 560 through 562' Processing helix chain '8' and resid 591 through 604 removed outlier: 3.658A pdb=" N SER 8 598 " --> pdb=" O LYS 8 594 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA 8 600 " --> pdb=" O ALA 8 596 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE 8 601 " --> pdb=" O ALA 8 597 " (cutoff:3.500A) Processing helix chain '8' and resid 605 through 609 removed outlier: 4.175A pdb=" N ALA 8 608 " --> pdb=" O PHE 8 605 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS 8 609 " --> pdb=" O LYS 8 606 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 605 through 609' Processing helix chain '8' and resid 627 through 632 removed outlier: 3.549A pdb=" N VAL 8 631 " --> pdb=" O ASN 8 627 " (cutoff:3.500A) Processing helix chain '8' and resid 659 through 663 removed outlier: 4.181A pdb=" N GLU 8 662 " --> pdb=" O PRO 8 659 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 33 removed outlier: 4.150A pdb=" N LEU b 32 " --> pdb=" O PHE b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 201 removed outlier: 4.309A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 262 through 266 removed outlier: 3.556A pdb=" N ILE b 266 " --> pdb=" O ASP b 263 " (cutoff:3.500A) Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'c' and resid 61 through 70 removed outlier: 4.313A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 103 removed outlier: 3.569A pdb=" N ALA c 102 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 37 removed outlier: 3.965A pdb=" N VAL d 28 " --> pdb=" O ASN d 24 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL d 32 " --> pdb=" O VAL d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 40 No H-bonds generated for 'chain 'd' and resid 38 through 40' Processing helix chain 'd' and resid 97 through 112 removed outlier: 3.759A pdb=" N ARG d 102 " --> pdb=" O LYS d 98 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER d 107 " --> pdb=" O GLY d 103 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER d 110 " --> pdb=" O LYS d 106 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 140 removed outlier: 4.022A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 161 Processing helix chain 'd' and resid 177 through 183 removed outlier: 3.666A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA d 182 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 177 through 183' Processing helix chain 'd' and resid 189 through 200 Processing helix chain 'e' and resid 3 through 20 removed outlier: 4.117A pdb=" N ASP e 9 " --> pdb=" O ASP e 5 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 27 Processing helix chain 'e' and resid 47 through 60 removed outlier: 3.512A pdb=" N ASN e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP e 55 " --> pdb=" O ASN e 51 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA e 58 " --> pdb=" O ALA e 54 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 105 removed outlier: 3.811A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 110 Processing helix chain 'e' and resid 161 through 171 Processing helix chain 'f' and resid 2 through 6 Processing helix chain 'f' and resid 59 through 64 Processing helix chain 'f' and resid 66 through 78 removed outlier: 4.177A pdb=" N LEU f 71 " --> pdb=" O ALA f 67 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 138 through 149 removed outlier: 3.770A pdb=" N GLN f 142 " --> pdb=" O GLN f 138 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 30 removed outlier: 3.651A pdb=" N ASN g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU g 30 " --> pdb=" O ALA g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.530A pdb=" N ILE g 44 " --> pdb=" O THR g 40 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE g 46 " --> pdb=" O LYS g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.507A pdb=" N VAL g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 105 removed outlier: 3.574A pdb=" N VAL g 103 " --> pdb=" O ILE g 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 13 removed outlier: 3.903A pdb=" N GLU a 13 " --> pdb=" O ARG a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 34 removed outlier: 3.889A pdb=" N GLU a 32 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU a 33 " --> pdb=" O LEU a 30 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA a 34 " --> pdb=" O LYS a 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 29 through 34' Processing helix chain 'a' and resid 54 through 58 removed outlier: 3.692A pdb=" N GLN a 57 " --> pdb=" O LYS a 54 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN a 58 " --> pdb=" O SER a 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 54 through 58' Processing helix chain 'a' and resid 181 through 183 No H-bonds generated for 'chain 'a' and resid 181 through 183' Processing helix chain 'a' and resid 184 through 197 removed outlier: 3.866A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 29 removed outlier: 4.148A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 43 removed outlier: 3.629A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 83 removed outlier: 3.713A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 95 Processing helix chain 'i' and resid 102 through 106 Processing helix chain 'i' and resid 107 through 112 removed outlier: 4.150A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 125 Processing helix chain 'i' and resid 125 through 133 removed outlier: 4.220A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 37 removed outlier: 3.823A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG j 34 " --> pdb=" O THR j 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG j 35 " --> pdb=" O GLU j 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 95 Processing helix chain 'j' and resid 98 through 107 removed outlier: 3.849A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE j 103 " --> pdb=" O ARG j 99 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA j 104 " --> pdb=" O VAL j 100 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY j 107 " --> pdb=" O ILE j 103 " (cutoff:3.500A) Processing helix chain 'k' and resid 113 through 118 removed outlier: 3.730A pdb=" N SER k 117 " --> pdb=" O MET k 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 6 removed outlier: 3.877A pdb=" N THR l 5 " --> pdb=" O ARG l 2 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU l 6 " --> pdb=" O LEU l 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 2 through 6' Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.838A pdb=" N ARG l 41 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 60 Processing helix chain 'l' and resid 129 through 138 removed outlier: 3.581A pdb=" N ALA l 134 " --> pdb=" O GLY l 130 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE l 135 " --> pdb=" O ALA l 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU l 136 " --> pdb=" O ARG l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 55 removed outlier: 4.404A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 117 removed outlier: 3.827A pdb=" N GLU m 115 " --> pdb=" O GLU m 111 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE m 117 " --> pdb=" O ALA m 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 117 through 122 removed outlier: 4.445A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 25 removed outlier: 3.819A pdb=" N GLN n 18 " --> pdb=" O SER n 14 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE n 21 " --> pdb=" O ARG n 17 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA n 25 " --> pdb=" O PHE n 21 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 49 removed outlier: 3.945A pdb=" N GLU n 43 " --> pdb=" O PRO n 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 54 removed outlier: 3.819A pdb=" N LEU n 54 " --> pdb=" O PRO n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 60 through 69 removed outlier: 3.547A 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 'n' and resid 83 through 87 Processing helix chain 'o' and resid 3 through 21 removed outlier: 3.627A pdb=" N ILE o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR o 12 " --> pdb=" O ILE o 8 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.662A pdb=" N GLU o 60 " --> pdb=" O LYS o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 84 removed outlier: 3.727A pdb=" N ALA o 73 " --> pdb=" O ASP o 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 113 removed outlier: 3.834A pdb=" N ALA o 105 " --> pdb=" O GLY o 101 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA o 110 " --> pdb=" O LEU o 106 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 9 removed outlier: 3.795A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 97 through 101 removed outlier: 3.889A pdb=" N ARG p 100 " --> pdb=" O TYR p 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 19 removed outlier: 3.676A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS q 13 " --> pdb=" O ALA q 9 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS q 14 " --> pdb=" O ARG q 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS q 15 " --> pdb=" O ALA q 11 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 removed outlier: 3.553A pdb=" N ARG q 27 " --> pdb=" O TYR q 24 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER q 28 " --> pdb=" O GLY q 25 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG q 29 " --> pdb=" O ALA q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 24 through 29' Processing helix chain 'q' and resid 31 through 70 removed outlier: 4.061A pdb=" N ILE q 39 " --> pdb=" O PHE q 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR q 44 " --> pdb=" O LYS q 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA q 62 " --> pdb=" O GLN q 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG q 63 " --> pdb=" O LEU q 59 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE q 64 " --> pdb=" O TRP q 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG q 69 " --> pdb=" O ASN q 65 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN q 70 " --> pdb=" O ALA q 66 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 83 removed outlier: 3.556A pdb=" N ASN q 80 " --> pdb=" O SER q 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 99 Processing helix chain 'q' and resid 101 through 117 removed outlier: 3.726A pdb=" N ALA q 107 " --> pdb=" O VAL q 103 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 18 Processing helix chain 's' and resid 31 through 36 Processing helix chain 's' and resid 37 through 39 No H-bonds generated for 'chain 's' and resid 37 through 39' Processing helix chain 's' and resid 42 through 56 removed outlier: 3.574A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL s 47 " --> pdb=" O ALA s 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE s 55 " --> pdb=" O LEU s 51 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 8 removed outlier: 3.741A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 28 removed outlier: 3.563A pdb=" N THR t 22 " --> pdb=" O GLU t 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET t 24 " --> pdb=" O ALA t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 removed outlier: 4.157A pdb=" N GLN t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 14 through 18 removed outlier: 4.144A pdb=" N LYS u 18 " --> pdb=" O GLY u 15 " (cutoff:3.500A) Processing helix chain 'v' and resid 14 through 22 Processing helix chain 'v' and resid 44 through 48 removed outlier: 3.822A pdb=" N MET v 48 " --> pdb=" O HIS v 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 44 through 48' Processing helix chain 'v' and resid 53 through 58 removed outlier: 3.631A pdb=" N PHE v 56 " --> pdb=" O LYS v 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 52 through 59 removed outlier: 3.516A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 73 removed outlier: 3.655A pdb=" N GLU x 69 " --> pdb=" O THR x 65 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG x 71 " --> pdb=" O LEU x 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 6 removed outlier: 3.541A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 2 through 6' Processing helix chain 'y' and resid 9 through 22 removed outlier: 3.690A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU y 22 " --> pdb=" O LEU y 18 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 35 removed outlier: 3.921A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 removed outlier: 4.173A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN y 45 " --> pdb=" O HIS y 41 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG y 47 " --> pdb=" O LEU y 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS y 54 " --> pdb=" O VAL y 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR y 55 " --> pdb=" O ALA y 51 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.585A pdb=" N ALA z 21 " --> pdb=" O PRO z 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU z 24 " --> pdb=" O LYS z 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 50 removed outlier: 3.535A pdb=" N GLY z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'D' and resid 9 through 14 removed outlier: 3.532A pdb=" N ARG D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 29 through 36 Processing helix chain 'E' and resid 6 through 11 removed outlier: 4.251A pdb=" N ALA E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 6 through 11' Processing helix chain 'E' and resid 36 through 42 removed outlier: 3.865A pdb=" N HIS E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 removed outlier: 4.138A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.798A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 Processing helix chain 'G' and resid 44 through 61 removed outlier: 3.669A pdb=" N MET G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN G 50 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA G 52 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 54 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 102 through 123 removed outlier: 3.994A pdb=" N VAL G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.659A pdb=" N THR G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 205 through 221 removed outlier: 3.599A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 10 removed outlier: 4.040A pdb=" N ILE H 9 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 5 through 10' Processing helix chain 'H' and resid 27 through 46 removed outlier: 3.922A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU H 32 " --> pdb=" O PHE H 28 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.950A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE H 76 " --> pdb=" O PRO H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 86 Processing helix chain 'H' and resid 86 through 94 removed outlier: 4.254A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.624A pdb=" N ALA H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 142 removed outlier: 3.925A pdb=" N ALA H 132 " --> pdb=" O MET H 128 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.146A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.695A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS I 57 " --> pdb=" O GLN I 53 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG I 62 " --> pdb=" O GLN I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 80 removed outlier: 3.586A pdb=" N PHE I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 94 removed outlier: 3.829A pdb=" N ASN I 88 " --> pdb=" O ASN I 84 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 removed outlier: 4.911A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 116 removed outlier: 3.523A pdb=" N GLN I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 160 removed outlier: 3.638A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 164 removed outlier: 3.962A pdb=" N ARG I 164 " --> pdb=" O ALA I 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 164' Processing helix chain 'I' and resid 196 through 203 removed outlier: 4.019A pdb=" N VAL I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 63 removed outlier: 3.505A pdb=" N ALA J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 118 removed outlier: 3.732A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 removed outlier: 4.236A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 138 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR J 139 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN J 145 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.784A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 164 Processing helix chain 'K' and resid 12 through 17 removed outlier: 5.061A pdb=" N GLU K 16 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 50 through 54 removed outlier: 3.831A pdb=" N LYS K 53 " --> pdb=" O PRO K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 4.720A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 4.113A pdb=" N ALA L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 47 removed outlier: 3.787A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA L 45 " --> pdb=" O ILE L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 63 removed outlier: 3.589A pdb=" N ALA L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 108 removed outlier: 4.073A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA L 106 " --> pdb=" O TRP L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 123 removed outlier: 3.563A pdb=" N LEU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 147 removed outlier: 3.554A pdb=" N ASP L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.640A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG M 12 " --> pdb=" O ASP M 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE M 13 " --> pdb=" O MET M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.555A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 119 Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.911A pdb=" N TYR N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 33 through 38' Processing helix chain 'N' and resid 44 through 53 removed outlier: 4.237A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.167A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 85 removed outlier: 3.696A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS N 80 " --> pdb=" O GLY N 76 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 99 removed outlier: 3.577A pdb=" N ARG N 94 " --> pdb=" O ASP N 90 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 removed outlier: 3.779A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR O 22 " --> pdb=" O ILE O 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 88 removed outlier: 3.887A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 57 Processing helix chain 'P' and resid 58 through 72 removed outlier: 3.873A pdb=" N ALA P 62 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL P 64 " --> pdb=" O PHE