Starting phenix.real_space_refine on Sun Mar 3 10:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/03_2024/7ohx_12912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/03_2024/7ohx_12912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/03_2024/7ohx_12912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/03_2024/7ohx_12912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/03_2024/7ohx_12912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohx_12912/03_2024/7ohx_12912.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1774 5.49 5 S 123 5.16 5 C 48264 2.51 5 N 15763 2.21 5 O 21063 1.98 5 H 70039 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 GLU 4": "OE1" <-> "OE2" Residue "3 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ASP 56": "OD1" <-> "OD2" Residue "3 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 68": "OE1" <-> "OE2" Residue "3 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 122": "OE1" <-> "OE2" Residue "3 ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 165": "OE1" <-> "OE2" Residue "4 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 36": "OE1" <-> "OE2" Residue "4 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 68": "OE1" <-> "OE2" Residue "4 ASP 78": "OD1" <-> "OD2" Residue "4 ASP 114": "OD1" <-> "OD2" Residue "4 ASP 147": "OD1" <-> "OD2" Residue "4 ASP 179": "OD1" <-> "OD2" Residue "4 ASP 216": "OD1" <-> "OD2" Residue "4 TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 236": "OE1" <-> "OE2" Residue "4 GLU 240": "OE1" <-> "OE2" Residue "4 ASP 241": "OD1" <-> "OD2" Residue "5 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 55": "OE1" <-> "OE2" Residue "5 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 104": "OD1" <-> "OD2" Residue "5 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 210": "OE1" <-> "OE2" Residue "5 ASP 220": "OD1" <-> "OD2" Residue "5 ASP 241": "OD1" <-> "OD2" Residue "5 ARG 252": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 262": "OE1" <-> "OE2" Residue "5 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ARG 300": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ASP 359": "OD1" <-> "OD2" Residue "5 ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 411": "OD1" <-> "OD2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 375": "OE1" <-> "OE2" Residue "C ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ARG 340": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 376": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 153": "OD1" <-> "OD2" Residue "H ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "K ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K GLU 203": "OE1" <-> "OE2" Residue "K TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 257": "OE1" <-> "OE2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "K ASP 261": "OD1" <-> "OD2" Residue "K GLU 264": "OE1" <-> "OE2" Residue "K ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 40": "OD1" <-> "OD2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 8": "OE1" <-> "OE2" Residue "N ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 145": "OD1" <-> "OD2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 100": "OE1" <-> "OE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 187": "OE1" <-> "OE2" Residue "P ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 108": "OD1" <-> "OD2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 21": "OE1" <-> "OE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 24": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 108": "OD1" <-> "OD2" Residue "W PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 224": "OD1" <-> "OD2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y GLU 67": "OE1" <-> "OE2" Residue "Y PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 164": "OD1" <-> "OD2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 210": "OD1" <-> "OD2" Residue "b GLU 325": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 423": "OE1" <-> "OE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 464": "OE1" <-> "OE2" Residue "b GLU 466": "OE1" <-> "OE2" Residue "b PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 8": "OE1" <-> "OE2" Residue "h ASP 79": "OD1" <-> "OD2" Residue "h ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m GLU 251": "OE1" <-> "OE2" Residue "m PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m GLU 272": "OE1" <-> "OE2" Residue "m GLU 342": "OE1" <-> "OE2" Residue "m GLU 355": "OE1" <-> "OE2" Residue "n ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 107": "OE1" <-> "OE2" Residue "n ASP 131": "OD1" <-> "OD2" Residue "n ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ASP 214": "OD1" <-> "OD2" Residue "n PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 223": "OE1" <-> "OE2" Residue "n TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ASP 413": "OD1" <-> "OD2" Residue "n ARG 414": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 451": "OE1" <-> "OE2" Residue "o TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ASP 83": "OD1" <-> "OD2" Residue "t ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "t TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t GLU 226": "OE1" <-> "OE2" Residue "t ASP 241": "OD1" <-> "OD2" Residue "u ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 28": "OE1" <-> "OE2" Residue "u ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 62": "OE1" <-> "OE2" Residue "u ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 84": "OE1" <-> "OE2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v ASP 202": "OD1" <-> "OD2" Residue "v TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x GLU 25": "OE1" <-> "OE2" Residue "x ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "x ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "x TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x GLU 116": "OE1" <-> "OE2" Residue "x TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ASP 146": "OD1" <-> "OD2" Residue "x PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x GLU 196": "OE1" <-> "OE2" Residue "x GLU 225": "OE1" <-> "OE2" Residue "x PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "x ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "x GLU 285": "OE1" <-> "OE2" Residue "x GLU 289": "OE1" <-> "OE2" Residue "x TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "y ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y ASP 90": "OD1" <-> "OD2" Residue "y GLU 99": "OE1" <-> "OE2" Residue "y ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "y GLU 126": "OE1" <-> "OE2" Residue "y TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 157028 Number of models: 1 Model: "" Number of chains: 39 Chain: "1" Number of atoms: 50227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 50227 Classifications: {'RNA': 1561} Modifications used: {'3*END': 1, 'rna2p_pur': 158, 'rna2p_pyr': 105, 'rna3p_pur': 719, 'rna3p_pyr': 579} Link IDs: {'rna2p': 262, 'rna3p': 1298} Chain breaks: 39 Chain: "2" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 4736 Classifications: {'RNA': 148} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 61, 'rna3p_pyr': 61} Link IDs: {'rna2p': 25, 'rna3p': 122} Chain breaks: 3 Chain: "3" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2908 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 5, 'TRANS': 167} Chain: "4" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3744 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 3 Chain: "5" Number of atoms: 6170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 6170 Classifications: {'peptide': 385} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 3 Chain: "6" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 2061 Classifications: {'RNA': 65} Modifications used: {'3*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 18, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 25, 'rna3p': 39} Chain breaks: 1 Chain: "B" Number of atoms: 5093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5093 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 10, 'TRANS': 304} Chain breaks: 1 Chain: "C" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5336 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain: "D" Number of atoms: 6897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6897 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 20, 'TRANS': 403} Chain breaks: 3 Chain: "E" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2497 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain breaks: 1 Chain: "F" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3969 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "G" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2345 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 2 Chain: "H" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2008 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 122} Chain breaks: 4 Chain: "K" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3956 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 2 Chain: "L" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1782 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2179 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3079 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3080 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 179} Chain breaks: 1 Chain: "P" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2014 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 3 Chain: "Q" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2101 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "S" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2904 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "W" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2075 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 7 Chain: "Y" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2060 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "b" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 4030 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Chain breaks: 8 Chain: "e" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2057 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "f" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1731 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "i" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 413 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "j" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1137 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'TRANS': 69} Chain: "m" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1790 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 12, 'TRANS': 93} Chain breaks: 3 Chain: "n" Number of atoms: 4111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 4111 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain breaks: 12 Chain: "o" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1901 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "t" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3287 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 193} Chain breaks: 6 Chain: "u" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1729 