P 60 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.728A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 102 Processing helix chain 'Q' and resid 3 through 8 removed outlier: 3.924A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 18 removed outlier: 4.133A pdb=" N LEU R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 21 No H-bonds generated for 'chain 'R' and resid 19 through 21' Processing helix chain 'R' and resid 25 through 36 removed outlier: 3.775A pdb=" N ILE R 32 " --> pdb=" O ARG R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 60 removed outlier: 3.574A pdb=" N VAL R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 55 through 60' Processing helix chain 'R' and resid 64 through 81 removed outlier: 3.624A pdb=" N LEU R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP R 81 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.573A pdb=" N LEU R 88 " --> pdb=" O CYS R 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG R 91 " --> pdb=" O GLY R 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 17 removed outlier: 3.864A pdb=" N GLU S 9 " --> pdb=" O MET S 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP S 17 " --> pdb=" O VAL S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 removed outlier: 3.850A pdb=" N ILE S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 47 removed outlier: 3.715A pdb=" N LEU S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 59 removed outlier: 3.809A pdb=" N GLN S 59 " --> pdb=" O PRO S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 88 removed outlier: 4.024A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.615A pdb=" N ALA T 8 " --> pdb=" O THR T 4 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE T 14 " --> pdb=" O ILE T 10 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY T 15 " --> pdb=" O VAL T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 41 removed outlier: 3.770A pdb=" N ALA T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU T 31 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR T 32 " --> pdb=" O VAL T 28 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 44 No H-bonds generated for 'chain 'T' and resid 42 through 44' Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.595A pdb=" N ARG T 52 " --> pdb=" O ASP T 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET T 58 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU T 66 " --> pdb=" O ARG T 62 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 removed outlier: 3.553A pdb=" N LEU T 80 " --> pdb=" O ARG T 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 removed outlier: 3.758A pdb=" N TRP U 60 " --> pdb=" O ARG U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 78 Processing helix chain 'W' and resid 24 through 29 Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 60 removed outlier: 3.727A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA W 57 " --> pdb=" O GLN W 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 22 removed outlier: 3.870A pdb=" N LYS X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 41 removed outlier: 4.012A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA Y 16 " --> pdb=" O GLN Y 12 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 52 removed outlier: 4.244A pdb=" N ASN Y 51 " --> pdb=" O GLN Y 47 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 69 through 86 removed outlier: 3.682A pdb=" N ASN Y 77 " --> pdb=" O ARG Y 73 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA Y 80 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.053A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 44 removed outlier: 3.645A pdb=" N THR Z 42 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG Z 44 " --> pdb=" O PRO Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 49 Processing helix chain 'Z' and resid 52 through 59 Processing sheet with id=AA1, first strand: chain '8' and resid 417 through 418 Processing sheet with id=AA2, first strand: chain '8' and resid 492 through 493 removed outlier: 7.464A pdb=" N LEU 8 612 " --> pdb=" O GLU 8 689 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU 8 689 " --> pdb=" O LEU 8 612 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU 8 614 " --> pdb=" O TYR 8 687 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR 8 687 " --> pdb=" O GLU 8 614 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE 8 616 " --> pdb=" O LEU 8 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '8' and resid 505 through 507 Processing sheet with id=AA4, first strand: chain '8' and resid 621 through 623 removed outlier: 3.524A pdb=" N VAL 8 652 " --> pdb=" O THR 8 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 2 through 4 removed outlier: 4.167A pdb=" N VAL b 3 " --> pdb=" O LYS b 17 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS b 17 " --> pdb=" O VAL b 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'b' and resid 101 through 104 removed outlier: 3.841A pdb=" N ILE b 103 " --> pdb=" O ALA b 91 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'c' and resid 170 through 171 removed outlier: 4.013A pdb=" N GLY c 6 " --> pdb=" O LEU c 201 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL c 26 " --> pdb=" O GLY c 10 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 79 through 82 removed outlier: 6.636A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 115 through 118 Processing sheet with id=AB2, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AB3, first strand: chain 'd' and resid 118 through 120 Processing sheet with id=AB4, first strand: chain 'e' and resid 65 through 68 removed outlier: 3.813A pdb=" N LEU e 65 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN e 36 " --> pdb=" O ASP e 152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 18 through 19 removed outlier: 3.663A pdb=" N ASN f 19 " --> pdb=" O VAL f 22 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL f 22 " --> pdb=" O ASN f 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE f 23 " --> pdb=" O ARG f 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 40 through 43 Processing sheet with id=AB7, first strand: chain 'f' and resid 82 through 85 removed outlier: 6.853A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'f' and resid 88 through 89 Processing sheet with id=AB9, first strand: chain 'f' and resid 94 through 97 removed outlier: 3.671A pdb=" N LEU f 104 " --> pdb=" O VAL f 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL f 112 " --> pdb=" O LEU f 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'g' and resid 19 through 20 removed outlier: 3.621A pdb=" N ILE g 4 " --> pdb=" O VAL g 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 77 through 82 removed outlier: 3.562A pdb=" N VAL g 78 " --> pdb=" O ILE g 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 43 through 45 Processing sheet with id=AC4, first strand: chain 'a' and resid 62 through 63 removed outlier: 4.039A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'i' and resid 8 through 10 removed outlier: 4.282A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE i 58 " --> pdb=" O VAL i 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU i 10 " --> pdb=" O VAL i 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'i' and resid 99 through 101 removed outlier: 3.749A pdb=" N ILE i 100 " --> pdb=" O VAL i 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'j' and resid 122 through 124 removed outlier: 7.118A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'j' and resid 75 through 77 removed outlier: 3.501A pdb=" N HIS j 76 " --> pdb=" O LYS j 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.716A pdb=" N THR k 42 " --> pdb=" O MET k 20 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.785A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE k 77 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE p 58 " --> pdb=" O PHE p 73 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA p 57 " --> pdb=" O ILE p 49 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE p 49 " --> pdb=" O ALA p 57 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR p 59 " --> pdb=" O ILE p 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 74 through 77 removed outlier: 7.248A pdb=" N ALA l 108 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AD4, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.315A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'm' and resid 40 through 42 removed outlier: 3.527A pdb=" N ASN m 88 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU m 90 " --> pdb=" O ILE m 73 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 33 through 37 removed outlier: 3.632A pdb=" N ILE n 34 " --> pdb=" O ILE n 113 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE n 113 " --> pdb=" O ILE n 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'o' and resid 47 through 49 removed outlier: 6.741A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU o 26 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'p' and resid 36 through 40 removed outlier: 6.453A pdb=" N GLU p 26 " --> pdb=" O ILE p 83 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE p 83 " --> pdb=" O GLU p 26 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS p 28 " --> pdb=" O ASP p 81 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 11 through 15 removed outlier: 7.248A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.709A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 7.146A 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 76 Processing sheet with id=AE3, first strand: chain 's' and resid 4 through 10 removed outlier: 3.606A pdb=" N VAL s 105 " --> pdb=" O ALA s 5 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS s 9 " --> pdb=" O SER s 101 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 's' and resid 81 through 86 Processing sheet with id=AE5, first strand: chain 't' and resid 11 through 14 removed outlier: 4.312A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AE7, first strand: chain 'u' and resid 63 through 65 removed outlier: 6.985A pdb=" N LYS u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL u 27 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL u 10 " --> pdb=" O GLY u 22 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE9, first strand: chain 'u' and resid 82 through 85 removed outlier: 4.076A pdb=" N PHE u 94 " --> pdb=" O GLY u 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG u 85 " --> pdb=" O VAL u 92 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'v' and resid 3 through 5 removed outlier: 6.521A pdb=" N ILE v 4 " --> pdb=" O VAL v 64 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASP v 90 " --> pdb=" O GLN v 75 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL v 77 " --> pdb=" O HIS v 88 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N HIS v 88 " --> pdb=" O VAL v 77 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG v 79 " --> pdb=" O LEU v 86 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU v 86 " --> pdb=" O ARG v 79 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN v 87 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE v 26 " --> pdb=" O LEU v 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU v 42 " --> pdb=" O PHE v 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE v 40 " --> pdb=" O ALA v 28 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'w' and resid 18 through 19 removed outlier: 3.913A pdb=" N SER w 31 " --> pdb=" O ALA w 57 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'w' and resid 26 through 27 removed outlier: 3.768A pdb=" N GLY w 61 " --> pdb=" O VAL w 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS w 64 " --> pdb=" O SER w 77 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER w 77 " --> pdb=" O LYS w 64 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'x' and resid 13 through 16 removed outlier: 3.963A pdb=" N ARG x 26 " --> pdb=" O GLY x 14 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'x' and resid 33 through 34 Processing sheet with id=AF6, first strand: chain 'x' and resid 37 through 39 removed outlier: 3.668A pdb=" N VAL x 39 " --> pdb=" O ARG x 44 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG x 44 " --> pdb=" O VAL x 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'z' and resid 35 through 38 Processing sheet with id=AF8, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AF9, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AG1, first strand: chain 'C' and resid 35 through 38 removed outlier: 4.176A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 48 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 37 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.841A pdb=" N ALA E 47 " --> pdb=" O HIS E 23 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 2 through 3 removed outlier: 6.521A pdb=" N LYS F 2 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 16 through 17 Processing sheet with id=AG5, first strand: chain 'G' and resid 66 through 69 removed outlier: 5.765A pdb=" N LEU G 160 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE G 185 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL G 162 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL G 182 " --> pdb=" O PHE G 197 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE G 199 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA G 184 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.629A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 55 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 57 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA H 103 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE H 67 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 163 through 168 removed outlier: 4.157A pdb=" N ARG H 163 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY H 154 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 150 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 202 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL H 199 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE H 201 " --> pdb=" O ASP H 182 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.848A pdb=" N ARG I 127 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL I 124 " --> pdb=" O ARG I 127 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AH1, first strand: chain 'J' and resid 18 through 24 Processing sheet with id=AH2, first strand: chain 'J' and resid 94 through 96 removed outlier: 3.709A pdb=" N LEU J 123 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AH4, first strand: chain 'K' and resid 41 through 45 removed outlier: 5.128A pdb=" N ASP K 41 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU K 61 " --> pdb=" O ASP K 41 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY K 43 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR K 59 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS K 58 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL K 10 " --> pdb=" O HIS K 58 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 72 through 77 removed outlier: 4.192A pdb=" N ARG L 77 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR L 84 " --> pdb=" O ARG L 77 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 23 through 27 removed outlier: 4.241A pdb=" N VAL M 24 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU M 60 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU M 57 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL M 50 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU M 59 " --> pdb=" O PHE M 48 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE M 48 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR M 61 " --> pdb=" O GLU M 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 75 through 76 removed outlier: 6.726A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 5 through 10 removed outlier: 3.910A pdb=" N TYR N 5 " --> pdb=" O ILE N 20 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA N 15 " --> pdb=" O LYS N 67 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 45 through 46 removed outlier: 3.749A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.641A pdb=" N LYS S 96 " --> pdb=" O GLU O 66 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 29 through 35 removed outlier: 3.560A pdb=" N ILE P 30 " --> pdb=" O HIS P 23 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE P 22 " --> pdb=" O MET P 84 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL P 83 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE P 109 " --> pdb=" O VAL P 83 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL P 85 " --> pdb=" O ILE P 109 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP P 111 " --> pdb=" O VAL P 85 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 28 through 31 Processing sheet with id=AI4, first strand: chain 'Q' and resid 38 through 39 Processing sheet with id=AI5, first strand: chain 'U' and resid 34 through 35 removed outlier: 3.515A pdb=" N GLU U 34 " --> pdb=" O VAL U 21 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL U 2 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 37 through 39 Processing sheet with id=AI7, first strand: chain 'V' and resid 10 through 11 removed outlier: 3.586A pdb=" N VAL V 28 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'X' and resid 47 through 51 1270 hydrogen bonds defined for protein. 3483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1984 hydrogen bonds 3246 hydrogen bond angles 0 basepair planarities 823 basepair parallelities 2455 stacking parallelities Total time for adding SS restraints: 223.66 Time building geometry restraints manager: 63.67 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: 22013 1.33 - 1.46: 69610 1.46 - 1.58: 61282 1.58 - 1.71: 9464 1.71 - 1.83: 283 Bond restraints: 162652 Sorted by residual: bond pdb=" CA PRO i 73 " pdb=" C PRO i 73 " ideal model delta sigma weight residual 1.514 1.483 0.031 5.50e-03 3.31e+04 3.14e+01 bond pdb=" C GLY n 101 " pdb=" O GLY n 101 " ideal model delta sigma weight residual 1.235 1.301 -0.067 1.35e-02 5.49e+03 2.44e+01 bond pdb=" O5' A 31014 " pdb=" C5' A 31014 " ideal model delta sigma weight residual 1.420 1.480 -0.060 1.50e-02 4.44e+03 1.62e+01 bond pdb=" O5' G 31013 " pdb=" C5' G 31013 " ideal model delta sigma weight residual 1.420 1.476 -0.056 1.50e-02 4.44e+03 1.39e+01 bond pdb=" O5' G 1 757 " pdb=" C5' G 1 757 " ideal model delta sigma weight residual 1.420 1.473 -0.053 1.50e-02 4.44e+03 1.25e+01 ... (remaining 162647 not shown) Histogram of bond angle deviations from ideal: 97.29 - 105.49: 23486 105.49 - 113.68: 100306 113.68 - 121.87: 82733 121.87 - 130.07: 33605 130.07 - 138.26: 2944 Bond angle restraints: 243074 Sorted by residual: angle pdb=" C2' A 12430 " pdb=" C1' A 12430 " pdb=" N9 A 12430 " ideal model delta sigma weight residual 112.00 123.41 -11.41 1.50e+00 4.44e-01 5.79e+01 angle pdb=" N GLY r 44 " pdb=" CA GLY r 44 " pdb=" C GLY r 44 " ideal model delta sigma weight residual 113.79 105.05 8.74 1.17e+00 7.31e-01 5.58e+01 angle pdb=" C2' C 1 873 " pdb=" C1' C 1 873 " pdb=" N1 C 1 873 " ideal model delta sigma weight residual 114.00 124.78 -10.78 1.50e+00 4.44e-01 5.16e+01 angle pdb=" C3' A 31227 " pdb=" C2' A 31227 " pdb=" O2' A 31227 " ideal model delta sigma weight residual 110.70 121.38 -10.68 1.50e+00 4.44e-01 5.07e+01 angle pdb=" C3' C 31397 " pdb=" C2' C 31397 " pdb=" O2' C 31397 " ideal model delta sigma weight residual 110.70 121.23 -10.53 1.50e+00 4.44e-01 4.93e+01 ... (remaining 243069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 91416 35.15 - 70.30: 11410 70.30 - 105.46: 1347 105.46 - 140.61: 20 140.61 - 175.76: 21 Dihedral angle restraints: 104214 sinusoidal: 86644 harmonic: 17570 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 -41.80 123.80 1 8.00e+00 1.56e-02 2.33e+02 dihedral pdb=" CA LYS g 8 " pdb=" C LYS g 8 " pdb=" N VAL g 9 " pdb=" CA VAL g 9 " ideal model delta harmonic sigma weight residual 180.00 128.95 51.05 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" O4' C 1 873 " pdb=" C2' C 1 873 " pdb=" C1' C 1 873 " pdb=" C3' C 1 873 " ideal model delta sinusoidal sigma weight residual -35.00 36.65 -71.65 1 8.00e+00 1.56e-02 1.03e+02 ... (remaining 104211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 31029 0.948 - 1.896: 0 1.896 - 2.843: 0 2.843 - 3.791: 0 3.791 - 4.739: 2 Chirality restraints: 31031 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 2.24 -4.74 2.00e-01 2.50e+01 5.61e+02 chirality pdb=" C1' C 1 873 " pdb=" O4' C 1 873 " pdb=" C2' C 1 873 " pdb=" N1 C 1 873 " both_signs ideal model delta sigma weight residual False 2.45 -1.59 4.03 2.00e-01 2.50e+01 4.06e+02 chirality pdb=" P C 5 1 " pdb=" OP1 C 5 1 " pdb=" OP2 C 5 1 " pdb=" O5' C 5 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.71e+00 ... (remaining 31028 not shown) Planarity restraints: 13221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 31049 " 0.180 2.00e-02 2.50e+03 1.20e-01 3.26e+02 pdb=" N1 U 31049 " 0.017 2.00e-02 2.50e+03 pdb=" C2 U 31049 " -0.029 2.00e-02 2.50e+03 pdb=" O2 U 31049 " -0.066 2.00e-02 2.50e+03 pdb=" N3 U 31049 " -0.075 2.00e-02 2.50e+03 pdb=" C4 U 31049 " -0.085 2.00e-02 2.50e+03 pdb=" O4 U 31049 " 0.246 2.00e-02 2.50e+03 pdb=" C5 U 31049 " -0.125 2.00e-02 2.50e+03 pdb=" C6 U 31049 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 31148 " 0.207 2.00e-02 2.50e+03 1.18e-01 3.14e+02 pdb=" N1 U 31148 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U 31148 " -0.033 2.00e-02 2.50e+03 pdb=" O2 U 31148 " -0.088 2.00e-02 2.50e+03 pdb=" N3 U 31148 " -0.030 2.00e-02 2.50e+03 pdb=" C4 U 31148 " -0.041 2.00e-02 2.50e+03 pdb=" O4 U 31148 " 0.212 2.00e-02 2.50e+03 pdb=" C5 U 31148 " -0.128 2.00e-02 2.50e+03 pdb=" C6 U 31148 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 31397 " -0.183 2.00e-02 2.50e+03 9.33e-02 1.96e+02 pdb=" N1 C 31397 " 0.012 2.00e-02 2.50e+03 pdb=" C2 C 31397 " 0.031 2.00e-02 2.50e+03 pdb=" O2 C 31397 " 0.089 2.00e-02 2.50e+03 pdb=" N3 C 31397 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 31397 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C 31397 " -0.132 2.00e-02 2.50e+03 pdb=" C5 C 31397 " 0.096 2.00e-02 2.50e+03 pdb=" C6 C 31397 " 0.094 2.00e-02 2.50e+03 ... (remaining 13218 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 7184 2.68 - 3.24: 125534 3.24 - 3.79: 287716 3.79 - 4.35: 373067 4.35 - 4.90: 507130 Nonbonded interactions: 1300631 Sorted by model distance: nonbonded pdb=" OG1 THR I 85 " pdb=" OG1 THR J 102 " model vdw 2.130 2.440 nonbonded pdb=" O THR K 26 " pdb=" OG1 THR K 30 " model vdw 2.194 2.440 nonbonded pdb=" OE1 GLU b 81 " pdb=" OH TYR b 102 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR c 25 " pdb=" O VAL c 189 " model vdw 2.229 2.440 nonbonded pdb=" O ARG o 33 " pdb=" OG1 THR o 65 " model vdw 2.245 2.440 ... (remaining 1300626 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: 4.250 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: 23.100 Check model and map are aligned: 1.650 Set scattering table: 1.030 Process input model: 495.420 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 531.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.121 162652 Z= 0.585 Angle : 1.069 16.252 243074 Z= 0.659 Chirality : 0.091 4.739 31031 Planarity : 0.013 0.120 13221 Dihedral : 23.535 175.762 92880 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.72 % Favored : 87.80 % Rotamer: Outliers : 1.63 % Allowed : 16.42 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.54 % 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: -4.79 (0.08), residues: 6067 helix: -4.36 (0.07), residues: 1494 sheet: -2.33 (0.15), residues: 940 loop : -2.99 (0.09), residues: 3633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP b 212 HIS 0.028 0.003 HIS b 52 PHE 0.032 0.004 PHE s 75 TYR 0.037 0.004 TYR s 38 ARG 0.016 0.002 ARG Z 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1538 time to evaluate : 5.674 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: 8 431 MET cc_start: 0.4621 (ppp) cc_final: 0.4395 (ppp) REVERT: 8 497 LYS cc_start: 0.7882 (pttp) cc_final: 0.7026 (ttmt) REVERT: 8 522 MET cc_start: 0.1543 (ttp) cc_final: 0.1155 (ttp) REVERT: 8 584 HIS cc_start: 0.8093 (m90) cc_final: 0.7491 (m170) REVERT: 8 663 MET cc_start: 0.2395 (mpp) cc_final: -0.1636 (ptt) REVERT: 8 682 MET cc_start: 0.2315 (mmm) cc_final: 0.1961 (ttt) REVERT: b 97 ASP cc_start: 0.7932 (p0) cc_final: 0.7598 (p0) REVERT: b 142 ASN cc_start: 0.8575 (t0) cc_final: 0.8204 (t0) REVERT: b 147 PRO cc_start: 0.9296 (Cg_exo) cc_final: 0.9034 (Cg_endo) REVERT: b 155 ARG cc_start: 0.7352 (ptm160) cc_final: 0.7024 (ptp-170) REVERT: b 184 GLU cc_start: 0.6522 (mt-10) cc_final: 0.5921 (mm-30) REVERT: b 260 LYS cc_start: 0.7622 (mttt) cc_final: 0.7415 (mttt) REVERT: d 73 ILE cc_start: 0.9008 (tt) cc_final: 0.8714 (tt) REVERT: d 101 TYR cc_start: 0.8686 (t80) cc_final: 0.8484 (t80) REVERT: e 37 MET cc_start: 0.8215 (ttm) cc_final: 0.7681 (tpp) REVERT: e 95 MET cc_start: 0.8251 (ttp) cc_final: 0.7520 (ttp) REVERT: e 101 ARG cc_start: 0.6602 (ttp-170) cc_final: 0.5643 (tmt-80) REVERT: e 111 ARG cc_start: 0.6881 (ttt90) cc_final: 0.5863 (ttt90) REVERT: f 89 VAL cc_start: 0.8666 (m) cc_final: 0.8110 (m) REVERT: f 104 LEU cc_start: 0.8261 (mt) cc_final: 0.7640 (tp) REVERT: f 106 LEU cc_start: 0.8663 (mm) cc_final: 0.8404 (mm) REVERT: f 115 GLN cc_start: 0.8310 (tt0) cc_final: 0.7294 (mp10) REVERT: f 116 LEU cc_start: 0.8123 (tp) cc_final: 0.7870 (tp) REVERT: f 148 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7365 (ttt90) REVERT: f 174 LYS cc_start: 0.7427 (pttt) cc_final: 0.7132 (pttt) REVERT: g 135 HIS cc_start: 0.8196 (t70) cc_final: 0.7697 (t70) REVERT: i 96 LYS cc_start: 0.7785 (tmtt) cc_final: 0.7575 (tptt) REVERT: i 124 MET cc_start: 0.7356 (tpt) cc_final: 0.6948 (ttt) REVERT: j 14 ASP cc_start: 0.8100 (p0) cc_final: 0.7785 (p0) REVERT: j 19 ASP cc_start: 0.7305 (t70) cc_final: 0.7038 (p0) REVERT: j 39 LYS cc_start: 0.8240 (tttt) cc_final: 0.7794 (ttmm) REVERT: j 131 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8937 (p0) REVERT: k 113 MET cc_start: 0.5934 (mmt) cc_final: 0.4294 (tmm) REVERT: l 55 MET cc_start: 0.7727 (tpp) cc_final: 0.6971 (tpp) REVERT: l 63 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7672 (mttt) REVERT: l 86 GLU cc_start: 0.7740 (pp20) cc_final: 0.7470 (pp20) REVERT: l 129 LYS cc_start: 0.7729 (mttp) cc_final: 0.7273 (mptt) REVERT: l 143 GLU cc_start: 0.6585 (pm20) cc_final: 0.6023 (pm20) REVERT: m 31 PHE cc_start: 0.8221 (m-80) cc_final: 0.7419 (m-10) REVERT: n 72 ASP cc_start: 0.8303 (t0) cc_final: 0.7971 (m-30) REVERT: o 13 ARG cc_start: 0.6726 (tpt170) cc_final: 0.6389 (tpt90) REVERT: o 38 GLN cc_start: 0.7479 (mt0) cc_final: 0.6993 (tm-30) REVERT: o 55 GLU cc_start: 0.7122 (mp0) cc_final: 0.6493 (mm-30) REVERT: o 84 GLU cc_start: 0.8776 (pt0) cc_final: 0.8494 (tm-30) REVERT: o 111 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.6632 (ttp-170) REVERT: p 5 LYS cc_start: 0.7579 (tptt) cc_final: 0.7214 (tptt) REVERT: q 35 PHE cc_start: 0.8427 (t80) cc_final: 0.8192 (t80) REVERT: q 113 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8115 (pptt) REVERT: r 11 GLN cc_start: 0.7955 (mp10) cc_final: 0.7128 (mt0) REVERT: s 2 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8006 (mm-30) REVERT: s 66 ILE cc_start: 0.8860 (tt) cc_final: 0.8399 (mm) REVERT: s 106 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.7821 (p) REVERT: s 109 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7780 (p0) REVERT: t 52 GLU cc_start: 0.7745 (mp0) cc_final: 0.7497 (mp0) REVERT: u 60 LYS cc_start: 0.8995 (tppt) cc_final: 0.8731 (tptp) REVERT: v 11 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7549 (mt-10) REVERT: v 38 LEU cc_start: 0.7833 (tp) cc_final: 0.7620 (tt) REVERT: v 65 VAL cc_start: 0.7304 (t) cc_final: 0.7092 (t) REVERT: v 73 LYS cc_start: 0.7450 (mmmm) cc_final: 0.7238 (mmmm) REVERT: w 40 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8434 (ttpp) REVERT: x 33 HIS cc_start: 0.7040 (m-70) cc_final: 0.6512 (m170) REVERT: x 49 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7020 (ttt180) REVERT: x 58 ILE cc_start: 0.8551 (tp) cc_final: 0.8093 (mm) REVERT: y 14 LEU cc_start: 0.7943 (mt) cc_final: 0.7681 (mt) REVERT: z 57 GLU cc_start: 0.7864 (tp30) cc_final: 0.7135 (tm-30) REVERT: D 11 LYS cc_start: 0.9246 (ttmt) cc_final: 0.8882 (ttmm) REVERT: E 4 LYS cc_start: 0.6296 (mttt) cc_final: 0.5757 (mttt) REVERT: F 20 ASP cc_start: 0.7320 (t0) cc_final: 0.7118 (t0) REVERT: F 23 ILE cc_start: 0.8260 (mt) cc_final: 0.7974 (mt) REVERT: F 34 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8380 (mttp) REVERT: G 87 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8370 (p0) REVERT: G 150 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7721 (pt) REVERT: G 199 ILE cc_start: 0.8176 (mt) cc_final: 0.7934 (mt) REVERT: H 27 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.4738 (mm-30) REVERT: I 50 TYR cc_start: 0.7313 (t80) cc_final: 0.6881 (t80) REVERT: I 69 ARG cc_start: 0.7445 (pmt-80) cc_final: 0.7222 (mmm-85) REVERT: I 70 GLN cc_start: 0.8077 (tt0) cc_final: 0.6690 (tt0) REVERT: I 74 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: J 25 LYS cc_start: 0.6286 (ptpp) cc_final: 0.6010 (ptpp) REVERT: J 49 TYR cc_start: 0.7460 (m-10) cc_final: 0.7172 (m-10) REVERT: J 67 ARG cc_start: 0.8235 (mmt-90) cc_final: 0.7529 (mmm160) REVERT: J 69 ASN cc_start: 0.8275 (t0) cc_final: 0.7418 (t0) REVERT: J 73 VAL cc_start: 0.7124 (OUTLIER) cc_final: 0.6923 (t) REVERT: K 21 MET cc_start: 0.6676 (mtp) cc_final: 0.6461 (mtp) REVERT: K 52 ASN cc_start: 0.8478 (t0) cc_final: 0.8159 (t0) REVERT: K 82 ASP cc_start: 0.7720 (t70) cc_final: 0.7379 (t70) REVERT: K 86 ARG cc_start: 0.6846 (ptp-170) cc_final: 0.6562 (ptp-170) REVERT: K 88 MET cc_start: 0.7299 (ptm) cc_final: 0.6697 (ptm) REVERT: N 28 VAL cc_start: 0.5428 (t) cc_final: 0.5194 (t) REVERT: P 28 ASN cc_start: 0.6762 (t0) cc_final: 0.6323 (t0) REVERT: P 124 LYS cc_start: 0.7875 (pptt) cc_final: 0.7375 (pttp) REVERT: Q 4 ASN cc_start: 0.7458 (t0) cc_final: 0.7212 (t0) REVERT: Q 66 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7309 (mp) REVERT: Q 98 ARG cc_start: 0.7414 (mtp180) cc_final: 0.7097 (tpt90) REVERT: R 90 HIS cc_start: 0.5814 (m-70) cc_final: 0.5499 (m90) REVERT: S 46 LYS cc_start: 0.4780 (mmmt) cc_final: 0.4536 (mmpt) REVERT: S 70 HIS cc_start: 0.5321 (m-70) cc_final: 0.5013 (m-70) REVERT: T 34 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8165 (tp40) REVERT: U 31 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7430 (ptt90) REVERT: W 42 ARG cc_start: 0.7644 (ptm160) cc_final: 0.7425 (ptp90) REVERT: Z 45 LYS cc_start: 0.7354 (mttt) cc_final: 0.6975 (mmmt) outliers start: 82 outliers final: 46 residues processed: 1598 average time/residue: 1.4462 time to fit residues: 3858.7702 Evaluate side-chains 1234 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1179 time to evaluate : 6.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 53 VAL Chi-restraints excluded: chain D residue 16 HIS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 899 optimal weight: 9.9990 chunk 807 optimal weight: 2.9990 chunk 447 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 544 optimal weight: 1.9990 chunk 431 optimal weight: 10.0000 chunk 834 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 chunk 507 optimal weight: 7.9990 chunk 621 optimal weight: 2.9990 chunk 967 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 496 GLN ** 8 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 560 GLN ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 114 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 ASN ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN d 29 HIS ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN e 126 ASN ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN a 24 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN i 5 GLN i 33 ASN i 93 ASN ** i 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 ASN k 93 GLN l 38 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 16 HIS o 38 GLN o 43 ASN o 98 GLN o 104 GLN p 76 HIS q 36 GLN q 43 GLN ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN u 68 ASN ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN C 18 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN F 35 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN G 119 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN I 35 GLN I 58 GLN I 70 GLN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS K 17 GLN K 37 HIS L 67 ASN L 85 GLN M 15 ASN M 66 GLN N 30 ASN N 74 GLN N 80 HIS O 58 ASN P 21 HIS ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN P 39 ASN P 80 ASN P 100 ASN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS S 65 GLN T 34 GLN T 39 GLN T 41 HIS ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN X 42 ASN Y 67 HIS Y 74 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 162652 Z= 0.283 Angle : 0.814 13.184 243074 Z= 0.415 Chirality : 0.048 3.192 31031 Planarity : 0.006 0.071 13221 Dihedral : 24.100 177.071 80843 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.53 % Favored : 89.19 % Rotamer: Outliers : 6.45 % Allowed : 21.97 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.24 % 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: -4.18 (0.09), residues: 6067 helix: -3.24 (0.09), residues: 1635 sheet: -2.16 (0.15), residues: 1021 loop : -2.78 (0.09), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP G 95 HIS 0.022 0.002 HIS v 44 PHE 0.034 0.003 PHE I 71 TYR 0.037 0.003 TYR 8 490 ARG 0.011 0.001 ARG j 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1295 time to evaluate : 6.406 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: 8 497 LYS cc_start: 0.7906 (pttp) cc_final: 0.7081 (ttmt) REVERT: 8 560 GLN cc_start: 0.1261 (OUTLIER) cc_final: 0.0042 (tm130) REVERT: 8 571 VAL cc_start: 0.5399 (OUTLIER) cc_final: 0.4741 (p) REVERT: 8 584 HIS cc_start: 0.8068 (m90) cc_final: 0.7145 (m170) REVERT: 8 663 MET cc_start: 0.2221 (mpp) cc_final: -0.1622 (ptt) REVERT: 8 682 MET cc_start: 0.2358 (mmm) cc_final: 0.2151 (ttt) REVERT: b 48 ILE cc_start: 0.8812 (tp) cc_final: 0.8503 (tp) REVERT: b 97 ASP cc_start: 0.7911 (p0) cc_final: 0.7464 (p0) REVERT: b 155 ARG cc_start: 0.7263 (ptm160) cc_final: 0.6490 (ptp-170) REVERT: d 1 MET cc_start: 0.5833 (mmt) cc_final: 0.5250 (mmt) REVERT: d 16 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7962 (tm-30) REVERT: d 69 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6198 (ptp-110) REVERT: d 73 ILE cc_start: 0.8906 (tt) cc_final: 0.8647 (tt) REVERT: d 95 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8217 (ptmt) REVERT: d 117 ARG cc_start: 0.7649 (mtp180) cc_final: 0.7241 (mtm-85) REVERT: e 8 LYS cc_start: 0.7417 (mtmm) cc_final: 0.7109 (mtmt) REVERT: e 19 PHE cc_start: 0.6458 (m-80) cc_final: 0.6188 (m-10) REVERT: e 21 TYR cc_start: 0.6244 (m-80) cc_final: 0.5998 (m-80) REVERT: e 95 MET cc_start: 0.8089 (ttp) cc_final: 0.7180 (ttp) REVERT: e 101 ARG cc_start: 0.6681 (ttp-170) cc_final: 0.5643 (tmt-80) REVERT: e 111 ARG cc_start: 0.6766 (ttt90) cc_final: 0.5696 (ttt90) REVERT: e 132 ARG cc_start: 0.7235 (mpt180) cc_final: 0.6836 (mpt180) REVERT: f 89 VAL cc_start: 0.8556 (m) cc_final: 0.8084 (m) REVERT: f 115 GLN cc_start: 0.8100 (tt0) cc_final: 0.7300 (pm20) REVERT: f 116 LEU cc_start: 0.8113 (tp) cc_final: 0.7823 (tp) REVERT: f 148 ARG cc_start: 0.7946 (ttt-90) cc_final: 0.7611 (ttt90) REVERT: g 135 HIS cc_start: 0.8238 (t70) cc_final: 0.7754 (t70) REVERT: a 166 ASP cc_start: 0.5558 (m-30) cc_final: 0.5306 (m-30) REVERT: i 96 LYS cc_start: 0.7952 (tmtt) cc_final: 0.7728 (tptt) REVERT: i 124 MET cc_start: 0.7084 (tpt) cc_final: 0.6653 (ttt) REVERT: j 16 TYR cc_start: 0.8183 (m-80) cc_final: 0.7922 (m-10) REVERT: j 19 ASP cc_start: 0.7423 (t70) cc_final: 0.6899 (p0) REVERT: j 39 LYS cc_start: 0.8363 (tttt) cc_final: 0.7848 (ttmm) REVERT: j 67 ASN cc_start: 0.7251 (m-40) cc_final: 0.6716 (t0) REVERT: j 90 GLU cc_start: 0.8304 (pp20) cc_final: 0.7683 (pp20) REVERT: j 131 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8926 (p0) REVERT: k 23 LYS cc_start: 0.8374 (tppt) cc_final: 0.8155 (mttm) REVERT: k 98 ARG cc_start: 0.5247 (mpt180) cc_final: 0.4630 (tmm-80) REVERT: k 113 MET cc_start: 0.6080 (mmt) cc_final: 0.5149 (ptt) REVERT: l 55 MET cc_start: 0.7892 (tpp) cc_final: 0.7060 (tpp) REVERT: l 143 GLU cc_start: 0.6393 (pm20) cc_final: 0.5964 (pm20) REVERT: m 31 PHE cc_start: 0.7723 (m-80) cc_final: 0.7394 (m-10) REVERT: n 42 LYS cc_start: 0.7874 (mttm) cc_final: 0.7673 (tmtt) REVERT: n 72 ASP cc_start: 0.7796 (t0) cc_final: 0.7287 (m-30) REVERT: o 13 ARG cc_start: 0.6921 (tpt170) cc_final: 0.6327 (tpt90) REVERT: o 30 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7180 (ttp80) REVERT: o 33 ARG cc_start: 0.8860 (ttt180) cc_final: 0.8617 (tpp-160) REVERT: o 55 GLU cc_start: 0.7306 (mp0) cc_final: 0.6380 (mm-30) REVERT: o 76 LYS cc_start: 0.8598 (tptt) cc_final: 0.8181 (tppt) REVERT: o 84 GLU cc_start: 0.8670 (pt0) cc_final: 0.8454 (tm-30) REVERT: p 101 GLU cc_start: 0.9064 (mp0) cc_final: 0.8766 (mp0) REVERT: q 2 ARG cc_start: 0.7210 (ttt180) cc_final: 0.6999 (ttt180) REVERT: q 14 LYS cc_start: 0.8172 (tptp) cc_final: 0.7742 (tptp) REVERT: q 35 PHE cc_start: 0.8479 (t80) cc_final: 0.7986 (t80) REVERT: r 11 GLN cc_start: 0.7867 (mp10) cc_final: 0.7077 (mt0) REVERT: r 43 ASN cc_start: 0.6247 (OUTLIER) cc_final: 0.5563 (p0) REVERT: r 62 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7725 (tm-30) REVERT: r 92 TRP cc_start: 0.7619 (m100) cc_final: 