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "v" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2223 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 2 Chain: "x" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4573 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 2 Chain: "y" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2854 Classifications: {'peptide': 189} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain breaks: 3 Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0PU8 SG CYS j 19 144.826 94.410 134.368 1.00109.48 S ATOM A0PVL SG CYS j 22 141.760 94.676 132.119 1.00 87.45 S ATOM A0Q1A SG CYS j 34 143.349 97.832 133.608 1.00 98.44 S ATOM A0Q27 SG CYS j 37 141.466 95.430 135.828 1.00 75.92 S ATOM A0ZAX SG CYS u 6 186.903 148.386 51.756 1.00170.73 S ATOM A0ZC9 SG CYS u 9 187.483 145.390 50.881 1.00221.58 S ATOM A0ZM6 SG CYS u 32 183.575 145.494 50.822 1.00299.18 S Residues with excluded nonbonded symmetry interactions: 189 residue: pdb=" N ASP 4 57 " occ=0.52 ... (10 atoms not shown) pdb=" HB3 ASP 4 57 " occ=0.52 residue: pdb=" N VAL O 3 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (13 atoms not shown) pdb=" HG3 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (12 atoms not shown) pdb=" HD3 PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (17 atoms not shown) pdb="HD13 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (10 atoms not shown) pdb=" HB3 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (20 atoms not shown) pdb=" HZ3 LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY O 13 " occ=0.50 ... (remaining 177 not shown) Time building chain proxies: 48.51, per 1000 atoms: 0.31 Number of scatterers: 157028 At special positions: 0 Unit cell: (219.081, 255.24, 285.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 123 16.00 P 1774 15.00 O 21063 8.00 N 15763 7.00 C 48264 6.00 H 70039 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 105.44 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " Number of angles added : 6 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11544 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 66 sheets defined 44.5% alpha, 15.2% beta 531 base pairs and 786 stacking pairs defined. Time for finding SS restraints: 55.25 Creating SS restraints... Processing helix chain '3' and resid 2 through 13 Processing helix chain '3' and resid 43 through 47 removed outlier: 3.541A pdb=" N ASN 3 47 " --> pdb=" O PRO 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 70 Processing helix chain '3' and resid 72 through 76 Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 118 Processing helix chain '3' and resid 119 through 127 Processing helix chain '3' and resid 138 through 157 removed outlier: 3.727A pdb=" N LYS 3 157 " --> pdb=" O LEU 3 153 " (cutoff:3.500A) Processing helix chain '3' and resid 157 through 171 Processing helix chain '4' and resid 6 through 11 Processing helix chain '4' and resid 14 through 29 removed outlier: 4.090A pdb=" N LYS 4 27 " --> pdb=" O GLU 4 23 " (cutoff:3.500A) Processing helix chain '4' and resid 31 through 36 removed outlier: 3.621A pdb=" N LYS 4 35 " --> pdb=" O ALA 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 55 removed outlier: 4.074A pdb=" N PHE 4 42 " --> pdb=" O LYS 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 58 through 76 removed outlier: 4.154A pdb=" N HIS 4 73 " --> pdb=" O LEU 4 69 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY 4 74 " --> pdb=" O GLY 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 109 removed outlier: 4.013A pdb=" N PHE 4 95 " --> pdb=" O ASN 4 91 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 132 Processing helix chain '4' and resid 142 through 155 removed outlier: 4.007A pdb=" N ARG 4 155 " --> pdb=" O LYS 4 151 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 182 removed outlier: 4.777A pdb=" N LEU 4 178 " --> pdb=" O VAL 4 174 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP 4 179 " --> pdb=" O ASP 4 175 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 185 No H-bonds generated for 'chain '4' and resid 183 through 185' Processing helix chain '4' and resid 213 through 214 No H-bonds generated for 'chain '4' and resid 213 through 214' Processing helix chain '4' and resid 216 through 218 No H-bonds generated for 'chain '4' and resid 216 through 218' Processing helix chain '4' and resid 221 through 227 Processing helix chain '4' and resid 231 through 242 Processing helix chain '5' and resid 42 through 45 Processing helix chain '5' and resid 119 through 126 removed outlier: 4.451A pdb=" N LEU 5 123 " --> pdb=" O ASP 5 119 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 301 removed outlier: 3.751A pdb=" N ARG 5 300 " --> pdb=" O LEU 5 297 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU 5 301 " --> pdb=" O PRO 5 298 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 297 through 301' Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.979A pdb=" N HIS B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.851A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.519A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.547A pdb=" N TYR C 194 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.427A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.001A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 4.140A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 320 through 328 removed outlier: 3.608A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.493A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 66 through 78 Proline residue: D 74 - end of helix Processing helix chain 'D' and resid 91 through 108 Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.743A pdb=" N GLY D 114 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.771A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.616A pdb=" N MET D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.859A pdb=" N LEU D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 206 through 217 removed outlier: 3.673A pdb=" N GLN D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 243 Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 324 through 339 removed outlier: 3.512A pdb=" N PHE D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 369 through 384 Processing helix chain 'D' and resid 395 through 400 removed outlier: 4.022A pdb=" N LEU D 399 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY D 400 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 408 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.623A pdb=" N LEU D 432 " --> pdb=" O GLN D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 92 through 96 removed outlier: 4.096A pdb=" N GLY E 95 " --> pdb=" O SER E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.864A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 9 through 72 removed outlier: 3.593A pdb=" N GLN F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 130 removed outlier: 4.018A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.633A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.532A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 97 removed outlier: 3.691A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 117 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.523A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 189 removed outlier: 4.007A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.501A pdb=" N ALA H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'K' and resid 33 through 48 removed outlier: 3.929A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 77 Processing helix chain 'K' and resid 106 through 114 removed outlier: 3.714A pdb=" N TRP K 110 " --> pdb=" O PHE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 117 No H-bonds generated for 'chain 'K' and resid 115 through 117' Processing helix chain 'K' and resid 128 through 134 Processing helix chain 'K' and resid 139 through 143 removed outlier: 4.185A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 139 through 143' Processing helix chain 'K' and resid 144 through 148 Processing helix chain 'K' and resid 157 through 163 removed outlier: 3.656A pdb=" N LYS K 161 " --> pdb=" O GLY K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 184 through 188 removed outlier: 4.543A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 190 through 195 Processing helix chain 'K' and resid 196 through 201 removed outlier: 3.969A pdb=" N LYS K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 255 through 274 removed outlier: 4.249A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.680A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.531A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.764A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.822A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 177 through 184 removed outlier: 5.796A pdb=" N ASN N 182 " --> pdb=" O LYS N 179 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS N 184 " --> pdb=" O ASN N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.595A pdb=" N THR N 190 " --> pdb=" O GLY N 186 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TRP N 191 " --> pdb=" O ARG N 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 29 removed outlier: 3.691A pdb=" N ASN O 29 " --> pdb=" O LYS O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 54 through 59 Processing helix chain 'O' and resid 75 through 87 removed outlier: 3.661A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 162 Processing helix chain 'O' and resid 163 through 186 Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 75 removed outlier: 3.982A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 23 through 41 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.770A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 52 through 56 Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'W' and resid 20 through 34 removed outlier: 3.777A pdb=" N LEU W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 59 Processing helix chain 'W' and resid 69 through 76 Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 161 through 169 Processing helix chain 'W' and resid 198 through 207 removed outlier: 3.750A pdb=" N LEU W 203 " --> pdb=" O GLN W 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.820A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'b' and resid 62 through 67 removed outlier: 3.582A pdb=" N GLY b 67 " --> pdb=" O ASP b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 82 Processing helix chain 'b' and resid 87 through 97 Processing helix chain 'b' and resid 129 through 139 Processing helix chain 'b' and resid 147 through 160 removed outlier: 3.554A pdb=" N GLU b 151 " --> pdb=" O LEU b 147 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 181 No H-bonds generated for 'chain 'b' and resid 179 through 181' Processing helix chain 'b' and resid 182 through 188 removed outlier: 3.898A pdb=" N THR b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 197 through 202 removed outlier: 3.506A pdb=" N THR b 201 " --> pdb=" O ALA b 198 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS b 202 " --> pdb=" O PHE b 199 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 245 Processing helix chain 'b' and resid 265 through 275 removed outlier: 