0.7273 (m100) REVERT: s 11 ARG cc_start: 0.8096 (mpp-170) cc_final: 0.7864 (mpp-170) REVERT: s 66 ILE cc_start: 0.8594 (tt) cc_final: 0.8329 (mm) REVERT: t 52 GLU cc_start: 0.7623 (mp0) cc_final: 0.7056 (mp0) REVERT: u 60 LYS cc_start: 0.8937 (tppt) cc_final: 0.8423 (tptp) REVERT: v 53 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8208 (tttm) REVERT: v 86 LEU cc_start: 0.7392 (mt) cc_final: 0.6202 (mp) REVERT: w 40 LYS cc_start: 0.9079 (ttmt) cc_final: 0.8605 (ttpp) REVERT: x 33 HIS cc_start: 0.6997 (m-70) cc_final: 0.6464 (m90) REVERT: y 10 SER cc_start: 0.9496 (m) cc_final: 0.9291 (p) REVERT: y 37 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7611 (mt) REVERT: y 58 ASN cc_start: 0.7482 (p0) cc_final: 0.7271 (p0) REVERT: y 59 GLU cc_start: 0.7759 (tt0) cc_final: 0.7545 (tt0) REVERT: z 57 GLU cc_start: 0.7770 (tp30) cc_final: 0.7290 (tm-30) REVERT: D 11 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8649 (tttm) REVERT: F 1 MET cc_start: 0.6942 (tpp) cc_final: 0.6522 (tpt) REVERT: F 23 ILE cc_start: 0.8327 (mt) cc_final: 0.7966 (mt) REVERT: G 13 VAL cc_start: 0.3323 (OUTLIER) cc_final: 0.3051 (p) REVERT: G 55 GLU cc_start: 0.8470 (mp0) cc_final: 0.8247 (mp0) REVERT: G 92 ASN cc_start: 0.6593 (m-40) cc_final: 0.6052 (m-40) REVERT: G 150 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7412 (pt) REVERT: G 207 ARG cc_start: 0.7088 (tpt90) cc_final: 0.6209 (mpp80) REVERT: H 27 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.4516 (mm-30) REVERT: I 50 TYR cc_start: 0.7404 (t80) cc_final: 0.6919 (t80) REVERT: I 69 ARG cc_start: 0.7454 (pmt-80) cc_final: 0.7248 (mmm160) REVERT: I 74 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: J 53 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7137 (mmt180) REVERT: J 69 ASN cc_start: 0.8213 (t0) cc_final: 0.7296 (t0) REVERT: K 52 ASN cc_start: 0.8328 (t0) cc_final: 0.8049 (t0) REVERT: K 82 ASP cc_start: 0.7839 (t70) cc_final: 0.7422 (t70) REVERT: K 97 THR cc_start: 0.4560 (OUTLIER) cc_final: 0.4256 (t) REVERT: M 6 ILE cc_start: 0.8760 (mm) cc_final: 0.8503 (mt) REVERT: M 35 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7465 (tt) REVERT: P 28 ASN cc_start: 0.6792 (t0) cc_final: 0.6363 (t0) REVERT: Q 66 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7141 (mp) REVERT: Q 98 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7144 (tpt90) REVERT: S 46 LYS cc_start: 0.5178 (mmmt) cc_final: 0.4898 (mmpt) REVERT: U 13 LYS cc_start: 0.8250 (tptt) cc_final: 0.7759 (tptp) REVERT: U 31 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7516 (ptt90) REVERT: U 59 HIS cc_start: 0.7573 (t-90) cc_final: 0.7300 (t-170) REVERT: V 8 GLN cc_start: 0.7591 (tt0) cc_final: 0.7117 (tp40) REVERT: V 61 ARG cc_start: 0.7911 (ptt90) cc_final: 0.7429 (tpt170) REVERT: W 20 ILE cc_start: 0.4177 (OUTLIER) cc_final: 0.3640 (tp) REVERT: W 37 LYS cc_start: 0.8016 (mttt) cc_final: 0.7662 (tttt) REVERT: X 60 PHE cc_start: 0.7261 (t80) cc_final: 0.7047 (t80) REVERT: Y 20 ASN cc_start: 0.8525 (m-40) cc_final: 0.8324 (m-40) REVERT: Z 10 PRO cc_start: 0.7837 (Cg_endo) cc_final: 0.7618 (Cg_exo) REVERT: Z 45 LYS cc_start: 0.7457 (mttt) cc_final: 0.6928 (mmmt) outliers start: 325 outliers final: 201 residues processed: 1467 average time/residue: 1.4052 time to fit residues: 3516.6407 Evaluate side-chains 1396 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1179 time to evaluate : 6.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 560 GLN Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 631 VAL Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 693 ASN Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 242 HIS Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 146 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 69 ARG Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 71 ASN Chi-restraints excluded: chain q residue 97 ILE Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 16 HIS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 58 ASN Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 34 GLU Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 537 optimal weight: 50.0000 chunk 300 optimal weight: 20.0000 chunk 804 optimal weight: 0.9980 chunk 658 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 968 optimal weight: 20.0000 chunk 1046 optimal weight: 20.0000 chunk 862 optimal weight: 6.9990 chunk 960 optimal weight: 30.0000 chunk 330 optimal weight: 10.0000 chunk 777 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 ASN b 238 ASN ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 33 ASN ** i 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 45 GLN o 100 HIS ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 HIS ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS s 7 HIS ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 27 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 ASN M 75 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN T 36 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN W 30 ASN Y 67 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 162652 Z= 0.350 Angle : 0.862 14.011 243074 Z= 0.436 Chirality : 0.046 0.391 31031 Planarity : 0.006 0.090 13221 Dihedral : 24.540 177.222 80830 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 27.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.86 % Favored : 86.85 % Rotamer: Outliers : 8.77 % Allowed : 24.32 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -3.83 (0.09), residues: 6067 helix: -2.62 (0.10), residues: 1610 sheet: -2.13 (0.16), residues: 938 loop : -2.70 (0.10), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP U 60 HIS 0.013 0.002 HIS b 52 PHE 0.038 0.003 PHE r 77 TYR 0.034 0.003 TYR 8 490 ARG 0.012 0.001 ARG H 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1636 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 442 poor density : 1194 time to evaluate : 5.653 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: 8 584 HIS cc_start: 0.8053 (m90) cc_final: 0.7191 (m170) REVERT: 8 634 ASP cc_start: 0.6242 (t0) cc_final: 0.6022 (t0) REVERT: 8 663 MET cc_start: 0.2134 (mpp) cc_final: -0.1800 (ptt) REVERT: b 97 ASP cc_start: 0.7925 (p0) cc_final: 0.7416 (p0) REVERT: b 155 ARG cc_start: 0.7254 (ptm160) cc_final: 0.6462 (ptp-170) REVERT: b 224 MET cc_start: 0.7205 (mtt) cc_final: 0.6664 (mtt) REVERT: d 69 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6108 (ptp-110) REVERT: d 85 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6147 (m-10) REVERT: e 19 PHE cc_start: 0.6425 (m-80) cc_final: 0.6146 (m-10) REVERT: e 21 TYR cc_start: 0.6428 (m-80) cc_final: 0.6192 (m-80) REVERT: e 45 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6687 (p0) REVERT: e 95 MET cc_start: 0.8119 (ttp) cc_final: 0.7145 (ttp) REVERT: e 111 ARG cc_start: 0.6867 (ttt90) cc_final: 0.5608 (ttt180) REVERT: f 43 LYS cc_start: 0.7498 (mmtt) cc_final: 0.6836 (mmpt) REVERT: f 89 VAL cc_start: 0.8730 (m) cc_final: 0.8520 (m) REVERT: f 115 GLN cc_start: 0.8114 (tt0) cc_final: 0.7368 (pm20) REVERT: f 148 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7369 (ttm170) REVERT: g 35 LYS cc_start: 0.7804 (ptpt) cc_final: 0.7480 (ptpt) REVERT: g 135 HIS cc_start: 0.8224 (t70) cc_final: 0.7758 (t70) REVERT: a 166 ASP cc_start: 0.5555 (m-30) cc_final: 0.5281 (m-30) REVERT: i 124 MET cc_start: 0.7258 (tpt) cc_final: 0.6922 (ttt) REVERT: j 19 ASP cc_start: 0.7390 (t70) cc_final: 0.6797 (p0) REVERT: j 39 LYS cc_start: 0.8344 (tttt) cc_final: 0.7985 (ttmm) REVERT: j 90 GLU cc_start: 0.8277 (pp20) cc_final: 0.7759 (pp20) REVERT: j 131 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.8939 (p0) REVERT: k 23 LYS cc_start: 0.8436 (tppt) cc_final: 0.8190 (mmtt) REVERT: k 43 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8469 (mt) REVERT: k 59 LYS cc_start: 0.8274 (tmtt) cc_final: 0.8045 (tttt) REVERT: k 98 ARG cc_start: 0.5343 (mpt180) cc_final: 0.4665 (tmm-80) REVERT: k 105 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7966 (mmt90) REVERT: k 110 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7889 (mm-30) REVERT: k 113 MET cc_start: 0.6183 (mmt) cc_final: 0.5184 (ptt) REVERT: k 114 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7170 (tptt) REVERT: l 55 MET cc_start: 0.7959 (tpp) cc_final: 0.7126 (tpp) REVERT: l 143 GLU cc_start: 0.6519 (pm20) cc_final: 0.6169 (pm20) REVERT: m 31 PHE cc_start: 0.7672 (m-80) cc_final: 0.7377 (m-10) REVERT: m 47 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6948 (tm-30) REVERT: n 42 LYS cc_start: 0.7987 (mttm) cc_final: 0.7647 (tptp) REVERT: n 72 ASP cc_start: 0.7843 (t0) cc_final: 0.7215 (t0) REVERT: o 13 ARG cc_start: 0.7273 (tpt170) cc_final: 0.6752 (tpt90) REVERT: o 30 ARG cc_start: 0.7486 (ttp80) cc_final: 0.7164 (ttp80) REVERT: o 33 ARG cc_start: 0.8884 (ttt180) cc_final: 0.8504 (tpp-160) REVERT: o 55 GLU cc_start: 0.7518 (mp0) cc_final: 0.7013 (mm-30) REVERT: o 67 ASN cc_start: 0.7251 (p0) cc_final: 0.7027 (p0) REVERT: q 13 HIS cc_start: 0.7557 (m90) cc_final: 0.7342 (m90) REVERT: q 14 LYS cc_start: 0.8188 (tptp) cc_final: 0.7724 (tptp) REVERT: r 11 GLN cc_start: 0.8006 (mp10) cc_final: 0.7304 (mt0) REVERT: r 43 ASN cc_start: 0.6004 (OUTLIER) cc_final: 0.5436 (p0) REVERT: r 97 LYS cc_start: 0.8957 (tmmt) cc_final: 0.8476 (tmtt) REVERT: s 66 ILE cc_start: 0.8513 (tt) cc_final: 0.8207 (mm) REVERT: t 1 MET cc_start: 0.4788 (mmt) cc_final: 0.4212 (mtp) REVERT: u 60 LYS cc_start: 0.8921 (tppt) cc_final: 0.8458 (tptp) REVERT: v 46 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8926 (mmmm) REVERT: v 53 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8258 (tttm) REVERT: v 86 LEU cc_start: 0.7512 (mt) cc_final: 0.6589 (mp) REVERT: w 40 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8652 (ttpp) REVERT: x 33 HIS cc_start: 0.7169 (m-70) cc_final: 0.6623 (m90) REVERT: x 45 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: y 37 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7806 (mt) REVERT: y 58 ASN cc_start: 0.7713 (p0) cc_final: 0.7457 (p0) REVERT: z 57 GLU cc_start: 0.7882 (tp30) cc_final: 0.7517 (tm-30) REVERT: B 35 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8273 (mp0) REVERT: D 11 LYS cc_start: 0.9296 (ttmt) cc_final: 0.8643 (tttm) REVERT: F 1 MET cc_start: 0.7069 (tpp) cc_final: 0.6815 (tpp) REVERT: F 23 ILE cc_start: 0.8552 (mt) cc_final: 0.8221 (mt) REVERT: G 55 GLU cc_start: 0.8562 (mp0) cc_final: 0.8281 (mp0) REVERT: G 87 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8194 (p0) REVERT: G 150 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7466 (pt) REVERT: G 199 ILE cc_start: 0.8080 (mt) cc_final: 0.7644 (mm) REVERT: G 207 ARG cc_start: 0.6975 (tpt90) cc_final: 0.6137 (mpp80) REVERT: H 27 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.4212 (mm-30) REVERT: H 143 LEU cc_start: 0.7256 (tp) cc_final: 0.7053 (tt) REVERT: I 50 TYR cc_start: 0.7576 (t80) cc_final: 0.7125 (t80) REVERT: I 68 GLU cc_start: 0.7192 (tp30) cc_final: 0.6647 (tp30) REVERT: I 69 ARG cc_start: 0.7466 (pmt-80) cc_final: 0.7254 (mmm160) REVERT: J 25 LYS cc_start: 0.6802 (ptpp) cc_final: 0.6411 (ptpp) REVERT: J 88 HIS cc_start: 0.5650 (t-90) cc_final: 0.5314 (t-90) REVERT: K 52 ASN cc_start: 0.8371 (t0) cc_final: 0.8142 (t0) REVERT: K 97 THR cc_start: 0.4586 (OUTLIER) cc_final: 0.4247 (t) REVERT: M 28 SER cc_start: 0.8610 (p) cc_final: 0.8304 (p) REVERT: P 28 ASN cc_start: 0.6939 (t0) cc_final: 0.6573 (t0) REVERT: P 34 THR cc_start: 0.8157 (p) cc_final: 0.7861 (t) REVERT: Q 28 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: Q 66 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7364 (mp) REVERT: Q 71 HIS cc_start: 0.4001 (OUTLIER) cc_final: 0.3577 (p90) REVERT: Q 98 ARG cc_start: 0.7496 (mtp180) cc_final: 0.6997 (tpt90) REVERT: S 46 LYS cc_start: 0.4958 (mmmt) cc_final: 0.4725 (mmpt) REVERT: T 34 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8599 (tp-100) REVERT: U 1 MET cc_start: 0.2645 (tpt) cc_final: 0.2235 (tpp) REVERT: U 4 ILE cc_start: 0.4158 (OUTLIER) cc_final: 0.3920 (mt) REVERT: U 13 LYS cc_start: 0.8037 (tptt) cc_final: 0.7584 (tptp) REVERT: U 31 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7583 (ptt90) REVERT: U 66 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8063 (p) REVERT: V 47 ASP cc_start: 0.6266 (t70) cc_final: 0.5706 (t0) REVERT: V 72 TRP cc_start: 0.6883 (m100) cc_final: 0.6468 (m100) REVERT: W 37 LYS cc_start: 0.8151 (mttt) cc_final: 0.7940 (tttt) REVERT: W 54 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6803 (tt) REVERT: X 68 HIS cc_start: 0.5511 (m90) cc_final: 0.5222 (m90) REVERT: Y 43 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6800 (mptt) REVERT: Y 67 HIS cc_start: 0.6171 (OUTLIER) cc_final: 0.5497 (t-170) REVERT: Z 10 PRO cc_start: 0.7986 (Cg_endo) cc_final: 0.7768 (Cg_exo) REVERT: Z 45 LYS cc_start: 0.7431 (mttt) cc_final: 0.6970 (mmmt) outliers start: 442 outliers final: 295 residues processed: 1469 average time/residue: 1.3484 time to fit residues: 3387.8675 Evaluate side-chains 1454 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1137 time to evaluate : 6.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 631 VAL Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 693 ASN Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 242 HIS Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 69 ARG Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 85 PHE Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 136 GLN Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain g residue 149 GLU Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain i residue 4 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 3 THR Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 56 SER Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 35 PHE Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 38 TYR Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain u residue 23 LYS Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 31 TYR Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 45 PHE Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 34 SER Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 16 HIS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 63 TYR Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 34 GLU Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 67 HIS Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 957 optimal weight: 20.0000 chunk 728 optimal weight: 5.9990 chunk 502 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 462 optimal weight: 0.9980 chunk 650 optimal weight: 0.9990 chunk 972 optimal weight: 20.0000 chunk 1029 optimal weight: 5.9990 chunk 508 optimal weight: 9.9990 chunk 921 optimal weight: 0.4980 chunk 277 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 514 GLN ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN b 116 GLN d 30 GLN e 62 GLN ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN i 110 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN l 99 ASN n 31 HIS o 29 HIS o 43 ASN o 100 HIS ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS s 40 ASN t 15 HIS ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 87 GLN ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN P 27 ASN Q 5 GLN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 162652 Z= 0.186 Angle : 0.666 14.275 243074 Z= 0.344 Chirality : 0.038 0.324 31031 Planarity : 0.005 0.066 13221 Dihedral : 24.388 178.101 80823 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.23 % Favored : 90.51 % Rotamer: Outliers : 6.85 % Allowed : 26.80 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.19 % 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: -3.45 (0.10), residues: 6067 helix: -2.06 (0.11), residues: 1641 sheet: -2.05 (0.16), residues: 933 loop : -2.54 (0.10), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 95 HIS 0.043 0.001 HIS Y 67 PHE 0.027 0.002 PHE u 95 TYR 0.032 0.002 TYR f 93 ARG 0.017 0.001 ARG e 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1248 time to evaluate : 6.256 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: 8 491 ARG cc_start: 0.2083 (OUTLIER) cc_final: 0.0892 (mmp80) REVERT: 8 497 LYS cc_start: 0.7812 (pttp) cc_final: 0.6928 (ttmt) REVERT: 8 548 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.4452 (pt0) REVERT: 8 571 VAL cc_start: 0.5300 (OUTLIER) cc_final: 0.4677 (p) REVERT: 8 584 HIS cc_start: 0.8007 (m90) cc_final: 0.7446 (m170) REVERT: 8 663 MET cc_start: 0.1815 (mpp) cc_final: -0.2080 (ptt) REVERT: 8 682 MET cc_start: 0.3018 (OUTLIER) cc_final: 0.0997 (ttp) REVERT: b 48 ILE cc_start: 0.8931 (tp) cc_final: 0.8687 (tp) REVERT: b 155 ARG cc_start: 0.7026 (ptm160) cc_final: 0.5749 (ptp-170) REVERT: c 29 VAL cc_start: 0.6553 (t) cc_final: 0.6167 (m) REVERT: c 79 LEU cc_start: 0.8837 (mp) cc_final: 0.8629 (mp) REVERT: c 125 TRP cc_start: 0.8403 (m100) cc_final: 0.8041 (m100) REVERT: d 115 GLN cc_start: 0.8838 (tt0) cc_final: 0.8631 (tt0) REVERT: e 3 LEU cc_start: 0.7632 (mm) cc_final: 0.7352 (mm) REVERT: e 8 LYS cc_start: 0.7327 (mtmm) cc_final: 0.7035 (mtmt) REVERT: e 19 PHE cc_start: 0.6349 (m-80) cc_final: 0.6118 (m-10) REVERT: e 21 TYR cc_start: 0.6509 (m-80) cc_final: 0.6190 (m-80) REVERT: e 95 MET cc_start: 0.8189 (ttp) cc_final: 0.7308 (ttp) REVERT: e 101 ARG cc_start: 0.6221 (mtt180) cc_final: 0.5282 (tmt170) REVERT: e 111 ARG cc_start: 0.6828 (ttt90) cc_final: 0.5587 (ttt180) REVERT: f 43 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6962 (mmmt) REVERT: f 66 THR cc_start: 0.7802 (t) cc_final: 0.7589 (t) REVERT: f 89 VAL cc_start: 0.8692 (m) cc_final: 0.8485 (m) REVERT: f 115 GLN cc_start: 0.7973 (tt0) cc_final: 0.7248 (pm20) REVERT: f 116 LEU cc_start: 0.8035 (tp) cc_final: 0.7773 (tp) REVERT: g 73 ASN cc_start: 0.4620 (OUTLIER) cc_final: 0.3613 (t0) REVERT: g 135 HIS cc_start: 0.8152 (t70) cc_final: 0.7693 (t70) REVERT: a 27 ILE cc_start: -0.0031 (OUTLIER) cc_final: -0.0412 (mt) REVERT: j 14 ASP cc_start: 0.8281 (p0) cc_final: 0.7917 (p0) REVERT: j 19 ASP cc_start: 0.7331 (t70) cc_final: 0.6929 (p0) REVERT: j 39 LYS cc_start: 0.8383 (tttt) cc_final: 0.7925 (ttmm) REVERT: j 131 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8951 (p0) REVERT: k 23 LYS cc_start: 0.8181 (tppt) cc_final: 0.7953 (mttm) REVERT: k 43 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8362 (mt) REVERT: k 59 LYS cc_start: 0.8207 (tmtt) cc_final: 0.7983 (tttt) REVERT: k 110 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7852 (mm-30) REVERT: k 113 MET cc_start: 0.5992 (mmt) cc_final: 0.5056 (ttp) REVERT: l 55 MET cc_start: 0.7934 (tpp) cc_final: 0.7050 (tpp) REVERT: l 104 GLN cc_start: 0.7322 (mm110) cc_final: 0.6947 (tp40) REVERT: l 143 GLU cc_start: 0.6028 (pm20) cc_final: 0.5481 (mp0) REVERT: m 31 PHE cc_start: 0.7685 (m-80) cc_final: 0.6931 (m-10) REVERT: n 52 ILE cc_start: 0.8005 (mm) cc_final: 0.7769 (mp) REVERT: n 72 ASP cc_start: 0.7815 (t0) cc_final: 0.7130 (t0) REVERT: o 3 LYS cc_start: 0.7816 (pptt) cc_final: 0.7613 (pptt) REVERT: o 13 ARG cc_start: 0.7059 (tpt170) cc_final: 0.6373 (tpt90) REVERT: o 30 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7252 (ttp80) REVERT: o 33 ARG cc_start: 0.8881 (ttt180) cc_final: 0.8478 (tpp-160) REVERT: o 55 GLU cc_start: 0.7201 (mp0) cc_final: 0.6746 (mm-30) REVERT: o 67 ASN cc_start: 0.7483 (p0) cc_final: 0.7208 (p0) REVERT: o 76 LYS cc_start: 0.8617 (tptt) cc_final: 0.8209 (tppt) REVERT: q 13 HIS cc_start: 0.7321 (m90) cc_final: 0.6842 (m-70) REVERT: q 14 LYS cc_start: 0.8132 (tptp) cc_final: 0.7636 (tptp) REVERT: q 111 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8308 (tptp) REVERT: r 11 GLN cc_start: 0.7672 (mp10) cc_final: 0.6828 (mt0) REVERT: r 43 ASN cc_start: 0.6054 (OUTLIER) cc_final: 0.5271 (m-40) REVERT: r 92 TRP cc_start: 0.7474 (m100) cc_final: 0.7044 (m100) REVERT: r 97 LYS cc_start: 0.8818 (tmmt) cc_final: 0.7953 (mttm) REVERT: s 66 ILE cc_start: 0.8494 (tt) cc_final: 0.8153 (mm) REVERT: t 1 MET cc_start: 0.4494 (mmt) cc_final: 0.4136 (mtp) REVERT: t 89 GLU cc_start: 0.5084 (OUTLIER) cc_final: 0.4548 (mm-30) REVERT: u 60 LYS cc_start: 0.8920 (tppt) cc_final: 0.8487 (tptp) REVERT: v 46 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8811 (mmmm) REVERT: v 53 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8101 (tmtt) REVERT: v 57 TYR cc_start: 0.8440 (m-80) cc_final: 0.8226 (m-80) REVERT: w 40 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8662 (ttpp) REVERT: x 5 GLN cc_start: 0.8796 (mp10) cc_final: 0.8502 (mp10) REVERT: x 32 LEU cc_start: 0.8414 (mm) cc_final: 0.8047 (mt) REVERT: x 33 HIS cc_start: 0.7011 (m-70) cc_final: 0.6559 (m90) REVERT: x 45 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: x 51 SER cc_start: 0.8897 (p) cc_final: 0.8391 (p) REVERT: y 20 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8346 (t0) REVERT: y 58 ASN cc_start: 0.7657 (p0) cc_final: 0.7393 (p0) REVERT: z 57 GLU cc_start: 0.7804 (tp30) cc_final: 0.7449 (tm-30) REVERT: B 35 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8166 (mp0) REVERT: D 11 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8507 (tttm) REVERT: E 39 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8122 (ttm170) REVERT: F 23 ILE cc_start: 0.8445 (mt) cc_final: 0.8097 (mt) REVERT: G 55 GLU cc_start: 0.8552 (mp0) cc_final: 0.8262 (mp0) REVERT: G 150 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7366 (pt) REVERT: G 191 ASP cc_start: 0.7352 (t0) cc_final: 0.7134 (t0) REVERT: H 27 GLU cc_start: 0.5350 (OUTLIER) cc_final: 0.3663 (mm-30) REVERT: H 178 ARG cc_start: 0.8202 (ptp-170) cc_final: 0.7977 (ptm160) REVERT: I 50 TYR cc_start: 0.7615 (t80) cc_final: 0.7043 (t80) REVERT: I 68 GLU cc_start: 0.7129 (tp30) cc_final: 0.6870 (tp30) REVERT: J 25 LYS cc_start: 0.6706 (ptpp) cc_final: 0.6341 (ptpp) REVERT: J 127 TYR cc_start: 0.6744 (m-80) cc_final: 0.6244 (m-80) REVERT: K 1 MET cc_start: 0.6010 (mmt) cc_final: 0.5639 (mmm) REVERT: K 97 THR cc_start: 0.4641 (OUTLIER) cc_final: 0.4414 (t) REVERT: L 4 ARG cc_start: 0.5744 (tmt-80) cc_final: 0.3867 (mmt180) REVERT: M 28 SER cc_start: 0.8422 (p) cc_final: 0.8115 (p) REVERT: N 17 ARG cc_start: 0.3388 (mtp180) cc_final: 0.2649 (ptp-170) REVERT: P 28 ASN cc_start: 0.6710 (t0) cc_final: 0.6344 (t0) REVERT: P 60 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7127 (t80) REVERT: Q 66 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7335 (mp) REVERT: Q 71 HIS cc_start: 0.3860 (OUTLIER) cc_final: 0.3500 (p90) REVERT: Q 98 ARG cc_start: 0.7348 (mtp180) cc_final: 0.6922 (tpt170) REVERT: S 12 ARG cc_start: 0.4886 (ttt180) cc_final: 0.4629 (ttt180) REVERT: S 46 LYS cc_start: 0.5168 (mmmt) cc_final: 0.4870 (mmpt) REVERT: T 61 GLN cc_start: 0.8626 (tt0) cc_final: 0.8377 (mt0) REVERT: U 1 MET cc_start: 0.3132 (tpt) cc_final: 0.2763 (tpp) REVERT: U 13 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7690 (tptp) REVERT: U 31 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7672 (ptt90) REVERT: V 8 GLN cc_start: 0.7237 (tt0) cc_final: 0.6844 (tp40) REVERT: V 37 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6552 (tp) REVERT: V 47 ASP cc_start: 0.6086 (t70) cc_final: 0.5542 (t0) REVERT: V 61 ARG cc_start: 0.7845 (ptt90) cc_final: 0.7323 (tpt170) REVERT: W 37 LYS cc_start: 0.7989 (mttt) cc_final: 0.7785 (tttt) REVERT: W 59 LYS cc_start: 0.8759 (mttt) cc_final: 0.8376 (mttm) REVERT: X 68 HIS cc_start: 0.5222 (m90) cc_final: 0.5013 (m90) REVERT: Y 43 LYS cc_start: 0.6775 (mptt) cc_final: 0.6248 (mptt) REVERT: Z 16 ARG cc_start: 0.6187 (mtp180) cc_final: 0.5739 (mtp180) REVERT: Z 45 LYS cc_start: 0.7570 (mttt) cc_final: 0.7040 (mmmt) outliers start: 345 outliers final: 229 residues processed: 1455 average time/residue: 1.3750 time to fit residues: 3406.4999 Evaluate side-chains 1421 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1170 time to evaluate : 5.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 491 ARG Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 548 GLU Chi-restraints excluded: chain 8 residue 571 VAL Chi-restraints excluded: chain 8 residue 591 LEU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 682 MET Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 136 GLN Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain a residue 27 ILE Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 99 ASN 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 25 ASP Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 35 PHE Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 68 ARG Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 89 GLU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 45 PHE Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 20 ASN Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 60 PHE Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 109 ARG Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 857 optimal weight: 0.0570 chunk 584 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 766 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 chunk 878 optimal weight: 0.9990 chunk 711 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 525 optimal weight: 8.9990 chunk 923 optimal weight: 7.9990 chunk 259 optimal weight: 30.0000 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN e 22 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN o 98 GLN o 100 HIS ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN r 89 HIS t 15 HIS u 39 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN H 139 ASN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 HIS ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS V 49 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 162652 Z= 0.194 Angle : 0.663 14.622 243074 Z= 0.340 Chirality : 0.038 0.316 31031 Planarity : 0.005 0.065 13221 Dihedral : 24.364 179.484 80819 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.85 % Favored : 88.92 % Rotamer: Outliers : 7.46 % Allowed : 27.73 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.19 % 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: -3.21 (0.10), residues: 6067 helix: -1.71 (0.12), residues: 1640 sheet: -1.99 (0.16), residues: 941 loop : -2.45 (0.10), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP V 72 HIS 0.009 0.001 HIS K 11 PHE 0.031 0.002 PHE e 137 TYR 0.026 0.002 TYR 8 490 ARG 0.012 0.001 ARG j 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1578 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1202 time to evaluate : 6.323 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: 8 491 ARG cc_start: 0.1991 (OUTLIER) cc_final: 0.0444 (mmp-170) REVERT: 8 497 LYS cc_start: 0.7838 (pttp) cc_final: 0.6957 (ttmm) REVERT: 8 522 MET cc_start: 0.2542 (OUTLIER) cc_final: 0.1056 (mtp) REVERT: 8 548 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.4380 (pt0) REVERT: 8 574 MET cc_start: 0.4933 (tpp) cc_final: 0.3918 (mtm) REVERT: 8 584 HIS cc_start: 0.8005 (m90) cc_final: 0.7458 (m170) REVERT: 8 663 MET cc_start: 0.1220 (mpp) cc_final: -0.2268 (ptt) REVERT: b 155 ARG cc_start: 0.6898 (ptm160) cc_final: 0.5550 (ptm160) REVERT: c 125 TRP cc_start: 0.8337 (m100) cc_final: 0.7937 (m100) REVERT: d 57 LYS cc_start: 0.7574 (tmtt) cc_final: 0.7232 (tmtt) REVERT: d 69 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6139 (ptp-110) REVERT: d 85 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.5801 (m-10) REVERT: d 115 GLN cc_start: 0.8850 (tt0) cc_final: 0.7372 (tt0) REVERT: d 117 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7264 (mtm-85) REVERT: e 3 LEU cc_start: 0.7650 (mm) cc_final: 0.7447 (mm) REVERT: e 6 TYR cc_start: 0.6937 (t80) cc_final: 0.6218 (t80) REVERT: e 19 PHE cc_start: 0.6397 (m-80) cc_final: 0.6175 (m-10) REVERT: e 21 TYR cc_start: 0.6546 (m-80) cc_final: 0.6224 (m-80) REVERT: e 89 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6797 (p) REVERT: e 95 MET cc_start: 0.8042 (ttp) cc_final: 0.7175 (ttp) REVERT: e 111 ARG cc_start: 0.6845 (ttt90) cc_final: 0.5583 (ttt180) REVERT: f 21 GLN cc_start: 0.8317 (mm110) cc_final: 0.7934 (tp40) REVERT: f 115 GLN cc_start: 0.7941 (tt0) cc_final: 0.7249 (pm20) REVERT: f 116 LEU cc_start: 0.8027 (tp) cc_final: 0.7795 (tp) REVERT: g 73 ASN cc_start: 0.4570 (OUTLIER) cc_final: 0.3544 (t0) REVERT: g 135 HIS cc_start: 0.8164 (t70) cc_final: 0.7635 (t70) REVERT: j 7 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6020 (mmtp) REVERT: j 19 ASP cc_start: 0.7329 (t70) cc_final: 0.6921 (p0) REVERT: j 39 LYS cc_start: 0.8379 (tttt) cc_final: 0.7929 (ttmm) REVERT: j 131 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8953 (p0) REVERT: k 23 LYS cc_start: 0.8225 (tppt) cc_final: 0.8004 (mttm) REVERT: k 43 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8346 (mt) REVERT: k 59 LYS cc_start: 0.8205 (tmtt) cc_final: 0.7950 (tttt) REVERT: k 110 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7821 (mm-30) REVERT: k 113 MET cc_start: 0.6137 (mmt) cc_final: 0.5082 (ptm) REVERT: l 55 MET cc_start: 0.7936 (tpp) cc_final: 0.7069 (tpp) REVERT: l 143 GLU cc_start: 0.6161 (pm20) cc_final: 0.5531 (mp0) REVERT: m 31 PHE cc_start: 0.7642 (m-80) cc_final: 0.6950 (m-10) REVERT: m 62 LYS cc_start: 0.7833 (pttm) cc_final: 0.7603 (pttm) REVERT: n 42 LYS cc_start: 0.7952 (tptp) cc_final: 0.7731 (tptp) REVERT: n 72 ASP cc_start: 0.7643 (t0) cc_final: 0.7054 (t0) REVERT: o 13 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6493 (tpt90) REVERT: o 30 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7212 (ttp80) REVERT: o 33 ARG cc_start: 0.8901 (ttt180) cc_final: 0.8494 (tpp-160) REVERT: o 67 ASN cc_start: 0.7527 (p0) cc_final: 0.7152 (p0) REVERT: p 100 ARG cc_start: 0.8481 (mtt180) cc_final: 0.8116 (mtm-85) REVERT: q 13 HIS cc_start: 0.7229 (m90) cc_final: 0.6894 (m-70) REVERT: r 11 GLN cc_start: 0.7685 (mp10) cc_final: 0.6681 (mt0) REVERT: r 43 ASN cc_start: 0.6058 (OUTLIER) cc_final: 0.5754 (m-40) REVERT: r 68 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7069 (mtm180) REVERT: r 92 TRP cc_start: 0.7482 (m100) cc_final: 0.7073 (m100) REVERT: r 97 LYS cc_start: 0.8809 (tmmt) cc_final: 0.7909 (mttp) REVERT: s 66 ILE cc_start: 0.8485 (tt) cc_final: 0.8136 (mm) REVERT: t 1 MET cc_start: 0.4319 (mmt) cc_final: 0.3739 (mmm) REVERT: t 89 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.4464 (mm-30) REVERT: u 60 LYS cc_start: 0.8904 (tppt) cc_final: 0.8439 (tptp) REVERT: v 46 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8831 (mmmm) REVERT: v 86 LEU cc_start: 0.7419 (mt) cc_final: 0.6544 (mp) REVERT: w 40 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8709 (ttpp) REVERT: w 65 PHE cc_start: 0.7221 (m-10) cc_final: 0.6911 (m-10) REVERT: x 5 GLN cc_start: 0.8809 (mp10) cc_final: 0.8513 (mp10) REVERT: x 33 HIS cc_start: 0.6861 (m-70) cc_final: 0.6453 (m90) REVERT: x 51 SER cc_start: 0.8905 (p) cc_final: 0.8394 (p) REVERT: x 67 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6765 (tt) REVERT: y 58 ASN cc_start: 0.7647 (p0) cc_final: 0.7410 (p0) REVERT: z 37 ARG cc_start: 0.7062 (tpp-160) cc_final: 0.6798 (tpp-160) REVERT: z 57 GLU cc_start: 0.7825 (tp30) cc_final: 0.7495 (tm-30) REVERT: B 14 MET cc_start: 0.6849 (ttm) cc_final: 0.6649 (ttt) REVERT: B 35 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8253 (mp0) REVERT: D 11 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8705 (mtpp) REVERT: F 1 MET cc_start: 0.6538 (tpp) cc_final: 0.5284 (mpp) REVERT: F 23 ILE cc_start: 0.8488 (mt) cc_final: 0.8149 (mt) REVERT: G 55 GLU cc_start: 0.8536 (mp0) cc_final: 0.8248 (mp0) REVERT: G 144 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: G 150 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7378 (pt) REVERT: G 191 ASP cc_start: 0.7500 (t0) cc_final: 0.7289 (t0) REVERT: G 199 ILE cc_start: 0.8007 (mt) cc_final: 0.7580 (mm) REVERT: H 27 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.3833 (mm-30) REVERT: H 39 ARG cc_start: -0.1439 (OUTLIER) cc_final: -0.1661 (tmm160) REVERT: H 110 LEU cc_start: 0.7334 (tp) cc_final: 0.6732 (mt) REVERT: H 143 LEU cc_start: 0.6667 (tp) cc_final: 0.6329 (tp) REVERT: H 178 ARG cc_start: 0.8177 (ptp-170) cc_final: 0.7948 (ptm160) REVERT: I 50 TYR cc_start: 0.7663 (t80) cc_final: 0.7151 (t80) REVERT: I 94 GLU cc_start: 0.7416 (tt0) cc_final: 0.7213 (tt0) REVERT: J 25 LYS cc_start: 0.6678 (ptpp) cc_final: 0.6289 (ptpp) REVERT: J 70 MET cc_start: 0.3771 (OUTLIER) cc_final: 0.3514 (mmp) REVERT: K 1 MET cc_start: 0.6021 (mmt) cc_final: 0.5667 (mmm) REVERT: K 21 MET cc_start: 0.6283 (mtp) cc_final: 0.5785 (mtp) REVERT: K 52 ASN cc_start: 0.8356 (t0) cc_final: 0.8101 (t0) REVERT: K 91 ARG cc_start: 0.5928 (ttt-90) cc_final: 0.4784 (ttt-90) REVERT: K 97 THR cc_start: 0.4554 (p) cc_final: 0.4326 (t) REVERT: M 28 SER cc_start: 0.8418 (p) cc_final: 0.8092 (p) REVERT: N 17 ARG cc_start: 0.3635 (mtp180) cc_final: 0.2833 (ptp-170) REVERT: P 28 ASN cc_start: 0.6795 (t0) cc_final: 0.6458 (t0) REVERT: P 60 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7105 (t80) REVERT: Q 28 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: Q 66 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7352 (mp) REVERT: Q 98 ARG cc_start: 0.7378 (mtp180) cc_final: 0.6963 (tpt170) REVERT: S 46 LYS cc_start: 0.5078 (mmmt) cc_final: 0.4814 (mmpt) REVERT: T 34 GLN cc_start: 0.8903 (tp40) cc_final: 0.8588 (tp-100) REVERT: T 61 GLN cc_start: 0.8709 (tt0) cc_final: 0.8399 (mt0) REVERT: U 1 MET cc_start: 0.3026 (tpt) cc_final: 0.2616 (tpp) REVERT: U 4 ILE cc_start: 0.4318 (OUTLIER) cc_final: 0.4012 (mt) REVERT: U 13 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7505 (tptp) REVERT: U 31 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7703 (ptt90) REVERT: U 33 ILE cc_start: 0.8952 (mt) cc_final: 0.8731 (mp) REVERT: U 66 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7840 (p) REVERT: V 47 ASP cc_start: 0.6045 (t70) cc_final: 0.5554 (t0) REVERT: W 37 LYS cc_start: 0.7995 (mttt) cc_final: 0.7773 (tttt) REVERT: Y 24 ARG cc_start: 0.8761 (ttm110) cc_final: 0.7890 (ttm110) REVERT: Y 28 ARG cc_start: 0.8769 (mtt-85) cc_final: 0.8187 (mtt-85) REVERT: Y 43 LYS cc_start: 0.6825 (mptt) cc_final: 0.6380 (mptt) REVERT: Y 67 HIS cc_start: 0.5861 (OUTLIER) cc_final: 0.5508 (t-170) REVERT: Z 16 ARG cc_start: 0.6008 (mtp180) cc_final: 0.5517 (mtp-110) REVERT: Z 23 GLU cc_start: 0.0573 (OUTLIER) cc_final: -0.0586 (pp20) REVERT: Z 45 LYS cc_start: 0.7576 (mttt) cc_final: 0.7021 (mmmt) outliers start: 376 outliers final: 280 residues processed: 1428 average time/residue: 1.3637 time to fit residues: 3323.9602 Evaluate side-chains 1442 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1135 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 433 LEU Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 491 ARG Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 522 MET Chi-restraints excluded: chain 8 residue 548 GLU Chi-restraints excluded: chain 8 residue 573 ASP Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 661 SER Chi-restraints excluded: chain 8 residue 685 LEU Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 11 MET Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 69 ARG Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 85 PHE Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 136 GLN Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 110 HIS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 56 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 35 PHE Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 68 ARG Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 89 GLU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 69 GLU Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 60 PHE Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 17 ASP Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 67 HIS Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 346 optimal weight: 10.0000 chunk 927 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 604 optimal weight: 0.1980 chunk 254 optimal weight: 10.0000 chunk 1030 optimal weight: 4.9990 chunk 855 optimal weight: 20.0000 chunk 477 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 340 optimal weight: 20.0000 chunk 540 optimal weight: 0.6980 overall best weight: 5.