4.823A pdb=" N PHE b 271 " --> pdb=" O GLN b 267 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS b 272 " --> pdb=" O VAL b 268 " (cutoff:3.500A) Processing helix chain 'b' and resid 276 through 282 removed outlier: 5.442A pdb=" N ASN b 280 " --> pdb=" O LEU b 277 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 342 removed outlier: 3.754A pdb=" N LEU b 340 " --> pdb=" O CYS b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 445 Processing helix chain 'b' and resid 449 through 466 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 60 through 64 Processing helix chain 'e' and resid 78 through 84 removed outlier: 3.730A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 89 removed outlier: 4.114A pdb=" N THR e 89 " --> pdb=" O THR e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.167A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 43 removed outlier: 4.043A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 33 removed outlier: 3.670A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 Processing helix chain 'h' and resid 85 through 90 removed outlier: 3.718A pdb=" N ARG h 89 " --> pdb=" O THR h 85 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG h 90 " --> pdb=" O ARG h 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 85 through 90' Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 35 through 49 Processing helix chain 'i' and resid 53 through 57 Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 66 through 76 removed outlier: 3.739A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 267 Processing helix chain 'm' and resid 269 through 285 removed outlier: 3.563A pdb=" N ALA m 273 " --> pdb=" O SER m 269 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 298 Processing helix chain 'm' and resid 347 through 355 removed outlier: 3.860A pdb=" N GLU m 352 " --> pdb=" O PRO m 348 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA m 353 " --> pdb=" O GLU m 349 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 25 Processing helix chain 'n' and resid 64 through 70 removed outlier: 4.432A pdb=" N TYR n 70 " --> pdb=" O LYS n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 73 No H-bonds generated for 'chain 'n' and resid 71 through 73' Processing helix chain 'n' and resid 83 through 97 removed outlier: 4.006A pdb=" N ALA n 87 " --> pdb=" O HIS n 83 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG n 88 " --> pdb=" O LYS n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 107 Processing helix chain 'n' and resid 115 through 122 removed outlier: 3.549A pdb=" N GLU n 120 " --> pdb=" O HIS n 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 127 Processing helix chain 'n' and resid 128 through 145 removed outlier: 4.256A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 239 removed outlier: 3.928A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE n 231 " --> pdb=" O THR n 227 " (cutoff:3.500A) Processing helix chain 'n' and resid 250 through 255 Processing helix chain 'n' and resid 354 through 359 Processing helix chain 'n' and resid 391 through 394 Processing helix chain 'n' and resid 428 through 437 removed outlier: 4.094A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 3.807A pdb=" N PHE o 111 " --> pdb=" O LEU o 107 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE o 114 " --> pdb=" O TYR o 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 152 Processing helix chain 'o' and resid 195 through 212 removed outlier: 4.103A pdb=" N ALA o 212 " --> pdb=" O ILE o 208 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 87 removed outlier: 4.265A pdb=" N ILE t 61 " --> pdb=" O ARG t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 190 removed outlier: 3.882A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE t 190 " --> pdb=" O LEU t 186 " (cutoff:3.500A) Processing helix chain 't' and resid 191 through 194 Processing helix chain 't' and resid 200 through 212 Processing helix chain 't' and resid 231 through 240 removed outlier: 3.971A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 241 through 243 No H-bonds generated for 'chain 't' and resid 241 through 243' Processing helix chain 't' and resid 246 through 256 removed outlier: 3.590A pdb=" N ILE t 250 " --> pdb=" O CYS t 246 " (cutoff:3.500A) Processing helix chain 't' and resid 259 through 264 Processing helix chain 't' and resid 265 through 267 No H-bonds generated for 'chain 't' and resid 265 through 267' Processing helix chain 't' and resid 282 through 296 removed outlier: 4.186A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS t 288 " --> pdb=" O ASN t 284 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU t 293 " --> pdb=" O ILE t 289 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA t 294 " --> pdb=" O LYS t 290 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.504A pdb=" N LEU u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 57 Processing helix chain 'u' and resid 82 through 112 removed outlier: 3.511A pdb=" N THR u 89 " --> pdb=" O LEU u 85 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 Processing helix chain 'v' and resid 21 through 27 removed outlier: 3.500A pdb=" N GLN v 25 " --> pdb=" O ASN v 21 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG v 26 " --> pdb=" O LYS v 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS v 27 " --> pdb=" O ASP v 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 21 through 27' Processing helix chain 'v' and resid 33 through 40 removed outlier: 3.547A pdb=" N ALA v 37 " --> pdb=" O ASN v 33 " (cutoff:3.500A) Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 157 through 165 removed outlier: 3.702A pdb=" N LYS v 161 " --> pdb=" O GLU v 157 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU v 165 " --> pdb=" O LYS v 161 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 193 Processing helix chain 'v' and resid 195 through 201 removed outlier: 3.643A pdb=" N PHE v 201 " --> pdb=" O LYS v 197 " (cutoff:3.500A) Processing helix chain 'v' and resid 211 through 226 Processing helix chain 'x' and resid 12 through 44 removed outlier: 3.805A pdb=" N GLU x 43 " --> pdb=" O LYS x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 44 through 55 removed outlier: 3.712A pdb=" N ARG x 48 " --> pdb=" O ASN x 44 " (cutoff:3.500A) Processing helix chain 'x' and resid 60 through 64 Processing helix chain 'x' and resid 79 through 86 Processing helix chain 'x' and resid 104 through 118 Processing helix chain 'x' and resid 131 through 142 Processing helix chain 'x' and resid 204 through 218 Processing helix chain 'y' and resid 13 through 15 No H-bonds generated for 'chain 'y' and resid 13 through 15' Processing helix chain 'y' and resid 31 through 43 removed outlier: 3.589A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 Processing helix chain 'y' and resid 124 through 134 Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.698A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain '3' and resid 18 through 20 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 55 removed outlier: 3.528A pdb=" N ILE 3 80 " --> pdb=" O LEU 3 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 135 through 136 Processing sheet with id=AA4, first strand: chain '5' and resid 34 through 38 removed outlier: 3.771A pdb=" N ALA 5 36 " --> pdb=" O GLU 5 15 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG 5 2 " --> pdb=" O LEU 5 410 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE 5 406 " --> pdb=" O SER 5 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 47 through 51 removed outlier: 6.540A pdb=" N VAL 5 67 " --> pdb=" O SER 5 113 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER 5 113 " --> pdb=" O VAL 5 67 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU 5 69 " --> pdb=" O THR 5 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 140 through 145 removed outlier: 3.840A pdb=" N THR 5 142 " --> pdb=" O ALA 5 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS 5 144 " --> pdb=" O VAL 5 156 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU 5 163 " --> pdb=" O THR 5 159 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA 5 179 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS 5 168 " --> pdb=" O LYS 5 177 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LYS 5 177 " --> pdb=" O LYS 5 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 189 through 192 removed outlier: 3.589A pdb=" N PHE 5 189 " --> pdb=" O GLY 5 208 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY 5 208 " --> pdb=" O PHE 5 189 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLY 5 209 " --> pdb=" O LEU 5 213 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU 5 213 " --> pdb=" O GLY 5 209 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP 5 230 " --> pdb=" O LEU 5 216 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU 5 218 " --> pdb=" O GLN 5 228 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN 5 228 " --> pdb=" O GLU 5 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 248 through 254 removed outlier: 4.416A pdb=" N GLN 5 269 " --> pdb=" O LEU 5 254 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS 5 278 " --> pdb=" O THR 5 274 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA 5 292 " --> pdb=" O LYS 5 281 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 303 through 308 removed outlier: 5.198A pdb=" N GLN 5 305 " --> pdb=" O THR 5 336 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR 5 336 " --> pdb=" O GLN 5 305 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL 5 342 " --> pdb=" O LYS 5 354 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS 5 354 " --> pdb=" O VAL 5 342 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS 5 344 " --> pdb=" O LEU 5 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 366 through 370 removed outlier: 6.699A pdb=" N ASP 5 388 " --> pdb=" O MET 5 394 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET 5 394 " --> pdb=" O ASP 5 388 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.017A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 282 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 325 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG B 70 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP B 59 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.193A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 157 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.193A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 9 removed outlier: 6.748A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 63 Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.043A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB9, first strand: chain 'D' and resid 82 through 84 removed outlier: 6.486A pdb=" N VAL D 82 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 194 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 117 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA D 170 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL D 119 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 392 through 394 removed outlier: 6.597A pdb=" N GLN D 266 " --> pdb=" O ASN D 413 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 317 through 319 removed outlier: 4.002A