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 250 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN o 100 HIS ** q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS u 39 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 162652 Z= 0.264 Angle : 0.725 15.389 243074 Z= 0.368 Chirality : 0.040 0.317 31031 Planarity : 0.005 0.073 13221 Dihedral : 24.453 179.911 80819 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.64 % Favored : 88.10 % Rotamer: Outliers : 8.06 % Allowed : 28.44 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.19 % 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: -3.19 (0.10), residues: 6067 helix: -1.65 (0.12), residues: 1644 sheet: -1.92 (0.16), residues: 941 loop : -2.48 (0.10), residues: 3482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP V 72 HIS 0.049 0.002 HIS Y 67 PHE 0.039 0.002 PHE e 137 TYR 0.035 0.002 TYR f 93 ARG 0.012 0.001 ARG f 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 1165 time to evaluate : 8.525 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: 8 491 ARG cc_start: 0.1962 (OUTLIER) cc_final: 0.0488 (mmm160) REVERT: 8 497 LYS cc_start: 0.7853 (pttp) cc_final: 0.6966 (ttmm) REVERT: 8 522 MET cc_start: 0.3150 (ttp) cc_final: 0.1584 (ttt) REVERT: 8 548 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.4462 (pt0) REVERT: 8 574 MET cc_start: 0.4903 (tpp) cc_final: 0.3593 (mtp) REVERT: 8 584 HIS cc_start: 0.8026 (m90) cc_final: 0.7269 (m170) REVERT: 8 617 MET cc_start: -0.1832 (mpp) cc_final: -0.2159 (mpp) REVERT: 8 663 MET cc_start: 0.1326 (mpp) cc_final: -0.2287 (ptt) REVERT: 8 682 MET cc_start: 0.2815 (ttt) cc_final: 0.2043 (ttt) REVERT: b 155 ARG cc_start: 0.7019 (ptm160) cc_final: 0.5679 (ptm160) REVERT: c 125 TRP cc_start: 0.8368 (m100) cc_final: 0.7919 (m100) REVERT: d 57 LYS cc_start: 0.7715 (tmtt) cc_final: 0.7260 (tmtt) REVERT: d 69 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6199 (ptp-110) REVERT: d 85 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: e 3 LEU cc_start: 0.7846 (mm) cc_final: 0.7634 (mm) REVERT: e 8 LYS cc_start: 0.7495 (mtmt) cc_final: 0.7171 (UNCLASSIFIED) REVERT: e 21 TYR cc_start: 0.6609 (m-80) cc_final: 0.6270 (m-80) REVERT: e 31 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6798 (tp30) REVERT: e 95 MET cc_start: 0.8050 (ttp) cc_final: 0.7120 (ttp) REVERT: e 111 ARG cc_start: 0.6927 (ttt90) cc_final: 0.5621 (ttt180) REVERT: f 21 GLN cc_start: 0.8325 (mm110) cc_final: 0.8013 (tp40) REVERT: f 40 VAL cc_start: 0.8659 (m) cc_final: 0.8388 (p) REVERT: f 43 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6972 (mmmt) REVERT: f 105 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7733 (p) REVERT: f 115 GLN cc_start: 0.7991 (tt0) cc_final: 0.7276 (pm20) REVERT: f 116 LEU cc_start: 0.8068 (tp) cc_final: 0.7794 (tp) REVERT: g 135 HIS cc_start: 0.8146 (t70) cc_final: 0.7654 (t70) REVERT: a 7 ARG cc_start: 0.0205 (OUTLIER) cc_final: -0.2244 (mmt180) REVERT: a 218 MET cc_start: -0.0633 (ttt) cc_final: -0.2067 (ppp) REVERT: j 7 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6124 (mttp) REVERT: j 19 ASP cc_start: 0.7361 (t70) cc_final: 0.6973 (p0) REVERT: j 39 LYS cc_start: 0.8415 (tttt) cc_final: 0.7988 (ttmm) REVERT: j 103 ILE cc_start: 0.9013 (mt) cc_final: 0.8711 (mt) REVERT: j 131 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8959 (p0) REVERT: k 23 LYS cc_start: 0.8331 (tppt) cc_final: 0.8079 (mttm) REVERT: k 43 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8337 (mt) REVERT: k 59 LYS cc_start: 0.8300 (tmtt) cc_final: 0.7998 (tttt) REVERT: k 98 ARG cc_start: 0.5138 (mpt180) cc_final: 0.4671 (tmm-80) REVERT: k 110 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7860 (mm-30) REVERT: k 113 MET cc_start: 0.6203 (mmt) cc_final: 0.5203 (ptt) REVERT: l 33 ARG cc_start: 0.4093 (OUTLIER) cc_final: 0.2882 (mtt180) REVERT: l 55 MET cc_start: 0.7938 (tpp) cc_final: 0.7062 (tpp) REVERT: l 143 GLU cc_start: 0.6303 (pm20) cc_final: 0.5700 (mp0) REVERT: m 31 PHE cc_start: 0.7736 (m-80) cc_final: 0.7145 (m-10) REVERT: n 30 ARG cc_start: 0.7410 (mtm110) cc_final: 0.7092 (mtm110) REVERT: n 72 ASP cc_start: 0.7463 (t0) cc_final: 0.7083 (t70) REVERT: n 90 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6867 (pmt-80) REVERT: o 3 LYS cc_start: 0.7880 (pptt) cc_final: 0.7673 (pptt) REVERT: o 13 ARG cc_start: 0.7209 (tpt170) cc_final: 0.6508 (tpt90) REVERT: o 30 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7225 (ttp80) REVERT: o 33 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8470 (tpp-160) REVERT: o 67 ASN cc_start: 0.7559 (p0) cc_final: 0.7143 (p0) REVERT: p 5 LYS cc_start: 0.8639 (tptp) cc_final: 0.8073 (ttpt) REVERT: q 111 LYS cc_start: 0.8744 (tttm) cc_final: 0.8422 (tmtt) REVERT: r 11 GLN cc_start: 0.7773 (mp10) cc_final: 0.6562 (mt0) REVERT: r 43 ASN cc_start: 0.6126 (OUTLIER) cc_final: 0.5825 (m-40) REVERT: r 68 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7158 (mtm180) REVERT: r 92 TRP cc_start: 0.7487 (m100) cc_final: 0.7058 (m100) REVERT: r 97 LYS cc_start: 0.8847 (tmmt) cc_final: 0.7922 (mttm) REVERT: s 66 ILE cc_start: 0.8525 (tt) cc_final: 0.8176 (mm) REVERT: t 1 MET cc_start: 0.4420 (mmt) cc_final: 0.3959 (mmm) REVERT: t 89 GLU cc_start: 0.5011 (OUTLIER) cc_final: 0.4532 (mm-30) REVERT: u 60 LYS cc_start: 0.8933 (tppt) cc_final: 0.8476 (tptp) REVERT: v 46 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8799 (mmmm) REVERT: v 86 LEU cc_start: 0.7503 (mt) cc_final: 0.6720 (mp) REVERT: w 40 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8666 (ttpp) REVERT: w 65 PHE cc_start: 0.7169 (m-10) cc_final: 0.6958 (m-10) REVERT: x 33 HIS cc_start: 0.6913 (m-70) cc_final: 0.6497 (m90) REVERT: x 51 SER cc_start: 0.8924 (p) cc_final: 0.8404 (p) REVERT: x 67 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6893 (tt) REVERT: y 58 ASN cc_start: 0.7700 (p0) cc_final: 0.7421 (p0) REVERT: z 57 GLU cc_start: 0.7816 (tp30) cc_final: 0.7490 (tm-30) REVERT: B 3 GLN cc_start: 0.8679 (pp30) cc_final: 0.8389 (pp30) REVERT: B 14 MET cc_start: 0.6834 (ttm) cc_final: 0.6629 (ttt) REVERT: B 35 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8266 (mp0) REVERT: D 11 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8732 (mtpp) REVERT: F 23 ILE cc_start: 0.8498 (mt) cc_final: 0.8127 (mt) REVERT: G 55 GLU cc_start: 0.8564 (mp0) cc_final: 0.8263 (mp0) REVERT: G 150 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7346 (pt) REVERT: G 191 ASP cc_start: 0.7487 (t0) cc_final: 0.7246 (t0) REVERT: G 199 ILE cc_start: 0.7967 (mt) cc_final: 0.7742 (mt) REVERT: H 27 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.3677 (mm-30) REVERT: H 39 ARG cc_start: -0.1362 (OUTLIER) cc_final: -0.1623 (tmm160) REVERT: H 110 LEU cc_start: 0.7431 (tp) cc_final: 0.6791 (mt) REVERT: H 143 LEU cc_start: 0.7043 (tp) cc_final: 0.6688 (tp) REVERT: I 50 TYR cc_start: 0.7616 (t80) cc_final: 0.7174 (t80) REVERT: I 68 GLU cc_start: 0.7165 (tp30) cc_final: 0.6913 (mm-30) REVERT: I 77 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: J 25 LYS cc_start: 0.6750 (ptpp) cc_final: 0.6261 (ptpp) REVERT: K 21 MET cc_start: 0.6405 (mtp) cc_final: 0.5439 (mtp) REVERT: K 45 ARG cc_start: 0.8149 (mpp80) cc_final: 0.7810 (mpp80) REVERT: K 65 GLU cc_start: 0.4587 (OUTLIER) cc_final: 0.3347 (tm-30) REVERT: K 91 ARG cc_start: 0.6005 (ttt-90) cc_final: 0.4886 (ttt-90) REVERT: K 97 THR cc_start: 0.4577 (OUTLIER) cc_final: 0.4350 (t) REVERT: M 28 SER cc_start: 0.8482 (p) cc_final: 0.8155 (p) REVERT: N 17 ARG cc_start: 0.3863 (mtp180) cc_final: 0.3026 (ptp-170) REVERT: P 22 ILE cc_start: 0.7493 (mp) cc_final: 0.7122 (mm) REVERT: P 28 ASN cc_start: 0.6937 (t0) cc_final: 0.6605 (t0) REVERT: P 34 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7509 (t) REVERT: P 60 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7156 (t80) REVERT: Q 28 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: Q 66 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7349 (mp) REVERT: Q 71 HIS cc_start: 0.4003 (OUTLIER) cc_final: 0.3533 (p90) REVERT: Q 98 ARG cc_start: 0.7334 (mtp180) cc_final: 0.6920 (tpt170) REVERT: S 46 LYS cc_start: 0.4929 (mmmt) cc_final: 0.4666 (mmpt) REVERT: T 61 GLN cc_start: 0.8793 (tt0) cc_final: 0.8508 (mt0) REVERT: U 1 MET cc_start: 0.3160 (tpt) cc_final: 0.2943 (tpp) REVERT: U 4 ILE cc_start: 0.4147 (OUTLIER) cc_final: 0.3851 (mt) REVERT: U 5 ARG cc_start: 0.5871 (ptt-90) cc_final: 0.5359 (ptt-90) REVERT: U 13 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7357 (tptp) REVERT: W 37 LYS cc_start: 0.8089 (mttt) cc_final: 0.7882 (tttt) REVERT: W 60 ARG cc_start: 0.7343 (mmp-170) cc_final: 0.7019 (mtm180) REVERT: W 72 ARG cc_start: 0.7581 (ptt180) cc_final: 0.6703 (mmt-90) REVERT: X 68 HIS cc_start: 0.5409 (m90) cc_final: 0.5144 (m90) REVERT: Y 43 LYS cc_start: 0.6818 (mptt) cc_final: 0.6320 (mptt) REVERT: Z 16 ARG cc_start: 0.6203 (mtp180) cc_final: 0.5881 (mtp-110) REVERT: Z 23 GLU cc_start: 0.0788 (OUTLIER) cc_final: -0.0443 (pp20) REVERT: Z 45 LYS cc_start: 0.7595 (mttt) cc_final: 0.7043 (mmmt) outliers start: 406 outliers final: 314 residues processed: 1416 average time/residue: 1.3731 time to fit residues: 3340.8440 Evaluate side-chains 1479 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1135 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 491 ARG Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 548 GLU Chi-restraints excluded: chain 8 residue 573 ASP Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 693 ASN Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 11 MET Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 69 ARG Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 85 PHE Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 136 GLN Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 9 ASP Chi-restraints excluded: chain e residue 31 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain f residue 110 HIS Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain a residue 7 ARG Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 46 ASP Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 33 ARG Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 78 LYS Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 56 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 35 PHE Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 68 ARG Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 89 GLU Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain u residue 102 ILE Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 60 PHE Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 19 SER Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 993 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 587 optimal weight: 9.9990 chunk 752 optimal weight: 5.9990 chunk 583 optimal weight: 10.0000 chunk 867 optimal weight: 0.3980 chunk 575 optimal weight: 7.9990 chunk 1026 optimal weight: 0.3980 chunk 642 optimal weight: 6.9990 chunk 625 optimal weight: 9.9990 chunk 473 optimal weight: 20.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN n 107 ASN o 100 HIS r 89 HIS u 39 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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** M 3 GLN P 21 HIS ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN Y 60 GLN Y 67 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 162652 Z= 0.229 Angle : 0.691 15.985 243074 Z= 0.352 Chirality : 0.038 0.299 31031 Planarity : 0.005 0.063 13221 Dihedral : 24.500 179.642 80819 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.18 % Favored : 88.59 % Rotamer: Outliers : 7.60 % Allowed : 29.97 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.19 % 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: -3.07 (0.10), residues: 6067 helix: -1.46 (0.12), residues: 1634 sheet: -1.87 (0.16), residues: 948 loop : -2.44 (0.10), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP V 72 HIS 0.018 0.002 HIS Y 67 PHE 0.034 0.002 PHE e 76 TYR 0.040 0.002 TYR q 31 ARG 0.013 0.001 ARG V 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1161 time to evaluate : 6.317 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: 8 431 MET cc_start: 0.4821 (ppp) cc_final: 0.4528 (ppp) REVERT: 8 491 ARG cc_start: 0.1904 (OUTLIER) cc_final: 0.0439 (mmm160) REVERT: 8 497 LYS cc_start: 0.7888 (pttp) cc_final: 0.7033 (ttmm) REVERT: 8 522 MET cc_start: 0.3211 (ttp) cc_final: 0.2418 (ttt) REVERT: 8 548 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.4473 (pt0) REVERT: 8 584 HIS cc_start: 0.8049 (m90) cc_final: 0.7265 (m170) REVERT: 8 663 MET cc_start: 0.1328 (mpp) cc_final: -0.2281 (ptt) REVERT: b 155 ARG cc_start: 0.6930 (ptm160) cc_final: 0.5654 (ptm160) REVERT: c 125 TRP cc_start: 0.8347 (m100) cc_final: 0.7943 (m100) REVERT: d 57 LYS cc_start: 0.7602 (tmtt) cc_final: 0.7088 (tmtt) REVERT: d 69 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6146 (ptp-110) REVERT: d 85 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.5938 (m-80) REVERT: e 21 TYR cc_start: 0.6662 (m-80) cc_final: 0.6297 (m-80) REVERT: e 31 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6654 (tp30) REVERT: e 95 MET cc_start: 0.8067 (ttp) cc_final: 0.7485 (ttp) REVERT: e 111 ARG cc_start: 0.6989 (ttt90) cc_final: 0.5704 (ttt180) REVERT: f 21 GLN cc_start: 0.8375 (mm110) cc_final: 0.8096 (tp40) REVERT: f 34 ARG cc_start: 0.8768 (tpm170) cc_final: 0.8533 (tpm170) REVERT: f 43 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6905 (mmmt) REVERT: f 115 GLN cc_start: 0.7957 (tt0) cc_final: 0.7263 (pm20) REVERT: f 116 LEU cc_start: 0.8053 (tp) cc_final: 0.7798 (tp) REVERT: g 135 HIS cc_start: 0.8136 (t70) cc_final: 0.7594 (t70) REVERT: a 7 ARG cc_start: 0.0272 (OUTLIER) cc_final: -0.2358 (mmt180) REVERT: a 20 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6462 (mp10) REVERT: a 218 MET cc_start: -0.0479 (ttt) cc_final: -0.1815 (ttt) REVERT: j 7 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6110 (mttp) REVERT: j 19 ASP cc_start: 0.7374 (t70) cc_final: 0.6989 (p0) REVERT: j 39 LYS cc_start: 0.8390 (tttt) cc_final: 0.7994 (ttmm) REVERT: j 86 GLN cc_start: 0.7758 (pp30) cc_final: 0.7027 (pp30) REVERT: j 102 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7357 (mm-30) REVERT: j 122 LEU cc_start: 0.8834 (mt) cc_final: 0.8070 (pp) REVERT: k 23 LYS cc_start: 0.8287 (tppt) cc_final: 0.8038 (mttm) REVERT: k 43 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8320 (mt) REVERT: k 59 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7985 (tttt) REVERT: k 98 ARG cc_start: 0.5109 (mpt180) cc_final: 0.4671 (tmm-80) REVERT: k 110 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7838 (mm-30) REVERT: k 113 MET cc_start: 0.6251 (mmt) cc_final: 0.5153 (ptt) REVERT: l 55 MET cc_start: 0.7905 (tpp) cc_final: 0.7045 (tpp) REVERT: l 143 GLU cc_start: 0.6788 (pm20) cc_final: 0.5876 (mp0) REVERT: m 1 MET cc_start: 0.6087 (ppp) cc_final: 0.5762 (ppp) REVERT: m 31 PHE cc_start: 0.7692 (m-80) cc_final: 0.7015 (m-10) REVERT: m 47 GLU cc_start: 0.7293 (tp30) cc_final: 0.7012 (tp30) REVERT: m 90 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7196 (mm-30) REVERT: m 104 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6775 (mm-30) REVERT: n 72 ASP cc_start: 0.7383 (t0) cc_final: 0.6960 (t70) REVERT: o 13 ARG cc_start: 0.7217 (tpt170) cc_final: 0.6524 (tpt90) REVERT: o 30 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7281 (ttp80) REVERT: o 33 ARG cc_start: 0.8878 (ttt180) cc_final: 0.8391 (tpp-160) REVERT: o 67 ASN cc_start: 0.7560 (p0) cc_final: 0.7093 (p0) REVERT: p 100 ARG cc_start: 0.8524 (mtt180) cc_final: 0.8258 (mtm-85) REVERT: r 11 GLN cc_start: 0.7741 (mp10) cc_final: 0.6455 (mt0) REVERT: r 43 ASN cc_start: 0.6072 (OUTLIER) cc_final: 0.5606 (m110) REVERT: r 92 TRP cc_start: 0.7474 (m100) cc_final: 0.7065 (m100) REVERT: r 97 LYS cc_start: 0.8814 (tmmt) cc_final: 0.7910 (mttm) REVERT: s 66 ILE cc_start: 0.8536 (tt) cc_final: 0.8192 (mm) REVERT: t 1 MET cc_start: 0.4487 (mmt) cc_final: 0.3958 (mmm) REVERT: t 77 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7736 (ttm110) REVERT: t 89 GLU cc_start: 0.5091 (OUTLIER) cc_final: 0.4589 (mm-30) REVERT: u 34 ILE cc_start: 0.7607 (mp) cc_final: 0.6983 (tt) REVERT: u 60 LYS cc_start: 0.8927 (tppt) cc_final: 0.8583 (tptp) REVERT: v 86 LEU cc_start: 0.7482 (mt) cc_final: 0.6729 (mp) REVERT: w 40 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8674 (ttpp) REVERT: w 68 LYS cc_start: 0.6305 (mtpt) cc_final: 0.5814 (mtmt) REVERT: x 33 HIS cc_start: 0.6956 (m-70) cc_final: 0.6606 (m90) REVERT: x 51 SER cc_start: 0.8894 (p) cc_final: 0.8375 (p) REVERT: x 67 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6824 (tt) REVERT: y 58 ASN cc_start: 0.7702 (p0) cc_final: 0.7407 (p0) REVERT: z 28 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6866 (mt) REVERT: z 57 GLU cc_start: 0.7822 (tp30) cc_final: 0.7517 (tm-30) REVERT: B 3 GLN cc_start: 0.8633 (pp30) cc_final: 0.8354 (pp30) REVERT: D 11 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8690 (mtpp) REVERT: D 37 LYS cc_start: 0.8757 (tttt) cc_final: 0.8540 (tttt) REVERT: E 39 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8093 (ttm170) REVERT: F 1 MET cc_start: 0.5456 (tpt) cc_final: 0.5158 (tpt) REVERT: F 23 ILE cc_start: 0.8530 (mt) cc_final: 0.8163 (mt) REVERT: F 34 LYS cc_start: 0.7910 (tttt) cc_final: 0.7237 (tttt) REVERT: G 55 GLU cc_start: 0.8537 (mp0) cc_final: 0.8260 (mp0) REVERT: G 69 VAL cc_start: 0.8099 (t) cc_final: 0.7868 (t) REVERT: G 144 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: G 150 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7371 (pt) REVERT: G 199 ILE cc_start: 0.7988 (mt) cc_final: 0.7745 (mt) REVERT: G 207 ARG cc_start: 0.6442 (tpp-160) cc_final: 0.6190 (mpp80) REVERT: H 27 GLU cc_start: 0.5381 (OUTLIER) cc_final: 0.3692 (mm-30) REVERT: H 39 ARG cc_start: -0.1216 (OUTLIER) cc_final: -0.1473 (tmm160) REVERT: H 79 LYS cc_start: 0.3760 (mmmt) cc_final: 0.3538 (mmmt) REVERT: H 110 LEU cc_start: 0.7455 (tp) cc_final: 0.6830 (mt) REVERT: H 143 LEU cc_start: 0.7123 (tp) cc_final: 0.6802 (tp) REVERT: I 50 TYR cc_start: 0.7626 (t80) cc_final: 0.7228 (t80) REVERT: J 25 LYS cc_start: 0.6731 (ptpp) cc_final: 0.6144 (ptpp) REVERT: J 88 HIS cc_start: 0.6295 (t-90) cc_final: 0.5865 (t-90) REVERT: K 21 MET cc_start: 0.6276 (mtp) cc_final: 0.5627 (mtp) REVERT: K 88 MET cc_start: 0.7159 (ptm) cc_final: 0.6918 (ptm) REVERT: K 90 MET cc_start: 0.6532 (mmm) cc_final: 0.6254 (mmm) REVERT: K 91 ARG cc_start: 0.6192 (ttt-90) cc_final: 0.5101 (ttt-90) REVERT: M 28 SER cc_start: 0.8378 (p) cc_final: 0.8063 (p) REVERT: M 66 GLN cc_start: 0.5993 (OUTLIER) cc_final: 0.5596 (mt0) REVERT: N 17 ARG cc_start: 0.4147 (mtp180) cc_final: 0.3159 (ptp-170) REVERT: P 28 ASN cc_start: 0.6789 (t0) cc_final: 0.6497 (t0) REVERT: P 34 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7392 (t) REVERT: P 60 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7170 (t80) REVERT: P 120 CYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6638 (p) REVERT: Q 28 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: Q 66 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7250 (mp) REVERT: Q 71 HIS cc_start: 0.3771 (OUTLIER) cc_final: 0.3346 (p90) REVERT: S 46 LYS cc_start: 0.4979 (mmmt) cc_final: 0.4735 (mmpt) REVERT: T 61 GLN cc_start: 0.8843 (tt0) cc_final: 0.8602 (mt0) REVERT: U 1 MET cc_start: 0.2878 (tpt) cc_final: 0.2595 (tpp) REVERT: U 4 ILE cc_start: 0.4076 (OUTLIER) cc_final: 0.3817 (mt) REVERT: U 13 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7348 (tptp) REVERT: U 31 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7407 (ptt90) REVERT: V 47 ASP cc_start: 0.6214 (t70) cc_final: 0.5477 (t70) REVERT: W 37 LYS cc_start: 0.7865 (mttt) cc_final: 0.7661 (tttt) REVERT: Y 43 LYS cc_start: 0.6878 (mptt) cc_final: 0.6360 (mptt) REVERT: Z 16 ARG cc_start: 0.6329 (mtp180) cc_final: 0.5942 (mtp180) REVERT: Z 23 GLU cc_start: 0.0748 (OUTLIER) cc_final: -0.0353 (pp20) REVERT: Z 45 LYS cc_start: 0.7610 (mttt) cc_final: 0.7088 (mmmt) outliers start: 383 outliers final: 287 residues processed: 1405 average time/residue: 1.3654 time to fit residues: 3281.0651 Evaluate side-chains 1434 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1119 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 470 VAL Chi-restraints excluded: chain 8 residue 491 ARG Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 548 GLU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 11 MET Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 69 ARG Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 85 PHE Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 31 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 76 ILE Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 110 HIS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain g residue 149 GLU Chi-restraints excluded: chain a residue 7 ARG Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 123 LYS Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 56 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 89 GLU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 66 GLN Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 60 PHE Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 635 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 613 optimal weight: 50.0000 chunk 309 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 652 optimal weight: 0.0370 chunk 699 optimal weight: 10.0000 chunk 507 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 806 optimal weight: 0.0040 overall best weight: 4.