pdb=" N THR D 346 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE D 292 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N CYS D 345 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL D 294 " --> pdb=" O CYS D 345 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.533A pdb=" N ARG E 77 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 65 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.269A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 230 " --> pdb=" O VAL F 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.297A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.654A pdb=" N LYS H 26 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.468A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.857A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 97 through 101 Processing sheet with id=AD3, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AD4, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AD5, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.306A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD7, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.325A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN M 56 " --> pdb=" O ILE M 46 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE M 46 " --> pdb=" O GLN M 56 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.302A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE N 130 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AE2, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AE3, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.692A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE5, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE6, first strand: chain 'Q' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.202A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.930A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 65 through 66 removed outlier: 3.711A pdb=" N THR W 105 " --> pdb=" O TYR W 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR W 39 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR W 221 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 32 through 34 removed outlier: 3.604A pdb=" N ALA Y 33 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU Y 48 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'Y' and resid 79 through 82 removed outlier: 4.005A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AF4, first strand: chain 'b' and resid 205 through 211 Processing sheet with id=AF5, first strand: chain 'b' and resid 251 through 254 removed outlier: 3.547A pdb=" N VAL b 286 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET b 254 " --> pdb=" O VAL b 286 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AF7, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.014A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'f' and resid 8 through 18 removed outlier: 7.035A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR f 16 " --> pdb=" O VAL f 27 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL f 27 " --> pdb=" O TYR f 16 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ARG f 18 " --> pdb=" O PRO f 25 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG1, first strand: chain 'n' and resid 178 through 181 removed outlier: 3.827A pdb=" N LYS n 178 " --> pdb=" O GLN n 189 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL n 201 " --> pdb=" O VAL n 186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'n' and resid 388 through 389 removed outlier: 6.553A pdb=" N TYR n 366 " --> pdb=" O ILE n 411 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'o' and resid 117 through 124 removed outlier: 5.119A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN o 163 " --> pdb=" O SER o 96 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR o 155 " --> pdb=" O LEU o 162 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 't' and resid 133 through 134 Processing sheet with id=AG5, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.686A pdb=" N TYR u 4 " --> pdb=" O CYS u 13 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'x' and resid 121 through 123 removed outlier: 3.572A pdb=" N THR x 122 " --> pdb=" O ILE x 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE x 150 " --> pdb=" O THR x 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY x 159 " --> pdb=" O ASN x 151 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR x 158 " --> pdb=" O LEU x 175 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER x 176 " --> pdb=" O THR x 264 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR x 264 " --> pdb=" O SER x 176 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE x 178 " --> pdb=" O GLN x 262 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN x 262 " --> pdb=" O PHE x 178 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU x 196 " --> pdb=" O ILE x 230 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU x 232 " --> pdb=" O GLU x 196 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE x 198 " --> pdb=" O LEU x 232 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN x 234 " --> pdb=" O ILE x 198 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN x 200 " --> pdb=" O ASN x 234 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'x' and resid 121 through 123 removed outlier: 3.572A pdb=" N THR x 122 " --> pdb=" O ILE x 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE x 150 " --> pdb=" O THR x 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY x 159 " --> pdb=" O ASN x 151 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR x 158 " --> pdb=" O LEU x 175 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER x 176 " --> pdb=" O THR x 264 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR x 264 " --> pdb=" O SER x 176 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE x 178 " --> pdb=" O GLN x 262 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN x 262 " --> pdb=" O PHE x 178 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'y' and resid 2 through 5 removed outlier: 6.285A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.664A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.744A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'y' and resid 109 through 110 removed outlier: 3.547A pdb=" N CYS y 109 " --> pdb=" O LEU y 116 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'y' and resid 152 through 155 removed outlier: 3.506A pdb=" N GLY y 158 " --> pdb=" O SER y 155 " (cutoff:3.500A) 2064 hydrogen bonds defined for protein. 5832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1319 hydrogen bonds 2132 hydrogen bond angles 0 basepair planarities 531 basepair parallelities 786 stacking parallelities Total time for adding SS restraints: 84.64 Time building geometry restraints manager: 111.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.25: 79578 1.25 - 1.67: 82590 1.67 - 2.08: 202 2.08 - 2.50: 0 2.50 - 2.91: 1 Bond restraints: 162371 Sorted by residual: bond pdb=" O3' G 1 779 " pdb=" P G 1 781 " ideal model delta sigma weight residual 1.607 2.913 -1.306 1.50e-02 4.44e+03 7.58e+03 bond pdb=" N GLY N 2 " pdb=" CA GLY N 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.29e+00 bond pdb=" N ARG W 3 " pdb=" CA ARG W 3 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N HIS Q 15 " pdb=" CA HIS Q 15 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ALA h 2 " pdb=" CA ALA h 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 162366 not shown) Histogram of bond angle deviations from ideal: 58.69 - 73.79: 2 73.79 - 88.88: 0 88.88 - 103.97: 5729 103.97 - 119.06: 216140 119.06 - 134.15: 70882 Bond angle restraints: 292753 Sorted by residual: angle pdb=" O3' G 1 779 " pdb=" P G 1 781 " pdb=" O5' G 1 781 " ideal model delta sigma weight residual 104.00 58.98 45.02 1.50e+00 4.44e-01 9.01e+02 angle pdb=" O3' G 1 779 " pdb=" P G 1 781 " pdb=" OP2 G 1 781 " ideal model delta sigma weight residual 108.00 58.69 49.31 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C3' G 1 779 " pdb=" O3' G 1 779 " pdb=" P G 1 781 " ideal model delta sigma weight residual 120.20 106.35 13.85 1.50e+00 4.44e-01 8.53e+01 angle pdb=" N VAL b 411 " pdb=" CA VAL b 411 " pdb=" C VAL b 411 " ideal model delta sigma weight residual 113.71 109.73 3.98 9.50e-01 1.11e+00 1.75e+01 angle pdb=" O3' G 11097 " pdb=" C3' G 11097 " pdb=" C2' G 11097 " ideal model delta sigma weight residual 109.50 115.54 -6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 292748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 71734 35.93 - 71.86: 5588 71.86 - 107.80: 544 107.80 - 143.73: 27 143.73 - 179.66: 49 Dihedral angle restraints: 77942 sinusoidal: 57279 harmonic: 20663 Sorted by residual: dihedral pdb=" C4' A 11200 " pdb=" C3' A 11200 " pdb=" C2' A 11200 " pdb=" C1' A 11200 " ideal model delta sinusoidal sigma weight residual -35.00 36.54 -71.54 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' G 11097 " pdb=" C3' G 11097 " pdb=" C2' G 11097 " pdb=" C1' G 11097 " ideal model delta sinusoidal sigma weight residual -35.00 36.07 -71.07 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A 1 352 " pdb=" C3' A 1 352 " pdb=" C2' A 1 352 " pdb=" C1' A 1 352 " ideal model delta sinusoidal sigma weight residual -35.00 35.64 -70.64 1 8.00e+00 1.56e-02 1.00e+02 ... (remaining 77939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 15297 0.063 - 0.126: 956 0.126 - 0.189: 34 0.189 - 0.253: 51 0.253 - 0.316: 8 Chirality restraints: 16346 Sorted by residual: chirality pdb=" C3' G 11097 " pdb=" C4' G 11097 " pdb=" O3' G 11097 " pdb=" C2' G 11097 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3' G 11242 " pdb=" C4' G 11242 " pdb=" O3' G 11242 " pdb=" C2' G 11242 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' G 1 770 " pdb=" C4' G 1 770 " pdb=" O3' G 1 770 " pdb=" C2' G 1 770 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 16343 not shown) Planarity restraints: 17284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 14 " -0.036 2.00e-02 2.50e+03 1.68e-02 7.77e+00 pdb=" N1 C 2 14 " 0.039 2.00e-02 2.50e+03 pdb=" C2 C 2 14 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C 2 14 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C 2 14 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 2 14 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C 2 14 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C 2 14 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C 2 14 " 0.002 2.00e-02 2.50e+03 pdb=" H5 C 2 14 " -0.006 2.00e-02 2.50e+03 pdb=" H6 C 2 14 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 15 " 0.034 2.00e-02 2.50e+03 1.32e-02 6.09e+00 pdb=" N9 G 2 15 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G 2 15 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 2 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 15 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 2 15 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G 2 15 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G 2 15 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G 2 15 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G 2 15 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 2 15 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G 2 15 " -0.002 2.00e-02 2.50e+03 pdb=" H8 G 2 15 " -0.002 2.00e-02 2.50e+03 pdb=" H1 G 2 15 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 13212 " 0.031 2.00e-02 2.50e+03 1.46e-02 5.86e+00 pdb=" N1 C 13212 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C 13212 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C 13212 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C 13212 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C 13212 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C 13212 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 13212 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C 13212 " -0.003 2.00e-02 2.50e+03 pdb=" H5 C 13212 " 0.004 2.00e-02 2.50e+03 pdb=" H6 C 13212 " -0.006 2.00e-02 2.50e+03 ... (remaining 17281 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 6405 2.16 - 2.77: 266257 2.77 - 3.38: 425498 3.38 - 3.99: 565508 3.99 - 4.60: 857278 Nonbonded interactions: 2120946 Sorted by model distance: nonbonded pdb=" H21 G 11404 " pdb=" OP2 A 11407 " model vdw 1.551 1.850 nonbonded pdb=" OP2 G 1 297 " pdb=" H22 G 1 297 " model vdw 1.572 1.850 nonbonded pdb=" OP1 U 1 594 " pdb=" H1 G 1 609 " model vdw 1.578 1.850 nonbonded pdb=" OD1 ASN y 111 " pdb=" H VAL y 114 " model vdw 1.578 1.850 nonbonded pdb=" OP2 U 13214 " pdb="HH22 ARG M 128 " model vdw 1.580 1.850 ... (remaining 2120941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 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: 1.470 Extract box with map and model: 18.660 Check model and map are aligned: 1.630 Set scattering table: 1.050 Process input model: 471.070 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.380 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:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 504.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.005 1.306 92332 Z= 0.238 Angle : 0.493 49.306 133069 Z= 0.256 Chirality : 0.034 0.316 16346 Planarity : 0.002 0.051 10207 Dihedral : 21.715 179.660 46544 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.81 % Allowed : 10.98 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.12), residues: 5868 helix: 2.36 (0.12), residues: 2287 sheet: 0.28 (0.18), residues: 828 loop : -0.06 (0.12), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP K 253 HIS 0.002 0.000 HIS K 104 PHE 0.009 0.000 PHE 3 14 TYR 0.010 0.000 TYR D 450 ARG 0.004 0.000 ARG W 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1368 time to evaluate : 7.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 9 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8801 (t) REVERT: 3 104 PHE cc_start: 0.8483 (m-80) cc_final: 0.8271 (m-80) REVERT: 4 71 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8503 (tm-30) REVERT: 4 112 ASN cc_start: 0.8792 (m110) cc_final: 0.8489 (t0) REVERT: 4 124 LEU cc_start: 0.8912 (tp) cc_final: 0.8711 (tt) REVERT: 4 242 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8793 (tm) REVERT: 5 241 ASP cc_start: 0.8939 (m-30) cc_final: 0.8478 (t0) REVERT: C 176 SER cc_start: 0.9339 (m) cc_final: 0.9097 (p) REVERT: C 283 THR cc_start: 0.8852 (m) cc_final: 0.8557 (p) REVERT: D 176 LEU cc_start: 0.7814 (mt) cc_final: 0.7443 (mt) REVERT: F 25 GLN cc_start: 0.8213 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 26 VAL cc_start: 0.8653 (t) cc_final: 0.8437 (t) REVERT: G 80 TYR cc_start: 0.8869 (m-80) cc_final: 0.8504 (m-80) REVERT: G 161 GLU cc_start: 0.8438 (pm20) cc_final: 0.7709 (tm-30) REVERT: H 63 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8238 (tmtt) REVERT: K 160 LEU cc_start: 0.8221 (mt) cc_final: 0.7805 (tt) REVERT: M 27 GLN cc_start: 0.9340 (tt0) cc_final: 0.9075 (tp40) REVERT: O 72 HIS cc_start: 0.4079 (m90) cc_final: 0.3837 (m90) REVERT: P 91 VAL cc_start: 0.9423 (t) cc_final: 0.9200 (p) REVERT: S 104 GLU cc_start: 0.9635 (tt0) cc_final: 0.9406 (tm-30) REVERT: W 22 ASN cc_start: 0.5956 (t0) cc_final: 0.5483 (m110) REVERT: W 48 VAL cc_start: 0.8085 (m) cc_final: 0.7774 (p) REVERT: W 221 TYR cc_start: 0.8682 (t80) cc_final: 0.8372 (t80) REVERT: b 267 GLN cc_start: 0.7388 (mt0) cc_final: 0.7137 (tm-30) REVERT: b 284 MET cc_start: -0.0269 (ttm) cc_final: -0.0514 (mtp) REVERT: h 61 GLN cc_start: 0.8888 (mt0) cc_final: 0.8445 (mt0) REVERT: v 39 ASN cc_start: 0.8871 (m-40) cc_final: 0.8527 (m110) REVERT: v 183 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9188 (mm-30) REVERT: x 17 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9094 (tm-30) REVERT: x 100 ASN cc_start: 0.8278 (m110) cc_final: 0.7937 (m110) REVERT: x 127 LYS cc_start: 0.5375 (mttt) cc_final: 0.5030 (tttt) outliers start: 43 outliers final: 17 residues processed: 1403 average time/residue: 2.0670 time to fit residues: 4655.2770 Evaluate side-chains 890 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 871 time to evaluate : 7.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 3 residue 87 THR Chi-restraints excluded: chain 4 residue 29 LEU Chi-restraints excluded: chain 4 residue 242 LEU Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 200 ASN Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 137 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 649 optimal weight: 20.0000 chunk 582 optimal weight: 50.0000 chunk 323 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 chunk 311 optimal weight: 0.9980 chunk 602 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 448 optimal weight: 7.9990 chunk 698 optimal weight: 40.0000 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 73 HIS 5 269 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN C 116 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 260 GLN D 178 HIS D 330 ASN D 441 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS F 194 HIS H 59 ASN K 262 ASN P 121 GLN Q 45 ASN Q 58 ASN S 62 ASN S 142 GLN e 98 HIS f 75 HIS h 59 ASN h 99 GLN j 76 ASN o 113 GLN t 154 ASN ** u 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 25 GLN x 102 ASN x 187 HIS ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 92332 Z= 0.279 Angle : 0.587 12.995 133069 Z= 0.310 Chirality : 0.037 0.247 16346 Planarity : 0.004 0.056 10207 Dihedral : 22.621 179.898 34069 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 2.00 % Allowed : 16.11 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.11), residues: 5868 helix: 1.73 (0.11), residues: 2324 sheet: -0.27 (0.17), residues: 863 loop : -0.34 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP v 222 HIS 0.012 0.001 HIS E 172 PHE 0.027 0.002 PHE n 142 TYR 0.027 0.001 TYR u 108 ARG 0.010 0.000 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 882 time to evaluate : 7.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 95 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8766 (tm-30) REVERT: 4 71 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8485 (tm-30) REVERT: 4 112 ASN cc_start: 0.9206 (m-40) cc_final: 0.8642 (t0) REVERT: 4 242 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8813 (tm) REVERT: 5 241 ASP cc_start: 0.9039 (m-30) cc_final: 0.8709 (t0) REVERT: 5 374 TYR cc_start: 0.8256 (m-80) cc_final: 0.7910 (m-80) REVERT: D 276 ARG cc_start: 0.6769 (ttp80) cc_final: 0.6487 (ttm170) REVERT: F 25 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8054 (tm-30) REVERT: G 161 GLU cc_start: 0.8672 (pm20) cc_final: 0.7717 (tm-30) REVERT: G 173 MET cc_start: 0.9142 (mmm) cc_final: 0.8600 (mmt) REVERT: H 63 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8329 (tmtt) REVERT: K 160 LEU cc_start: 0.8186 (mt) cc_final: 0.7784 (tt) REVERT: N 29 GLU cc_start: 0.9396 (tm-30) cc_final: 0.9003 (tm-30) REVERT: P 91 VAL cc_start: 0.9535 (t) cc_final: 0.9310 (p) REVERT: W 22 ASN cc_start: 0.6014 (t0) cc_final: 0.5725 (m110) REVERT: W 48 VAL cc_start: 0.8120 (m) cc_final: 0.7799 (p) REVERT: W 171 ILE cc_start: 0.8701 (pt) cc_final: 0.8362 (pt) REVERT: W 221 TYR cc_start: 0.8518 (t80) cc_final: 0.8205 (t80) REVERT: b 267 GLN cc_start: 0.7449 (mt0) cc_final: 0.7068 (tm-30) REVERT: b 434 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.5136 (mt-10) REVERT: n 451 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6326 (pt0) REVERT: u 84 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7720 (pt0) REVERT: v 6 LYS cc_start: 0.8463 (mttt) cc_final: 0.8192 (mttm) REVERT: v 7 ARG cc_start: 0.6904 (mtt180) cc_final: 0.5852 (ttt90) REVERT: v 41 ASP cc_start: 0.8390 (t0) cc_final: 0.8174 (t0) REVERT: v 49 ASN cc_start: 0.8797 (m-40) cc_final: 0.8593 (m-40) REVERT: v 51 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9299 (mptt) REVERT: v 183 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9161 (mm-30) REVERT: x 17 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9128 (tm-30) REVERT: x 172 TYR cc_start: 0.8364 (t80) cc_final: 0.8144 (t80) outliers start: 106 outliers final: 70 residues processed: 957 average time/residue: 1.9557 time to fit residues: 3048.4493 Evaluate side-chains 859 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 786 time to evaluate : 6.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 87 THR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 120 ILE Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 29 LEU Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 4 residue 242 LEU Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 78 ASN Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 310 LEU Chi-restraints excluded: chain n residue 215 PHE Chi-restraints excluded: chain n residue 222 LEU Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain x residue 25 GLU Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 200 ASN Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 581 optimal weight: 6.9990 chunk 475 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 699 optimal weight: 20.0000 chunk 755 optimal weight: 30.0000 chunk 623 optimal weight: 9.9990 chunk 693 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 561 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN H 58 HIS H 59 ASN ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 284 ASN M 41 GLN O 42 ASN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN o 113 GLN ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 92332 Z= 0.282 Angle : 0.548 8.481 133069 Z= 0.292 Chirality : 0.036 0.227 16346 Planarity : 0.004 0.063 10207 Dihedral : 22.802 179.630 34060 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 2.29 % Allowed : 16.52 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 5868 helix: 1.47 (0.11), residues: 2321 sheet: -0.46 (0.17), residues: 830 loop : -0.62 (0.12), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP v 222 HIS 0.013 0.001 HIS D 141 PHE 0.022 0.001 PHE W 104 TYR 0.024 0.001 TYR G 80 ARG 0.010 0.000 ARG x 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 799 time to evaluate : 6.