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN o 100 HIS p 2 ASN r 89 HIS ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 162652 Z= 0.227 Angle : 0.695 16.168 243074 Z= 0.353 Chirality : 0.038 0.305 31031 Planarity : 0.005 0.070 13221 Dihedral : 24.506 179.588 80814 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.46 % Favored : 88.30 % Rotamer: Outliers : 7.50 % Allowed : 30.55 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.19 % 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: -3.05 (0.10), residues: 6067 helix: -1.41 (0.12), residues: 1631 sheet: -1.90 (0.16), residues: 965 loop : -2.44 (0.10), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP V 72 HIS 0.010 0.002 HIS J 88 PHE 0.035 0.002 PHE e 19 TYR 0.033 0.002 TYR v 57 ARG 0.014 0.001 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1514 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1136 time to evaluate : 6.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 491 ARG cc_start: 0.1839 (OUTLIER) cc_final: 0.0346 (mmm160) REVERT: 8 497 LYS cc_start: 0.7891 (pttp) cc_final: 0.7038 (ttmm) REVERT: 8 522 MET cc_start: 0.3000 (ttp) cc_final: 0.2241 (ttt) REVERT: 8 548 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.4276 (pt0) REVERT: 8 560 GLN cc_start: 0.1046 (OUTLIER) cc_final: 0.0308 (tm-30) REVERT: 8 584 HIS cc_start: 0.8041 (m90) cc_final: 0.7270 (m170) REVERT: 8 617 MET cc_start: -0.1788 (mpp) cc_final: -0.2308 (mpp) REVERT: 8 663 MET cc_start: 0.1419 (OUTLIER) cc_final: -0.1931 (ptt) REVERT: b 155 ARG cc_start: 0.6950 (ptm160) cc_final: 0.5634 (ptm160) REVERT: c 125 TRP cc_start: 0.8341 (m100) cc_final: 0.7938 (m100) REVERT: d 57 LYS cc_start: 0.7629 (tmtt) cc_final: 0.7124 (tmtt) REVERT: d 69 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6163 (ptp-110) REVERT: d 85 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5927 (m-80) REVERT: e 3 LEU cc_start: 0.7786 (mm) cc_final: 0.7526 (mm) REVERT: e 4 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.7948 (t-90) REVERT: e 21 TYR cc_start: 0.6692 (m-80) cc_final: 0.6267 (m-80) REVERT: e 31 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6723 (tp30) REVERT: e 95 MET cc_start: 0.7977 (ttp) cc_final: 0.7400 (ttp) REVERT: e 111 ARG cc_start: 0.7004 (ttt90) cc_final: 0.5701 (ttt180) REVERT: f 21 GLN cc_start: 0.8403 (mm110) cc_final: 0.8160 (tp40) REVERT: f 40 VAL cc_start: 0.8614 (m) cc_final: 0.8375 (p) REVERT: f 41 GLU cc_start: 0.8210 (pp20) cc_final: 0.7946 (pp20) REVERT: f 43 LYS cc_start: 0.7149 (mmtt) cc_final: 0.6863 (mmmt) REVERT: f 115 GLN cc_start: 0.7966 (tt0) cc_final: 0.7278 (pm20) REVERT: f 116 LEU cc_start: 0.8028 (tp) cc_final: 0.7804 (tp) REVERT: g 135 HIS cc_start: 0.8112 (t70) cc_final: 0.7579 (t70) REVERT: a 7 ARG cc_start: 0.0232 (OUTLIER) cc_final: -0.2352 (mmt180) REVERT: a 20 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6463 (mp10) REVERT: a 218 MET cc_start: -0.0265 (ttt) cc_final: -0.1606 (ttt) REVERT: j 7 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6079 (mttp) REVERT: j 16 TYR cc_start: 0.8167 (m-80) cc_final: 0.7883 (m-80) REVERT: j 19 ASP cc_start: 0.7360 (t70) cc_final: 0.7002 (p0) REVERT: j 39 LYS cc_start: 0.8403 (tttt) cc_final: 0.8001 (ttmm) REVERT: j 86 GLN cc_start: 0.7694 (pp30) cc_final: 0.6938 (pp30) REVERT: j 122 LEU cc_start: 0.8798 (mt) cc_final: 0.8195 (pp) REVERT: k 23 LYS cc_start: 0.8291 (tppt) cc_final: 0.8061 (mttm) REVERT: k 43 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8281 (mt) REVERT: k 59 LYS cc_start: 0.8283 (tmtt) cc_final: 0.7958 (tttt) REVERT: k 98 ARG cc_start: 0.5122 (mpt180) cc_final: 0.4645 (tmm-80) REVERT: k 110 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7829 (mm-30) REVERT: k 113 MET cc_start: 0.6296 (mmt) cc_final: 0.5185 (ptt) REVERT: l 55 MET cc_start: 0.7906 (tpp) cc_final: 0.7044 (tpp) REVERT: l 143 GLU cc_start: 0.6967 (pm20) cc_final: 0.6483 (mp0) REVERT: m 1 MET cc_start: 0.6123 (ppp) cc_final: 0.5797 (ppp) REVERT: m 31 PHE cc_start: 0.7689 (m-80) cc_final: 0.6991 (m-10) REVERT: m 90 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7151 (mm-30) REVERT: m 104 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6759 (mm-30) REVERT: n 72 ASP cc_start: 0.7380 (t0) cc_final: 0.6937 (t70) REVERT: n 90 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6826 (pmt-80) REVERT: o 13 ARG cc_start: 0.7222 (tpt170) cc_final: 0.6525 (tpt90) REVERT: o 30 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7246 (ttp80) REVERT: o 33 ARG cc_start: 0.8883 (ttt180) cc_final: 0.8395 (tpp-160) REVERT: o 67 ASN cc_start: 0.7555 (p0) cc_final: 0.7074 (p0) REVERT: p 100 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8277 (mtm-85) REVERT: q 35 PHE cc_start: 0.8535 (t80) cc_final: 0.8278 (t80) REVERT: r 11 GLN cc_start: 0.7696 (mp10) cc_final: 0.6730 (mt0) REVERT: r 43 ASN cc_start: 0.6044 (OUTLIER) cc_final: 0.5576 (m110) REVERT: r 92 TRP cc_start: 0.7463 (m100) cc_final: 0.7057 (m100) REVERT: r 97 LYS cc_start: 0.8772 (tmmt) cc_final: 0.7863 (mtpp) REVERT: s 66 ILE cc_start: 0.8538 (tt) cc_final: 0.8182 (mm) REVERT: t 1 MET cc_start: 0.4441 (OUTLIER) cc_final: 0.4023 (mmm) REVERT: t 89 GLU cc_start: 0.5158 (OUTLIER) cc_final: 0.4620 (mm-30) REVERT: u 60 LYS cc_start: 0.8999 (tppt) cc_final: 0.8521 (tptp) REVERT: v 53 LYS cc_start: 0.8432 (tttm) cc_final: 0.7977 (tmtt) REVERT: v 86 LEU cc_start: 0.7501 (mt) cc_final: 0.6772 (mp) REVERT: w 40 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8671 (ttpp) REVERT: w 64 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8456 (ttmt) REVERT: w 65 PHE cc_start: 0.7115 (m-10) cc_final: 0.6639 (m-10) REVERT: x 33 HIS cc_start: 0.6934 (m-70) cc_final: 0.6575 (m90) REVERT: x 51 SER cc_start: 0.8883 (p) cc_final: 0.8352 (p) REVERT: x 67 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6862 (tt) REVERT: y 58 ASN cc_start: 0.7716 (p0) cc_final: 0.7413 (p0) REVERT: z 57 GLU cc_start: 0.7819 (tp30) cc_final: 0.7462 (tm-30) REVERT: B 3 GLN cc_start: 0.8617 (pp30) cc_final: 0.8394 (pp30) REVERT: B 14 MET cc_start: 0.6713 (ttm) cc_final: 0.6292 (ttt) REVERT: D 11 LYS cc_start: 0.9204 (ttmt) cc_final: 0.8714 (mtpp) REVERT: F 1 MET cc_start: 0.5695 (tpt) cc_final: 0.5478 (mmm) REVERT: F 23 ILE cc_start: 0.8529 (mt) cc_final: 0.8163 (mt) REVERT: F 34 LYS cc_start: 0.7975 (tttt) cc_final: 0.7186 (tttt) REVERT: G 55 GLU cc_start: 0.8534 (mp0) cc_final: 0.8259 (mp0) REVERT: G 69 VAL cc_start: 0.8103 (t) cc_final: 0.7876 (t) REVERT: G 144 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: G 150 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7346 (pt) REVERT: G 199 ILE cc_start: 0.7929 (mt) cc_final: 0.7680 (mt) REVERT: G 207 ARG cc_start: 0.6399 (tpp-160) cc_final: 0.6151 (mpp80) REVERT: H 27 GLU cc_start: 0.5408 (OUTLIER) cc_final: 0.3703 (mm-30) REVERT: H 39 ARG cc_start: -0.1206 (OUTLIER) cc_final: -0.1456 (tmm160) REVERT: H 110 LEU cc_start: 0.7516 (tp) cc_final: 0.6883 (mt) REVERT: H 143 LEU cc_start: 0.7124 (tp) cc_final: 0.6827 (tp) REVERT: I 50 TYR cc_start: 0.7670 (t80) cc_final: 0.7256 (t80) REVERT: J 25 LYS cc_start: 0.6725 (ptpp) cc_final: 0.6161 (ptpp) REVERT: K 21 MET cc_start: 0.6291 (mtp) cc_final: 0.5539 (mtp) REVERT: K 23 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.4875 (tp30) REVERT: K 91 ARG cc_start: 0.6186 (ttt-90) cc_final: 0.5039 (ttt-90) REVERT: M 28 SER cc_start: 0.8447 (p) cc_final: 0.8144 (p) REVERT: M 66 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5602 (mt0) REVERT: N 17 ARG cc_start: 0.4302 (mtp180) cc_final: 0.3226 (ptp-170) REVERT: P 28 ASN cc_start: 0.6775 (t0) cc_final: 0.6512 (t0) REVERT: P 34 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7430 (t) REVERT: P 60 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7165 (t80) REVERT: P 120 CYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6526 (p) REVERT: Q 28 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: Q 66 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7189 (mp) REVERT: Q 71 HIS cc_start: 0.3803 (OUTLIER) cc_final: 0.3414 (p90) REVERT: S 46 LYS cc_start: 0.4995 (mmmt) cc_final: 0.4751 (mmpt) REVERT: T 61 GLN cc_start: 0.8836 (tt0) cc_final: 0.8591 (mt0) REVERT: T 62 ARG cc_start: 0.8969 (ttt180) cc_final: 0.8525 (ttt180) REVERT: U 1 MET cc_start: 0.2871 (tpt) cc_final: 0.2583 (tpp) REVERT: U 4 ILE cc_start: 0.4092 (OUTLIER) cc_final: 0.3829 (mt) REVERT: U 13 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7537 (tptp) REVERT: U 66 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7861 (p) REVERT: W 37 LYS cc_start: 0.7976 (mttt) cc_final: 0.7775 (tttt) REVERT: W 60 ARG cc_start: 0.7368 (mmp-170) cc_final: 0.7134 (mtm180) REVERT: Y 43 LYS cc_start: 0.6893 (mptt) cc_final: 0.6357 (mptt) REVERT: Z 16 ARG cc_start: 0.6341 (mtp180) cc_final: 0.5924 (mtp180) REVERT: Z 23 GLU cc_start: 0.0778 (OUTLIER) cc_final: -0.0394 (pp20) REVERT: Z 45 LYS cc_start: 0.7606 (mttt) cc_final: 0.7072 (mmmt) outliers start: 378 outliers final: 311 residues processed: 1368 average time/residue: 1.4074 time to fit residues: 3300.1030 Evaluate side-chains 1450 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1106 time to evaluate : 6.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 491 ARG Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 548 GLU Chi-restraints excluded: chain 8 residue 560 GLN Chi-restraints excluded: chain 8 residue 595 LEU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 661 SER Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 11 MET Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain d residue 27 LEU Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 69 ARG Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 85 PHE Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 31 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 110 HIS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain a residue 7 ARG Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain i residue 46 ASP Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 123 LYS Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 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 25 ASP Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 56 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 68 ARG Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 89 GLU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 34 SER Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 66 GLN Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 60 PHE Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 933 optimal weight: 3.9990 chunk 983 optimal weight: 7.9990 chunk 897 optimal weight: 0.7980 chunk 956 optimal weight: 40.0000 chunk 575 optimal weight: 8.9990 chunk 416 optimal weight: 10.0000 chunk 751 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 864 optimal weight: 7.9990 chunk 904 optimal weight: 6.9990 chunk 953 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 560 GLN ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN n 73 ASN o 100 HIS r 89 HIS ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 162652 Z= 0.265 Angle : 0.730 16.287 243074 Z= 0.368 Chirality : 0.039 0.307 31031 Planarity : 0.005 0.091 13221 Dihedral : 24.556 179.528 80814 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.20 % Favored : 87.56 % Rotamer: Outliers : 7.98 % Allowed : 30.19 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.17 % 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: -3.08 (0.10), residues: 6067 helix: -1.44 (0.12), residues: 1636 sheet: -1.90 (0.16), residues: 946 loop : -2.46 (0.10), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP V 72 HIS 0.014 0.002 HIS J 88 PHE 0.039 0.002 PHE e 76 TYR 0.024 0.002 TYR f 93 ARG 0.028 0.001 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1530 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 1128 time to evaluate : 6.174 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: 8 497 LYS cc_start: 0.7916 (pttp) cc_final: 0.7053 (ttmm) REVERT: 8 522 MET cc_start: 0.2977 (ttp) cc_final: 0.1220 (ttp) REVERT: 8 560 GLN cc_start: 0.1200 (OUTLIER) cc_final: 0.0286 (tm-30) REVERT: 8 574 MET cc_start: 0.5245 (OUTLIER) cc_final: 0.4390 (mtp) REVERT: 8 584 HIS cc_start: 0.8056 (m90) cc_final: 0.7287 (m170) REVERT: 8 617 MET cc_start: -0.1624 (mpp) cc_final: -0.2159 (mpp) REVERT: 8 663 MET cc_start: 0.1399 (OUTLIER) cc_final: -0.1936 (ptt) REVERT: b 155 ARG cc_start: 0.6993 (ptm160) cc_final: 0.5627 (ptm160) REVERT: d 57 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7174 (tmtt) REVERT: d 69 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6179 (ptp-110) REVERT: d 85 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6036 (m-80) REVERT: e 4 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.7571 (t-90) REVERT: e 8 LYS cc_start: 0.7447 (mtmt) cc_final: 0.7208 (mtmt) REVERT: e 21 TYR cc_start: 0.6729 (m-80) cc_final: 0.6292 (m-80) REVERT: e 31 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: e 95 MET cc_start: 0.7921 (ttp) cc_final: 0.6969 (ttp) REVERT: e 111 ARG cc_start: 0.7035 (ttt90) cc_final: 0.5701 (ttt180) REVERT: f 21 GLN cc_start: 0.8403 (mm110) cc_final: 0.8162 (tp40) REVERT: f 40 VAL cc_start: 0.8632 (m) cc_final: 0.8396 (p) REVERT: f 43 LYS cc_start: 0.7121 (mmtt) cc_final: 0.6855 (mmmt) REVERT: f 115 GLN cc_start: 0.8001 (tt0) cc_final: 0.7316 (pm20) REVERT: f 116 LEU cc_start: 0.8039 (tp) cc_final: 0.7773 (tp) REVERT: g 135 HIS cc_start: 0.8103 (t70) cc_final: 0.7581 (t70) REVERT: a 7 ARG cc_start: 0.0166 (OUTLIER) cc_final: -0.2289 (mmt180) REVERT: a 20 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6465 (mp10) REVERT: a 218 MET cc_start: -0.0037 (ttt) cc_final: -0.1447 (ttt) REVERT: j 7 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6170 (mttp) REVERT: j 16 TYR cc_start: 0.8124 (m-80) cc_final: 0.7822 (m-80) REVERT: j 19 ASP cc_start: 0.7369 (t70) cc_final: 0.7014 (p0) REVERT: j 39 LYS cc_start: 0.8419 (tttt) cc_final: 0.8018 (ttmm) REVERT: j 86 GLN cc_start: 0.7707 (pp30) cc_final: 0.6909 (pp30) REVERT: j 122 LEU cc_start: 0.8808 (mt) cc_final: 0.8286 (pp) REVERT: k 23 LYS cc_start: 0.8356 (tppt) cc_final: 0.8009 (mttm) REVERT: k 43 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8318 (mt) REVERT: k 59 LYS cc_start: 0.8334 (tmtt) cc_final: 0.7984 (tttt) REVERT: k 98 ARG cc_start: 0.5122 (mpt180) cc_final: 0.4702 (tmm-80) REVERT: k 110 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7820 (mm-30) REVERT: k 113 MET cc_start: 0.6299 (mmt) cc_final: 0.5223 (ptt) REVERT: l 33 ARG cc_start: 0.3966 (OUTLIER) cc_final: 0.2742 (mtt180) REVERT: l 55 MET cc_start: 0.7911 (tpp) cc_final: 0.7071 (tpp) REVERT: l 143 GLU cc_start: 0.7031 (pm20) cc_final: 0.6484 (mp0) REVERT: m 1 MET cc_start: 0.6113 (ppp) cc_final: 0.5772 (ppp) REVERT: m 31 PHE cc_start: 0.7712 (m-80) cc_final: 0.7011 (m-10) REVERT: m 104 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6828 (mm-30) REVERT: n 72 ASP cc_start: 0.7317 (t0) cc_final: 0.6900 (t70) REVERT: n 90 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6813 (pmt-80) REVERT: o 13 ARG cc_start: 0.7245 (tpt170) cc_final: 0.6540 (tpt90) REVERT: o 30 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7245 (ttp80) REVERT: o 33 ARG cc_start: 0.8906 (ttt180) cc_final: 0.8408 (tpp-160) REVERT: o 67 ASN cc_start: 0.7580 (p0) cc_final: 0.7097 (p0) REVERT: p 100 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8286 (mtm-85) REVERT: q 35 PHE cc_start: 0.8555 (t80) cc_final: 0.8301 (t80) REVERT: r 11 GLN cc_start: 0.7729 (mp10) cc_final: 0.6494 (mt0) REVERT: r 43 ASN cc_start: 0.5998 (OUTLIER) cc_final: 0.5518 (m110) REVERT: r 92 TRP cc_start: 0.7454 (m100) cc_final: 0.7030 (m100) REVERT: s 66 ILE cc_start: 0.8519 (tt) cc_final: 0.8150 (mm) REVERT: t 89 GLU cc_start: 0.5087 (OUTLIER) cc_final: 0.4517 (mm-30) REVERT: u 34 ILE cc_start: 0.7659 (mp) cc_final: 0.7015 (tt) REVERT: u 60 LYS cc_start: 0.8991 (tppt) cc_final: 0.8564 (tptp) REVERT: v 53 LYS cc_start: 0.8448 (tttm) cc_final: 0.7968 (tmtt) REVERT: w 40 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8688 (ttpp) REVERT: x 45 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: x 51 SER cc_start: 0.8873 (p) cc_final: 0.8346 (p) REVERT: x 67 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6905 (tt) REVERT: y 58 ASN cc_start: 0.7741 (p0) cc_final: 0.7422 (p0) REVERT: z 57 GLU cc_start: 0.7829 (tp30) cc_final: 0.7480 (tm-30) REVERT: B 3 GLN cc_start: 0.8638 (pp30) cc_final: 0.8412 (pp30) REVERT: B 14 MET cc_start: 0.6764 (ttm) cc_final: 0.6312 (ttt) REVERT: D 11 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8725 (mtpp) REVERT: E 39 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8091 (ttm170) REVERT: F 1 MET cc_start: 0.5936 (tpt) cc_final: 0.5575 (mmm) REVERT: F 23 ILE cc_start: 0.8564 (mt) cc_final: 0.8196 (mt) REVERT: G 55 GLU cc_start: 0.8530 (mp0) cc_final: 0.8231 (mp0) REVERT: G 69 VAL cc_start: 0.8118 (t) cc_final: 0.7892 (t) REVERT: G 144 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: G 150 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7343 (pt) REVERT: G 199 ILE cc_start: 0.7961 (mt) cc_final: 0.7707 (mt) REVERT: G 207 ARG cc_start: 0.6455 (tpp-160) cc_final: 0.6237 (mpp80) REVERT: H 27 GLU cc_start: 0.5462 (OUTLIER) cc_final: 0.3751 (mm-30) REVERT: H 39 ARG cc_start: -0.1123 (OUTLIER) cc_final: -0.1373 (tmm160) REVERT: H 110 LEU cc_start: 0.7557 (tp) cc_final: 0.6921 (mt) REVERT: H 143 LEU cc_start: 0.7140 (tp) cc_final: 0.6827 (tp) REVERT: I 50 TYR cc_start: 0.7653 (t80) cc_final: 0.7231 (t80) REVERT: I 69 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8267 (mmm160) REVERT: J 25 LYS cc_start: 0.6800 (ptpp) cc_final: 0.6375 (ptpp) REVERT: J 68 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7385 (mtm-85) REVERT: J 88 HIS cc_start: 0.6165 (t-90) cc_final: 0.5749 (t-90) REVERT: K 21 MET cc_start: 0.6343 (mtp) cc_final: 0.5550 (mtp) REVERT: K 23 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.4854 (tp30) REVERT: K 52 ASN cc_start: 0.8383 (t0) cc_final: 0.8164 (t0) REVERT: K 65 GLU cc_start: 0.4621 (OUTLIER) cc_final: 0.3390 (tm-30) REVERT: K 91 ARG cc_start: 0.6219 (ttt-90) cc_final: 0.5072 (ttt-90) REVERT: M 26 MET cc_start: 0.6269 (mpp) cc_final: 0.5502 (mpp) REVERT: M 28 SER cc_start: 0.8466 (p) cc_final: 0.8168 (p) REVERT: M 66 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5579 (mt0) REVERT: N 17 ARG cc_start: 0.4397 (mtp180) cc_final: 0.3449 (ptp-170) REVERT: P 22 ILE cc_start: 0.7493 (mp) cc_final: 0.6934 (mm) REVERT: P 28 ASN cc_start: 0.6780 (t0) cc_final: 0.6514 (t0) REVERT: P 34 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7535 (t) REVERT: P 60 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7177 (t80) REVERT: P 85 VAL cc_start: 0.8406 (t) cc_final: 0.8025 (p) REVERT: P 120 CYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6467 (p) REVERT: Q 28 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: Q 66 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7227 (mp) REVERT: Q 71 HIS cc_start: 0.3774 (OUTLIER) cc_final: 0.3424 (p90) REVERT: S 46 LYS cc_start: 0.4839 (mmmt) cc_final: 0.4600 (mmpt) REVERT: T 61 GLN cc_start: 0.8911 (tt0) cc_final: 0.8641 (mt0) REVERT: U 4 ILE cc_start: 0.4154 (OUTLIER) cc_final: 0.3870 (mt) REVERT: U 13 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7560 (tptp) REVERT: U 66 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7957 (p) REVERT: V 16 MET cc_start: 0.5530 (mmm) cc_final: 0.4959 (mmm) REVERT: W 37 LYS cc_start: 0.7967 (mttt) cc_final: 0.7765 (tttt) REVERT: W 72 ARG cc_start: 0.7611 (ptt180) cc_final: 0.6716 (mmt-90) REVERT: Y 24 ARG cc_start: 0.8632 (ttm110) cc_final: 0.7631 (ptp90) REVERT: Y 28 ARG cc_start: 0.8780 (mtt-85) cc_final: 0.8430 (mtt-85) REVERT: Y 43 LYS cc_start: 0.6909 (mptt) cc_final: 0.6358 (mptt) REVERT: Z 16 ARG cc_start: 0.6355 (mtp180) cc_final: 0.5970 (mtp180) REVERT: Z 23 GLU cc_start: 0.0753 (OUTLIER) cc_final: -0.0432 (pp20) REVERT: Z 45 LYS cc_start: 0.7653 (mttt) cc_final: 0.7116 (mmmt) outliers start: 402 outliers final: 329 residues processed: 1381 average time/residue: 1.3275 time to fit residues: 3134.4118 Evaluate side-chains 1471 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1106 time to evaluate : 6.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 458 ILE Chi-restraints excluded: chain 8 residue 470 VAL Chi-restraints excluded: chain 8 residue 491 ARG Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 560 GLN Chi-restraints excluded: chain 8 residue 573 ASP Chi-restraints excluded: chain 8 residue 574 MET Chi-restraints excluded: chain 8 residue 595 LEU Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 661 SER Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain 8 residue 693 ASN Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 11 MET Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 199 SER Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 69 ARG Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 85 PHE Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 31 GLU Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 110 HIS Chi-restraints excluded: chain f residue 162 ARG Chi-restraints excluded: chain f residue 168 VAL Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 137 GLU Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain a residue 7 ARG Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain i residue 46 ASP Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 123 LYS Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 33 ARG Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 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 25 ASP Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 91 TYR Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 95 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 56 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 68 ARG Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 89 GLU Chi-restraints excluded: chain u residue 6 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 55 GLU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 45 PHE Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 34 SER Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 149 LYS Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 66 GLN Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 60 PHE Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 51 SER Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 13 LYS Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 85 LEU Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 628 optimal weight: 0.9980 chunk 1011 optimal weight: 8.9990 chunk 617 optimal weight: 6.9990 chunk 479 optimal weight: 10.0000 chunk 703 optimal weight: 9.9990 chunk 1061 optimal weight: 0.2980 chunk 976 optimal weight: 0.5980 chunk 844 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 652 optimal weight: 4.9990 chunk 518 optimal weight: 7.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 496 GLN ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 ASN ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN l 38 GLN n 73 ASN o 100 HIS r 89 HIS s 57 ASN u 39 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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** N 74 GLN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 162652 Z= 0.155 Angle : 0.631 15.767 243074 Z= 0.321 Chirality : 0.035 0.295 31031 Planarity : 0.005 0.153 13221 Dihedral : 24.416 179.573 80813 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.36 % Favored : 90.39 % Rotamer: Outliers : 5.76 % Allowed : 32.37 % Favored : 61.87 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.10), residues: 6067 helix: -1.26 (0.12), residues: 1665 sheet: -1.77 (0.16), residues: 989 loop : -2.35 (0.10), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP V 72 HIS 0.009 0.001 HIS x 33 PHE 0.019 0.002 PHE u 95 TYR 0.023 0.002 TYR T 68 ARG 0.016 0.001 ARG V 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12134 Ramachandran restraints generated. 6067 Oldfield, 0 Emsley, 6067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1165 time to evaluate : 6.331 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: 8 497 LYS cc_start: 0.7906 (pttp) cc_final: 0.7152 (ttmm) REVERT: 8 522 MET cc_start: 0.2741 (ttp) cc_final: 0.1332 (mtp) REVERT: 8 574 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4121 (mtp) REVERT: 8 584 HIS cc_start: 0.8000 (m90) cc_final: 0.7442 (m170) REVERT: 8 617 MET cc_start: -0.1830 (mpp) cc_final: -0.2264 (mpp) REVERT: 8 663 MET cc_start: 0.1318 (OUTLIER) cc_final: -0.2074 (ptt) REVERT: b 155 ARG cc_start: 0.6759 (ptm160) cc_final: 0.5475 (ptm160) REVERT: c 4 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7782 (mt) REVERT: c 100 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6125 (tp) REVERT: c 125 TRP cc_start: 0.8342 (m100) cc_final: 0.7916 (m100) REVERT: d 57 LYS cc_start: 0.7499 (tmtt) cc_final: 0.7015 (tmtt) REVERT: d 85 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: e 3 LEU cc_start: 0.7723 (mm) cc_final: 0.7436 (mm) REVERT: e 4 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.7898 (t-90) REVERT: e 8 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7226 (mmtt) REVERT: e 21 TYR cc_start: 0.6440 (m-80) cc_final: 0.6227 (m-80) REVERT: e 41 GLU cc_start: 0.7465 (tp30) cc_final: 0.7180 (tp30) REVERT: e 95 MET cc_start: 0.7861 (ttp) cc_final: 0.7004 (ttp) REVERT: e 111 ARG cc_start: 0.6982 (ttt90) cc_final: 0.5578 (ttt180) REVERT: f 21 GLN cc_start: 0.8332 (mm110) cc_final: 0.8108 (tp40) REVERT: f 43 LYS cc_start: 0.7088 (mmtt) cc_final: 0.6786 (mmmt) REVERT: f 115 GLN cc_start: 0.7869 (tt0) cc_final: 0.7234 (pm20) REVERT: g 9 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7279 (p) REVERT: g 135 HIS cc_start: 0.8004 (t70) cc_final: 0.7438 (t70) REVERT: a 7 ARG cc_start: 0.0095 (OUTLIER) cc_final: -0.2556 (mmt180) REVERT: a 20 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6451 (mp10) REVERT: a 218 MET cc_start: -0.0298 (ttt) cc_final: -0.1818 (ppp) REVERT: j 16 TYR cc_start: 0.8180 (m-80) cc_final: 0.7875 (m-80) REVERT: j 19 ASP cc_start: 0.7509 (t70) cc_final: 0.7103 (p0) REVERT: j 39 LYS cc_start: 0.8332 (tttt) cc_final: 0.7896 (ttmm) REVERT: j 86 GLN cc_start: 0.7626 (pp30) cc_final: 0.6843 (pp30) REVERT: j 122 LEU cc_start: 0.8768 (mt) cc_final: 0.8310 (pp) REVERT: k 43 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8231 (mt) REVERT: k 59 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7837 (tttt) REVERT: k 110 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7850 (mm-30) REVERT: k 113 MET cc_start: 0.6160 (mmt) cc_final: 0.4996 (ptt) REVERT: l 55 MET cc_start: 0.7846 (tpp) cc_final: 0.7006 (tpp) REVERT: l 143 GLU cc_start: 0.6913 (pm20) cc_final: 0.6402 (mp0) REVERT: m 1 MET cc_start: 0.6002 (ppp) cc_final: 0.5654 (ppp) REVERT: m 31 PHE cc_start: 0.7467 (m-80) cc_final: 0.6776 (m-10) REVERT: m 104 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6689 (mm-30) REVERT: n 72 ASP cc_start: 0.7373 (t0) cc_final: 0.7064 (t0) REVERT: n 90 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6754 (pmt-80) REVERT: o 30 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7240 (ttp80) REVERT: o 33 ARG cc_start: 0.8840 (ttt180) cc_final: 0.8599 (tpp-160) REVERT: o 67 ASN cc_start: 0.7566 (p0) cc_final: 0.7062 (p0) REVERT: r 11 GLN cc_start: 0.7499 (mp10) cc_final: 0.6172 (mt0) REVERT: r 43 ASN cc_start: 0.6014 (OUTLIER) cc_final: 0.5739 (m-40) REVERT: r 92 TRP cc_start: 0.7452 (m100) cc_final: 0.6903 (m100) REVERT: r 97 LYS cc_start: 0.8720 (tmmt) cc_final: 0.7920 (mttp) REVERT: s 66 ILE cc_start: 0.8494 (tt) cc_final: 0.8135 (mm) REVERT: t 89 GLU cc_start: 0.4983 (OUTLIER) cc_final: 0.4504 (mm-30) REVERT: u 34 ILE cc_start: 0.7623 (mp) cc_final: 0.6987 (tt) REVERT: u 60 LYS cc_start: 0.8986 (tppt) cc_final: 0.8591 (tptp) REVERT: v 42 LEU cc_start: 0.8231 (mm) cc_final: 0.7885 (mm) REVERT: v 53 LYS cc_start: 0.8425 (tttm) cc_final: 0.8042 (tmtt) REVERT: v 86 LEU cc_start: 0.7447 (mt) cc_final: 0.6662 (mp) REVERT: w 40 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8723 (ttpp) REVERT: x 51 SER cc_start: 0.8798 (p) cc_final: 0.8275 (p) REVERT: x 67 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6873 (tt) REVERT: y 58 ASN cc_start: 0.7685 (p0) cc_final: 0.7335 (p0) REVERT: z 37 ARG cc_start: 0.6908 (tpp-160) cc_final: 0.6601 (tpp-160) REVERT: z 57 GLU cc_start: 0.7804 (tp30) cc_final: 0.7487 (tm-30) REVERT: B 3 GLN cc_start: 0.8564 (pp30) cc_final: 0.8327 (pp30) REVERT: B 14 MET cc_start: 0.6437 (ttm) cc_final: 0.6030 (ttt) REVERT: D 11 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8598 (mtpp) REVERT: F 1 MET cc_start: 0.5403 (tpt) cc_final: 0.5052 (tpt) REVERT: F 23 ILE cc_start: 0.8481 (mt) cc_final: 0.8138 (mt) REVERT: G 8 MET cc_start: 0.6962 (tpp) cc_final: 0.5609 (pmm) REVERT: G 55 GLU cc_start: 0.8518 (mp0) cc_final: 0.8223 (mp0) REVERT: G 69 VAL cc_start: 0.8058 (t) cc_final: 0.7826 (t) REVERT: G 144 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: G 150 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7190 (pt) REVERT: G 199 ILE cc_start: 0.7853 (mt) cc_final: 0.7613 (mt) REVERT: H 27 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.3773 (mm-30) REVERT: H 39 ARG cc_start: -0.1313 (OUTLIER) cc_final: -0.1553 (tmm160) REVERT: H 110 LEU cc_start: 0.7540 (tp) cc_final: 0.6916 (mt) REVERT: H 143 LEU cc_start: 0.7097 (tp) cc_final: 0.6850 (tp) REVERT: I 50 TYR cc_start: 0.7671 (t80) cc_final: 0.7213 (t80) REVERT: J 25 LYS cc_start: 0.6642 (ptpp) cc_final: 0.6050 (ptpp) REVERT: J 88 HIS cc_start: 0.6020 (t-90) cc_final: 0.5696 (t-90) REVERT: J 127 TYR cc_start: 0.6678 (m-80) cc_final: 0.6022 (m-80) REVERT: J 146 MET cc_start: 0.5677 (mtp) cc_final: 0.5435 (mtm) REVERT: K 1 MET cc_start: 0.5872 (mmt) cc_final: 0.5051 (mmm) REVERT: K 21 MET cc_start: 0.6280 (mtp) cc_final: 0.5735 (mtp) REVERT: K 52 ASN cc_start: 0.8443 (t0) cc_final: 0.8211 (t0) REVERT: K 65 GLU cc_start: 0.4207 (OUTLIER) cc_final: 0.3079 (tm-30) REVERT: K 90 MET cc_start: 0.6932 (mmm) cc_final: 0.5004 (mtp) REVERT: M 28 SER cc_start: 0.8063 (p) cc_final: 0.7772 (p) REVERT: M 66 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.5596 (mt0) REVERT: N 17 ARG cc_start: 0.4434 (mtp180) cc_final: 0.3541 (ptp-170) REVERT: P 22 ILE cc_start: 0.7201 (mp) cc_final: 0.6676 (mm) REVERT: P 28 ASN cc_start: 0.6691 (t0) cc_final: 0.6404 (t0) REVERT: P 60 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7044 (t80) REVERT: P 85 VAL cc_start: 0.8361 (t) cc_final: 0.7972 (p) REVERT: P 124 LYS cc_start: 0.7646 (pptt) cc_final: 0.7040 (pttp) REVERT: Q 28 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: Q 71 HIS cc_start: 0.3624 (OUTLIER) cc_final: 0.3298 (p90) REVERT: S 46 LYS cc_start: 0.4923 (mmmt) cc_final: 0.4672 (mmpt) REVERT: T 62 ARG cc_start: 0.8983 (ttt180) cc_final: 0.8576 (ttt180) REVERT: U 66 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7738 (p) REVERT: V 16 MET cc_start: 0.5250 (mmm) cc_final: 0.4647 (mmm) REVERT: V 56 ASP cc_start: 0.5247 (m-30) cc_final: 0.4917 (m-30) REVERT: W 37 LYS cc_start: 0.7855 (mttt) cc_final: 0.7646 (tttt) REVERT: W 49 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8015 (tppp) REVERT: W 63 TYR cc_start: 0.7744 (t80) cc_final: 0.7385 (t80) REVERT: Y 24 ARG cc_start: 0.8634 (ttm110) cc_final: 0.7896 (ptp-110) REVERT: Y 28 ARG cc_start: 0.8747 (mtt-85) cc_final: 0.8341 (mtt-85) REVERT: Y 43 LYS cc_start: 0.6970 (mptt) cc_final: 0.6494 (mptt) REVERT: Z 16 ARG cc_start: 0.6374 (mtp180) cc_final: 0.5909 (mtp-110) REVERT: Z 23 GLU cc_start: 0.0888 (OUTLIER) cc_final: -0.0160 (pp20) REVERT: Z 45 LYS cc_start: 0.7582 (mttt) cc_final: 0.7086 (mmmt) outliers start: 290 outliers final: 226 residues processed: 1348 average time/residue: 1.3505 time to fit residues: 3108.0788 Evaluate side-chains 1354 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1103 time to evaluate : 6.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 415 VAL Chi-restraints excluded: chain 8 residue 470 VAL Chi-restraints excluded: chain 8 residue 498 VAL Chi-restraints excluded: chain 8 residue 501 VAL Chi-restraints excluded: chain 8 residue 505 HIS Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 574 MET Chi-restraints excluded: chain 8 residue 623 THR Chi-restraints excluded: chain 8 residue 642 LEU Chi-restraints excluded: chain 8 residue 649 VAL Chi-restraints excluded: chain 8 residue 663 MET Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 156 SER Chi-restraints excluded: chain b residue 160 TYR Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 11 MET Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 85 PHE Chi-restraints excluded: chain d residue 90 GLN Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 4 HIS Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 127 TYR Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 19 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 88 LEU Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 162 ARG Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain g residue 143 ILE Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain a residue 7 ARG Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain i residue 46 ASP Chi-restraints excluded: chain i residue 66 PHE Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 40 HIS Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 47 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 123 LYS Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 23 ASN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 90 ARG Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 4 LYS Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 56 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 9 HIS Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 89 GLU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 67 SER Chi-restraints excluded: chain u residue 95 PHE Chi-restraints excluded: chain u residue 101 THR Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain v residue 82 TYR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 37 LEU Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 50 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 66 GLN Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 129 ARG Chi-restraints excluded: chain O residue 56 HIS Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain P residue 60 PHE Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 28 GLN Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 45 ASN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 59 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1065 random chunks: chunk 671 optimal weight: 6.9990 chunk 900 optimal weight: 5.9990 chunk 258 optimal weight: 30.0000 chunk 779 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 234 optimal weight: 10.0000 chunk 846 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 868 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 508 GLN ** 8 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 ASN ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN n 73 ASN o 100 HIS p 14 GLN q 36 GLN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN W 30 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.165724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.141160 restraints weight = 419203.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.144391 restraints weight = 185684.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.144482 restraints weight = 90442.481| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 162652 Z= 0.384 Angle : 0.869 17.300 243074 Z= 0.431 Chirality : 0.044 0.341 31031 Planarity : 0.007 0.194 13221 Dihedral : 24.754 179.064 80810 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.50 % Favored : 86.24 % Rotamer: Outliers : 6.51 % Allowed : 32.02 % Favored : 61.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -3.18 (0.10), residues: 6067 helix: -1.57 (0.12), residues: 1634 sheet: -1.87 (0.16), residues: 933 loop : -2.52 (0.10), residues: 3500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 42 HIS 0.016 0.002 HIS F 33 PHE 0.037 0.003 PHE e 76 TYR 0.039 0.003 TYR f 93 ARG 0.034 0.001 ARG b 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44202.44 seconds wall clock time: 772 minutes 41.00 seconds (46361.00 seconds total)