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 71 HIS cc_start: 0.6333 (OUTLIER) cc_final: 0.6084 (m-70) REVERT: 3 87 THR cc_start: 0.9325 (m) cc_final: 0.9112 (p) REVERT: 4 6 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8976 (t80) REVERT: 4 71 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8484 (tm-30) REVERT: 5 241 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8863 (t0) REVERT: 5 295 ASP cc_start: 0.9608 (OUTLIER) cc_final: 0.9406 (m-30) REVERT: D 194 ILE cc_start: 0.5095 (OUTLIER) cc_final: 0.4804 (pp) REVERT: D 233 THR cc_start: 0.8089 (p) cc_final: 0.7550 (p) REVERT: D 276 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6614 (ttm170) REVERT: F 25 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8060 (tm-30) REVERT: G 89 GLU cc_start: 0.9597 (tp30) cc_final: 0.9356 (tm-30) REVERT: G 144 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: G 161 GLU cc_start: 0.8805 (pm20) cc_final: 0.7745 (tm-30) REVERT: H 63 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8336 (tmtt) REVERT: K 74 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5806 (pt) REVERT: K 160 LEU cc_start: 0.8186 (mt) cc_final: 0.7790 (tt) REVERT: N 29 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9051 (tm-30) REVERT: P 82 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (tmm-80) REVERT: W 22 ASN cc_start: 0.5895 (t0) cc_final: 0.5687 (m110) REVERT: W 48 VAL cc_start: 0.8187 (m) cc_final: 0.7849 (p) REVERT: W 221 TYR cc_start: 0.8589 (t80) cc_final: 0.8304 (t80) REVERT: b 267 GLN cc_start: 0.7293 (mt0) cc_final: 0.6926 (tm-30) REVERT: b 432 MET cc_start: 0.1662 (tpt) cc_final: 0.1144 (tpt) REVERT: b 434 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4878 (mt-10) REVERT: h 102 GLU cc_start: 0.9521 (mm-30) cc_final: 0.9259 (tp30) REVERT: n 451 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6412 (pt0) REVERT: v 41 ASP cc_start: 0.8778 (t0) cc_final: 0.8570 (t0) REVERT: v 51 LYS cc_start: 0.9587 (mmmm) cc_final: 0.9320 (mptt) REVERT: v 199 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.9083 (mtm) REVERT: x 17 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9146 (tm-30) REVERT: x 139 CYS cc_start: 0.9247 (m) cc_final: 0.8958 (m) outliers start: 121 outliers final: 84 residues processed: 873 average time/residue: 1.8940 time to fit residues: 2710.3734 Evaluate side-chains 847 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 752 time to evaluate : 7.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 109 GLU Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 4 residue 242 LEU Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 241 ASP Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 39 TYR Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 215 PHE Chi-restraints excluded: chain n residue 222 LEU Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 284 ASN Chi-restraints excluded: chain v residue 163 GLU Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 200 ASN Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 20.0000 chunk 525 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 333 optimal weight: 30.0000 chunk 469 optimal weight: 8.9990 chunk 702 optimal weight: 40.0000 chunk 743 optimal weight: 7.9990 chunk 366 optimal weight: 7.9990 chunk 665 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN H 59 ASN L 99 HIS ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 92332 Z= 0.293 Angle : 0.557 6.591 133069 Z= 0.297 Chirality : 0.036 0.246 16346 Planarity : 0.004 0.067 10207 Dihedral : 22.826 179.758 34055 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 2.59 % Allowed : 17.58 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5868 helix: 1.33 (0.11), residues: 2319 sheet: -0.72 (0.17), residues: 824 loop : -0.76 (0.12), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP n 166 HIS 0.008 0.001 HIS j 69 PHE 0.015 0.001 PHE 4 102 TYR 0.030 0.001 TYR o 110 ARG 0.005 0.000 ARG i 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 762 time to evaluate : 6.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 71 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5491 (m-70) REVERT: 3 87 THR cc_start: 0.9340 (m) cc_final: 0.9137 (p) REVERT: 4 71 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8433 (tm-30) REVERT: 4 242 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8844 (tm) REVERT: 5 241 ASP cc_start: 0.9122 (m-30) cc_final: 0.8909 (t0) REVERT: 5 295 ASP cc_start: 0.9646 (OUTLIER) cc_final: 0.9446 (m-30) REVERT: C 284 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8676 (t) REVERT: D 115 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8119 (m) REVERT: D 194 ILE cc_start: 0.5555 (OUTLIER) cc_final: 0.5288 (pp) REVERT: D 276 ARG cc_start: 0.7256 (ttp80) cc_final: 0.6670 (ttm170) REVERT: F 25 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8053 (tm-30) REVERT: G 89 GLU cc_start: 0.9616 (tp30) cc_final: 0.9409 (tm-30) REVERT: G 161 GLU cc_start: 0.8829 (pm20) cc_final: 0.7823 (tm-30) REVERT: H 63 LYS cc_start: 0.8538 (mmtp) cc_final: 0.8275 (tmtt) REVERT: H 149 ASN cc_start: 0.7053 (m-40) cc_final: 0.6814 (m-40) REVERT: K 160 LEU cc_start: 0.8229 (mt) cc_final: 0.7819 (tt) REVERT: N 29 GLU cc_start: 0.9471 (tm-30) cc_final: 0.9094 (tm-30) REVERT: N 188 ARG cc_start: 0.7323 (mtm180) cc_final: 0.6901 (mtt180) REVERT: P 82 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8110 (ttm-80) REVERT: W 48 VAL cc_start: 0.8135 (m) cc_final: 0.7804 (p) REVERT: W 221 TYR cc_start: 0.8559 (t80) cc_final: 0.8276 (t80) REVERT: b 195 GLN cc_start: 0.5756 (mm-40) cc_final: 0.5555 (mm-40) REVERT: b 267 GLN cc_start: 0.7342 (mt0) cc_final: 0.6957 (tm-30) REVERT: b 432 MET cc_start: 0.1744 (tpt) cc_final: 0.1192 (tpt) REVERT: b 434 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.4876 (mt-10) REVERT: b 437 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6329 (t0) REVERT: h 102 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9286 (tp30) REVERT: n 451 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6486 (pt0) REVERT: v 41 ASP cc_start: 0.8844 (t0) cc_final: 0.8617 (t0) REVERT: v 51 LYS cc_start: 0.9583 (mmmm) cc_final: 0.9311 (mptt) REVERT: v 199 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9044 (mtm) REVERT: x 17 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9172 (tm-30) REVERT: x 139 CYS cc_start: 0.9265 (m) cc_final: 0.8942 (m) REVERT: x 287 ASP cc_start: 0.8445 (t0) cc_final: 0.7886 (t0) outliers start: 137 outliers final: 104 residues processed: 844 average time/residue: 1.8953 time to fit residues: 2615.3919 Evaluate side-chains 841 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 727 time to evaluate : 6.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 64 MET Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 120 ILE Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 4 residue 242 LEU Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 285 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 437 ASP Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 251 GLU Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 215 PHE Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 284 ASN Chi-restraints excluded: chain v residue 163 GLU Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 170 THR Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 9.9990 chunk 421 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 553 optimal weight: 30.0000 chunk 306 optimal weight: 0.7980 chunk 634 optimal weight: 10.0000 chunk 513 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 379 optimal weight: 3.9990 chunk 667 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 234 ASN B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN O 42 ASN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 92332 Z= 0.340 Angle : 0.599 12.720 133069 Z= 0.318 Chirality : 0.038 0.249 16346 Planarity : 0.004 0.077 10207 Dihedral : 23.009 179.843 34051 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 3.29 % Allowed : 17.66 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 5868 helix: 1.01 (0.11), residues: 2318 sheet: -1.00 (0.17), residues: 839 loop : -0.99 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP v 222 HIS 0.027 0.002 HIS D 178 PHE 0.035 0.002 PHE B 199 TYR 0.021 0.002 TYR h 75 ARG 0.014 0.000 ARG W 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 727 time to evaluate : 6.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 55 CYS cc_start: 0.9317 (p) cc_final: 0.8992 (p) REVERT: 3 71 HIS cc_start: 0.6037 (OUTLIER) cc_final: 0.4887 (m-70) REVERT: 3 147 ASN cc_start: 0.9586 (m110) cc_final: 0.9256 (m110) REVERT: 4 242 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8867 (tm) REVERT: 5 241 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8929 (t0) REVERT: 5 295 ASP cc_start: 0.9625 (OUTLIER) cc_final: 0.9423 (m-30) REVERT: C 284 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8723 (t) REVERT: D 115 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8197 (m) REVERT: D 194 ILE cc_start: 0.5632 (OUTLIER) cc_final: 0.5392 (pp) REVERT: D 276 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6834 (ttm170) REVERT: F 25 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8050 (tm-30) REVERT: G 144 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: G 161 GLU cc_start: 0.8855 (pm20) cc_final: 0.7981 (tm-30) REVERT: H 63 LYS cc_start: 0.8593 (mmtp) cc_final: 0.8318 (tmtt) REVERT: H 149 ASN cc_start: 0.7102 (m-40) cc_final: 0.6791 (m-40) REVERT: K 160 LEU cc_start: 0.8249 (mt) cc_final: 0.7767 (tt) REVERT: N 29 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9134 (tm-30) REVERT: N 188 ARG cc_start: 0.7526 (mtm180) cc_final: 0.6717 (ptp-170) REVERT: O 4 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6581 (mm-30) REVERT: P 82 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8245 (tmm-80) REVERT: W 48 VAL cc_start: 0.8197 (m) cc_final: 0.7869 (p) REVERT: W 221 TYR cc_start: 0.8528 (t80) cc_final: 0.8260 (t80) REVERT: b 267 GLN cc_start: 0.7420 (mt0) cc_final: 0.7028 (tm-30) REVERT: b 437 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6517 (t0) REVERT: h 102 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9291 (tp30) REVERT: n 120 GLU cc_start: 0.6700 (pp20) cc_final: 0.6407 (pp20) REVERT: n 451 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6424 (pt0) REVERT: v 41 ASP cc_start: 0.8900 (t0) cc_final: 0.8479 (t0) REVERT: v 49 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8675 (m-40) REVERT: v 51 LYS cc_start: 0.9623 (mmmm) cc_final: 0.9371 (mptt) REVERT: v 199 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9079 (mtm) REVERT: x 17 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9271 (tm-30) REVERT: x 21 ASP cc_start: 0.9281 (m-30) cc_final: 0.9071 (t0) REVERT: x 139 CYS cc_start: 0.9284 (m) cc_final: 0.8936 (m) outliers start: 174 outliers final: 125 residues processed: 844 average time/residue: 1.8598 time to fit residues: 2572.5130 Evaluate side-chains 833 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 695 time to evaluate : 7.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 64 MET Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 92 GLN Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 4 residue 242 LEU Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 241 ASP Chi-restraints excluded: chain 5 residue 295 ASP Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain 5 residue 358 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain K residue 285 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 73 GLN Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 39 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 437 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 52 LYS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 251 GLU Chi-restraints excluded: chain m residue 272 GLU Chi-restraints excluded: chain m residue 280 VAL Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 232 VAL Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 284 ASN Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 163 GLU Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 170 THR Chi-restraints excluded: chain x residue 200 ASN Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 20.0000 chunk 669 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 744 optimal weight: 0.4980 chunk 617 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 246 optimal weight: 40.0000 chunk 390 optimal weight: 3.9990 overall best weight: 6.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 ASN ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 34 HIS B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 92332 Z= 0.319 Angle : 0.582 8.348 133069 Z= 0.309 Chirality : 0.038 0.236 16346 Planarity : 0.004 0.074 10207 Dihedral : 23.072 179.595 34051 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 2.87 % Allowed : 18.87 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 5868 helix: 0.92 (0.11), residues: 2350 sheet: -1.08 (0.17), residues: 813 loop : -1.07 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP n 166 HIS 0.015 0.001 HIS O 72 PHE 0.015 0.001 PHE x 128 TYR 0.017 0.001 TYR Q 33 ARG 0.008 0.000 ARG b 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 713 time to evaluate : 7.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 55 CYS cc_start: 0.9324 (p) cc_final: 0.9031 (p) REVERT: 3 71 HIS cc_start: 0.6227 (OUTLIER) cc_final: 0.5171 (m-70) REVERT: 3 147 ASN cc_start: 0.9565 (m110) cc_final: 0.9232 (m110) REVERT: 5 76 LEU cc_start: 0.9178 (mp) cc_final: 0.8932 (pp) REVERT: 5 241 ASP cc_start: 0.9159 (m-30) cc_final: 0.8948 (t0) REVERT: C 284 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8704 (t) REVERT: D 115 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8226 (m) REVERT: D 276 ARG cc_start: 0.7389 (ttp80) cc_final: 0.6890 (ttm-80) REVERT: F 25 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8082 (tm-30) REVERT: G 144 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: G 161 GLU cc_start: 0.8870 (pm20) cc_final: 0.7966 (tm-30) REVERT: H 63 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8285 (tmtt) REVERT: K 160 LEU cc_start: 0.8203 (mt) cc_final: 0.7714 (tt) REVERT: N 29 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9168 (tm-30) REVERT: N 188 ARG cc_start: 0.7491 (mtm180) cc_final: 0.6635 (ptp-170) REVERT: O 4 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6613 (mm-30) REVERT: P 82 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: W 221 TYR cc_start: 0.8529 (t80) cc_final: 0.8271 (t80) REVERT: b 267 GLN cc_start: 0.7336 (mt0) cc_final: 0.6981 (tm-30) REVERT: b 437 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6501 (t0) REVERT: e 36 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8043 (mmtm) REVERT: h 102 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9295 (tp30) REVERT: n 451 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6501 (pt0) REVERT: v 20 ARG cc_start: 0.8397 (mtt90) cc_final: 0.7853 (mtm180) REVERT: v 41 ASP cc_start: 0.8912 (t0) cc_final: 0.8684 (t0) REVERT: v 199 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.9041 (mtm) REVERT: x 17 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9267 (tm-30) REVERT: x 139 CYS cc_start: 0.9282 (m) cc_final: 0.8927 (m) outliers start: 152 outliers final: 125 residues processed: 808 average time/residue: 1.8417 time to fit residues: 2428.4682 Evaluate side-chains 826 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 693 time to evaluate : 7.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 92 GLN Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 5 residue 25 SER Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain K residue 285 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 72 HIS Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 73 GLN Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 PHE Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 437 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 251 GLU Chi-restraints excluded: chain m residue 296 GLU Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 425 THR Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 284 ASN Chi-restraints excluded: chain v residue 163 GLU Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 423 optimal weight: 30.0000 chunk 543 optimal weight: 5.9990 chunk 420 optimal weight: 20.0000 chunk 626 optimal weight: 10.0000 chunk 415 optimal weight: 6.9990 chunk 741 optimal weight: 8.9990 chunk 463 optimal weight: 2.9990 chunk 451 optimal weight: 4.9990 chunk 342 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 GLN ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 ASN ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 92332 Z= 0.293 Angle : 0.572 9.344 133069 Z= 0.303 Chirality : 0.037 0.255 16346 Planarity : 0.004 0.075 10207 Dihedral : 23.124 179.838 34044 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.37 % Rotamer: Outliers : 3.12 % Allowed : 19.05 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 5868 helix: 1.00 (0.11), residues: 2338 sheet: -1.13 (0.17), residues: 812 loop : -1.06 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP n 166 HIS 0.011 0.001 HIS b 90 PHE 0.015 0.001 PHE F 229 TYR 0.017 0.001 TYR Q 33 ARG 0.009 0.000 ARG n 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 705 time to evaluate : 7.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 55 CYS cc_start: 0.9337 (p) cc_final: 0.9048 (p) REVERT: 3 71 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5278 (m-70) REVERT: 3 147 ASN cc_start: 0.9565 (m110) cc_final: 0.9233 (m110) REVERT: 5 76 LEU cc_start: 0.9170 (mp) cc_final: 0.8951 (pp) REVERT: C 284 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8741 (t) REVERT: D 115 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8243 (m) REVERT: D 276 ARG cc_start: 0.7372 (ttp80) cc_final: 0.6875 (ttm-80) REVERT: F 25 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8063 (tm-30) REVERT: G 144 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: G 161 GLU cc_start: 0.8828 (pm20) cc_final: 0.8010 (tm-30) REVERT: H 63 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8276 (tmtt) REVERT: H 69 ARG cc_start: 0.7227 (tpt90) cc_final: 0.7002 (ttt180) REVERT: H 149 ASN cc_start: 0.7097 (m-40) cc_final: 0.6849 (m-40) REVERT: K 160 LEU cc_start: 0.8298 (mt) cc_final: 0.7809 (tt) REVERT: N 29 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9173 (tm-30) REVERT: P 82 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8296 (ttm-80) REVERT: W 221 TYR cc_start: 0.8519 (t80) cc_final: 0.8261 (t80) REVERT: b 267 GLN cc_start: 0.7361 (mt0) cc_final: 0.6994 (tm-30) REVERT: b 434 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4637 (mt-10) REVERT: b 437 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6576 (t0) REVERT: h 102 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9280 (tp30) REVERT: n 451 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6565 (pt0) REVERT: u 20 MET cc_start: 0.4033 (ttt) cc_final: 0.3700 (tpt) REVERT: v 20 ARG cc_start: 0.8398 (mtt90) cc_final: 0.7869 (mtm180) REVERT: v 41 ASP cc_start: 0.8941 (t0) cc_final: 0.8538 (t0) REVERT: v 49 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8650 (m-40) REVERT: v 199 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9113 (mtt) REVERT: x 139 CYS cc_start: 0.9255 (m) cc_final: 0.8877 (m) REVERT: x 239 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8396 (pt) outliers start: 165 outliers final: 132 residues processed: 812 average time/residue: 1.8472 time to fit residues: 2442.7056 Evaluate side-chains 827 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 684 time to evaluate : 6.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 92 GLN Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 5 residue 25 SER Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain K residue 285 ARG Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 73 GLN Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 PHE Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 437 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 272 GLU Chi-restraints excluded: chain m residue 280 VAL Chi-restraints excluded: chain m residue 296 GLU Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 215 PHE Chi-restraints excluded: chain n residue 223 GLU Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 65 THR Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 284 ASN Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 200 ASN Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 239 ILE Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 286 MET Chi-restraints excluded: chain x residue 289 GLU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 442 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 471 optimal weight: 9.9990 chunk 504 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 582 optimal weight: 40.0000 overall best weight: 7.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 9 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 92332 Z= 0.362 Angle : 0.609 8.801 133069 Z= 0.323 Chirality : 0.039 0.267 16346 Planarity : 0.004 0.077 10207 Dihedral : 23.184 179.885 34044 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 3.14 % Allowed : 19.22 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 5868 helix: 0.74 (0.11), residues: 2349 sheet: -1.17 (0.17), residues: 808 loop : -1.19 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP n 166 HIS 0.011 0.001 HIS O 72 PHE 0.015 0.001 PHE x 128 TYR 0.051 0.002 TYR G 80 ARG 0.006 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 693 time to evaluate : 7.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 55 CYS cc_start: 0.9328 (p) cc_final: 0.9052 (p) REVERT: 3 71 HIS cc_start: 0.6311 (OUTLIER) cc_final: 0.5299 (m-70) REVERT: 3 147 ASN cc_start: 0.9578 (m110) cc_final: 0.9237 (m110) REVERT: 5 76 LEU cc_start: 0.9160 (mp) cc_final: 0.8957 (pp) REVERT: C 284 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8693 (t) REVERT: D 115 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8252 (m) REVERT: D 276 ARG cc_start: 0.7378 (ttp80) cc_final: 0.6882 (ttm-80) REVERT: G 80 TYR cc_start: 0.8207 (m-80) cc_final: 0.7985 (m-80) REVERT: G 144 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: G 161 GLU cc_start: 0.8839 (pm20) cc_final: 0.8158 (tm-30) REVERT: H 63 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8272 (tmtt) REVERT: H 69 ARG cc_start: 0.7154 (tpt90) cc_final: 0.6930 (ttt180) REVERT: H 149 ASN cc_start: 0.7019 (m-40) cc_final: 0.6769 (m-40) REVERT: K 160 LEU cc_start: 0.8300 (mt) cc_final: 0.7787 (tt) REVERT: N 29 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9208 (tm-30) REVERT: P 82 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8370 (ttm-80) REVERT: W 221 TYR cc_start: 0.8527 (t80) cc_final: 0.8273 (t80) REVERT: b 267 GLN cc_start: 0.7343 (mt0) cc_final: 0.6981 (tm-30) REVERT: b 437 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6518 (t0) REVERT: e 44 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: h 102 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9302 (tp30) REVERT: v 20 ARG cc_start: 0.8423 (mtt90) cc_final: 0.7894 (mtm180) REVERT: v 41 ASP cc_start: 0.8951 (t0) cc_final: 0.8725 (t0) REVERT: x 139 CYS cc_start: 0.9250 (m) cc_final: 0.8880 (m) outliers start: 166 outliers final: 141 residues processed: 802 average time/residue: 1.8294 time to fit residues: 2382.3467 Evaluate side-chains 831 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 683 time to evaluate : 6.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 64 MET Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 92 GLN Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 5 residue 25 SER Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 219 ILE Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain K residue 285 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 73 GLN Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 81 TYR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 104 PHE Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 437 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 272 GLU Chi-restraints excluded: chain m residue 280 VAL Chi-restraints excluded: chain m residue 296 GLU Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 215 PHE Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 128 THR Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 65 THR Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 284 ASN Chi-restraints excluded: chain v residue 163 GLU Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 170 THR Chi-restraints excluded: chain x residue 200 ASN Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 289 GLU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 674 optimal weight: 10.0000 chunk 710 optimal weight: 30.0000 chunk 647 optimal weight: 5.9990 chunk 690 optimal weight: 10.0000 chunk 709 optimal weight: 7.9990 chunk 415 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 542 optimal weight: 0.5980 chunk 211 optimal weight: 6.9990 chunk 624 optimal weight: 0.8980 chunk 653 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN e 26 HIS n 160 GLN n 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 92332 Z= 0.181 Angle : 0.534 7.793 133069 Z= 0.283 Chirality : 0.035 0.249 16346 Planarity : 0.004 0.072 10207 Dihedral : 23.162 179.659 34042 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.17 % Rotamer: Outliers : 2.44 % Allowed : 20.13 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 5868 helix: 1.12 (0.11), residues: 2350 sheet: -1.11 (0.18), residues: 800 loop : -0.95 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP n 166 HIS 0.011 0.001 HIS b 90 PHE 0.019 0.001 PHE G 94 TYR 0.025 0.001 TYR K 164 ARG 0.006 0.000 ARG W 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 710 time to evaluate : 7.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 55 CYS cc_start: 0.9280 (p) cc_final: 0.9010 (p) REVERT: 3 71 HIS cc_start: 0.6345 (OUTLIER) cc_final: 0.5333 (m-70) REVERT: 3 147 ASN cc_start: 0.9524 (m110) cc_final: 0.9181 (m110) REVERT: 5 76 LEU cc_start: 0.9145 (mp) cc_final: 0.8941 (pp) REVERT: C 284 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8786 (t) REVERT: D 115 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8226 (m) REVERT: D 276 ARG cc_start: 0.7299 (ttp80) cc_final: 0.6701 (ttm170) REVERT: G 161 GLU cc_start: 0.8828 (pm20) cc_final: 0.8128 (tm-30) REVERT: G 221 ASN cc_start: 0.9528 (m110) cc_final: 0.9251 (p0) REVERT: H 63 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8221 (tmtt) REVERT: H 149 ASN cc_start: 0.7055 (m-40) cc_final: 0.6806 (m-40) REVERT: K 164 TYR cc_start: 0.6470 (m-80) cc_final: 0.6237 (m-80) REVERT: N 29 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9166 (tm-30) REVERT: W 221 TYR cc_start: 0.8529 (t80) cc_final: 0.8273 (t80) REVERT: b 267 GLN cc_start: 0.7380 (mt0) cc_final: 0.7017 (tm-30) REVERT: b 437 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6607 (t0) REVERT: h 102 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9242 (tp30) REVERT: v 20 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7860 (mtm180) REVERT: v 41 ASP cc_start: 0.8935 (t0) cc_final: 0.8582 (t0) REVERT: v 49 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8746 (m-40) REVERT: v 199 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9143 (mtt) REVERT: x 139 CYS cc_start: 0.9244 (m) cc_final: 0.8855 (m) outliers start: 129 outliers final: 111 residues processed: 791 average time/residue: 1.8086 time to fit residues: 2320.5172 Evaluate side-chains 807 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 690 time to evaluate : 7.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 92 GLN Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 5 residue 25 SER Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain K residue 285 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 437 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 272 GLU Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 222 LEU Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 7.9990 chunk 453 optimal weight: 4.9990 chunk 730 optimal weight: 8.9990 chunk 445 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 507 optimal weight: 9.9990 chunk 766 optimal weight: 40.0000 chunk 705 optimal weight: 9.9990 chunk 610 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 471 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 92332 Z= 0.338 Angle : 0.602 8.295 133069 Z= 0.319 Chirality : 0.038 0.262 16346 Planarity : 0.004 0.077 10207 Dihedral : 23.187 179.751 34042 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.69 % Favored : 92.25 % Rotamer: Outliers : 2.50 % Allowed : 20.06 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 5868 helix: 0.82 (0.11), residues: 2350 sheet: -1.19 (0.17), residues: 810 loop : -1.17 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP n 166 HIS 0.011 0.001 HIS b 90 PHE 0.015 0.001 PHE n 142 TYR 0.019 0.002 TYR Q 33 ARG 0.007 0.000 ARG C 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 688 time to evaluate : 7.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 55 CYS cc_start: 0.9313 (p) cc_final: 0.9058 (p) REVERT: 3 71 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5285 (m-70) REVERT: 3 129 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8275 (tp30) REVERT: 3 147 ASN cc_start: 0.9565 (m110) cc_final: 0.9212 (m110) REVERT: 4 82 ASN cc_start: 0.8837 (t0) cc_final: 0.8465 (p0) REVERT: 5 76 LEU cc_start: 0.9184 (mp) cc_final: 0.8968 (pp) REVERT: C 284 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8672 (t) REVERT: D 115 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8229 (m) REVERT: D 276 ARG cc_start: 0.7354 (ttp80) cc_final: 0.6857 (ttm-80) REVERT: G 161 GLU cc_start: 0.8858 (pm20) cc_final: 0.8192 (tm-30) REVERT: G 221 ASN cc_start: 0.9528 (m110) cc_final: 0.9260 (p0) REVERT: H 63 LYS cc_start: 0.8514 (mmtp) cc_final: 0.8250 (tmtt) REVERT: H 149 ASN cc_start: 0.7097 (m-40) cc_final: 0.6844 (m-40) REVERT: K 164 TYR cc_start: 0.6454 (m-80) cc_final: 0.6205 (m-80) REVERT: N 29 GLU cc_start: 0.9502 (tm-30) cc_final: 0.9198 (tm-30) REVERT: P 23 ARG cc_start: 0.9021 (mtp180) cc_final: 0.8782 (tmt-80) REVERT: W 221 TYR cc_start: 0.8527 (t80) cc_final: 0.8273 (t80) REVERT: b 267 GLN cc_start: 0.7361 (mt0) cc_final: 0.7007 (tm-30) REVERT: b 437 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6653 (t0) REVERT: e 36 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8216 (mmmt) REVERT: e 44 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7399 (mtp85) REVERT: n 445 ASN cc_start: 0.6928 (m-40) cc_final: 0.6304 (p0) REVERT: o 153 ASN cc_start: 0.7578 (m-40) cc_final: 0.7368 (m-40) REVERT: v 20 ARG cc_start: 0.8450 (mtt90) cc_final: 0.7929 (mtm180) REVERT: v 41 ASP cc_start: 0.8941 (t0) cc_final: 0.8556 (t0) REVERT: v 49 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8725 (m-40) REVERT: v 51 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9304 (mptt) REVERT: x 139 CYS cc_start: 0.9244 (m) cc_final: 0.8858 (m) outliers start: 132 outliers final: 120 residues processed: 773 average time/residue: 1.7789 time to fit residues: 2243.9852 Evaluate side-chains 810 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 684 time to evaluate : 6.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 92 GLN Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 124 ARG Chi-restraints excluded: chain 4 residue 6 PHE Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 145 LEU Chi-restraints excluded: chain 4 residue 212 THR Chi-restraints excluded: chain 5 residue 25 SER Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 219 ILE Chi-restraints excluded: chain 5 residue 335 THR Chi-restraints excluded: chain 5 residue 336 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 253 TRP Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain K residue 285 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 437 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 95 GLU Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain m residue 272 GLU Chi-restraints excluded: chain n residue 118 ILE Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 217 ILE Chi-restraints excluded: chain n residue 222 LEU Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 451 GLU Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 144 ASP Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain t residue 65 THR Chi-restraints excluded: chain t residue 187 LEU Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 261 PHE Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 284 ASN Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 163 GLU Chi-restraints excluded: chain v residue 199 MET Chi-restraints excluded: chain v residue 214 ASP Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 170 THR Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 289 GLU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 3.9990 chunk 484 optimal weight: 9.9990 chunk 649 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 562 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 611 optimal weight: 0.2980 chunk 255 optimal weight: 10.0000 chunk 627 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.087786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.069004 restraints weight = 1371453.970| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.62 r_work: 0.3361 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 92332 Z= 0.262 Angle : 0.564 7.355 133069 Z= 0.298 Chirality : 0.037 0.253 16346 Planarity : 0.004 0.074 10207 Dihedral : 23.221 179.870 34042 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.30 % Rotamer: Outliers : 2.40 % Allowed : 20.19 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 5868 helix: 0.92 (0.11), residues: 2350 sheet: -1.16 (0.18), residues: 810 loop : -1.11 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP n 166 HIS 0.012 0.001 HIS b 90 PHE 0.016 0.001 PHE 4 102 TYR 0.018 0.001 TYR K 164 ARG 0.006 0.000 ARG C 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51354.43 seconds wall clock time: 883 minutes 14.54 seconds (52994.54 seconds total)