Starting phenix.real_space_refine on Fri Feb 16 00:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yly_10842/02_2024/6yly_10842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yly_10842/02_2024/6yly_10842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yly_10842/02_2024/6yly_10842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yly_10842/02_2024/6yly_10842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yly_10842/02_2024/6yly_10842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yly_10842/02_2024/6yly_10842.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 2899 5.49 5 S 126 5.16 5 C 64909 2.51 5 N 22089 2.21 5 O 30637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "a ASP 85": "OD1" <-> "OD2" Residue "a TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 117": "NH1" <-> "NH2" Residue "a PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "b ASP 7": "OD1" <-> "OD2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b GLU 62": "OE1" <-> "OE2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ASP 111": "OD1" <-> "OD2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 191": "OD1" <-> "OD2" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 210": "OD1" <-> "OD2" Residue "b ASP 255": "OD1" <-> "OD2" Residue "b PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 296": "OE1" <-> "OE2" Residue "b ASP 299": "OD1" <-> "OD2" Residue "b GLU 301": "OE1" <-> "OE2" Residue "b GLU 311": "OE1" <-> "OE2" Residue "b GLU 316": "OE1" <-> "OE2" Residue "b GLU 325": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "b ASP 370": "OD1" <-> "OD2" Residue "b GLU 380": "OE1" <-> "OE2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 459": "OE1" <-> "OE2" Residue "b GLU 466": "OE1" <-> "OE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c ASP 97": "OD1" <-> "OD2" Residue "d ASP 47": "OD1" <-> "OD2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "d GLU 83": "OE1" <-> "OE2" Residue "d ASP 84": "OD1" <-> "OD2" Residue "d PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 23": "OD1" <-> "OD2" Residue "e TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 3": "OE1" <-> "OE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ASP 219": "OD1" <-> "OD2" Residue "G ASP 224": "OD1" <-> "OD2" Residue "G TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "I ARG 3": "NH1" <-> "NH2" Residue "I TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 15": "OE1" <-> "OE2" Residue "h GLU 30": "OE1" <-> "OE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "i GLU 46": "OE1" <-> "OE2" Residue "i GLU 89": "OE1" <-> "OE2" Residue "j PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "j TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k ASP 7": "OD1" <-> "OD2" Residue "k ARG 39": "NH1" <-> "NH2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 98": "OD1" <-> "OD2" Residue "L PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 118": "OE1" <-> "OE2" Residue "L PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "L GLU 192": "OE1" <-> "OE2" Residue "L GLU 194": "OE1" <-> "OE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ASP 40": "OD1" <-> "OD2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "p TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 30": "OE1" <-> "OE2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "p TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 145": "OD1" <-> "OD2" Residue "N TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u GLU 97": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "u ARG 135": "NH1" <-> "NH2" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 187": "OE1" <-> "OE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ASP 108": "OD1" <-> "OD2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q ASP 22": "OD1" <-> "OD2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R ASP 148": "OD1" <-> "OD2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r GLU 21": "OE1" <-> "OE2" Residue "r GLU 22": "OE1" <-> "OE2" Residue "r GLU 28": "OE1" <-> "OE2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 82": "OD1" <-> "OD2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S GLU 130": "OE1" <-> "OE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U ASP 59": "OD1" <-> "OD2" Residue "U ASP 91": "OD1" <-> "OD2" Residue "U TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 46": "OD1" <-> "OD2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W GLU 107": "OE1" <-> "OE2" Residue "W TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 123": "OD1" <-> "OD2" Residue "W ARG 126": "NH1" <-> "NH2" Residue "W GLU 153": "OE1" <-> "OE2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W ASP 183": "OD1" <-> "OD2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "W GLU 212": "OE1" <-> "OE2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 78": "OD1" <-> "OD2" Residue "X ASP 106": "OD1" <-> "OD2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X ASP 134": "OD1" <-> "OD2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "Y GLU 38": "OE1" <-> "OE2" Residue "Y TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y GLU 127": "OE1" <-> "OE2" Residue "y GLU 8": "OE1" <-> "OE2" Residue "y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y ASP 120": "OD1" <-> "OD2" Residue "y GLU 124": "OE1" <-> "OE2" Residue "y GLU 127": "OE1" <-> "OE2" Residue "y ASP 169": "OD1" <-> "OD2" Residue "y GLU 171": "OE1" <-> "OE2" Residue "y ASP 201": "OD1" <-> "OD2" Residue "Z PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 31": "OE1" <-> "OE2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z GLU 120": "OE1" <-> "OE2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z ARG 19": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 30": "OE1" <-> "OE2" Residue "z ASP 35": "OD1" <-> "OD2" Residue "z ASP 48": "OD1" <-> "OD2" Residue "z GLU 54": "OE1" <-> "OE2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "K GLU 206": "OE1" <-> "OE2" Residue "K PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 245": "OE1" <-> "OE2" Residue "K ASP 253": "OD1" <-> "OD2" Residue "K ASP 271": "OD1" <-> "OD2" Residue "K ASP 275": "OD1" <-> "OD2" Residue "K ASP 285": "OD1" <-> "OD2" Residue "K TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 303": "NH1" <-> "NH2" Residue "K ASP 317": "OD1" <-> "OD2" Residue "K GLU 349": "OE1" <-> "OE2" Residue "K TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 373": "NH1" <-> "NH2" Residue "K GLU 401": "OE1" <-> "OE2" Residue "K ARG 410": "NH1" <-> "NH2" Residue "K PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 418": "NH1" <-> "NH2" Residue "K TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 34": "NH1" <-> "NH2" Residue "n PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 104": "NH1" <-> "NH2" Residue "n ARG 109": "NH1" <-> "NH2" Residue "n ASP 133": "OD1" <-> "OD2" Residue "n ARG 174": "NH1" <-> "NH2" Residue "n TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 239": "OD1" <-> "OD2" Residue "n ASP 253": "OD1" <-> "OD2" Residue "n TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 265": "OE1" <-> "OE2" Residue "n TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 353": "OD1" <-> "OD2" Residue "n PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 369": "NH1" <-> "NH2" Residue "n ASP 374": "OD1" <-> "OD2" Residue "n GLU 377": "OE1" <-> "OE2" Residue "n GLU 390": "OE1" <-> "OE2" Residue "n ASP 403": "OD1" <-> "OD2" Residue "n ARG 414": "NH1" <-> "NH2" Residue "n ARG 424": "NH1" <-> "NH2" Residue "n TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 116": "OD1" <-> "OD2" Residue "o ARG 121": "NH1" <-> "NH2" Residue "o TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 198": "OD1" <-> "OD2" Residue "o ARG 207": "NH1" <-> "NH2" Residue "o PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 208": "OD1" <-> "OD2" Residue "q GLU 210": "OE1" <-> "OE2" Residue "q PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 248": "NH1" <-> "NH2" Residue "q ASP 250": "OD1" <-> "OD2" Residue "q ARG 252": "NH1" <-> "NH2" Residue "q TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 263": "NH1" <-> "NH2" Residue "q ASP 391": "OD1" <-> "OD2" Residue "q GLU 395": "OE1" <-> "OE2" Residue "q GLU 401": "OE1" <-> "OE2" Residue "q ASP 404": "OD1" <-> "OD2" Residue "q ARG 421": "NH1" <-> "NH2" Residue "q ARG 432": "NH1" <-> "NH2" Residue "q TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 453": "OD1" <-> "OD2" Residue "q PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 43": "OE1" <-> "OE2" Residue "t GLU 73": "OE1" <-> "OE2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "t ARG 77": "NH1" <-> "NH2" Residue "t GLU 82": "OE1" <-> "OE2" Residue "t ASP 83": "OD1" <-> "OD2" Residue "t ARG 130": "NH1" <-> "NH2" Residue "t ASP 136": "OD1" <-> "OD2" Residue "t ARG 146": "NH1" <-> "NH2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 170": "OE1" <-> "OE2" Residue "t PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 205": "NH1" <-> "NH2" Residue "t ARG 211": "NH1" <-> "NH2" Residue "t ARG 213": "NH1" <-> "NH2" Residue "t GLU 259": "OE1" <-> "OE2" Residue "t PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 299": "NH1" <-> "NH2" Residue "s ARG 2": "NH1" <-> "NH2" Residue "s ARG 6": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 120663 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1391 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Chain: "a" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 652 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "B" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2866 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 12, 'TRANS': 347} Chain breaks: 1 Chain: "b" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3651 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1798 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "I" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain: "h" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "i" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "j" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'TRANS': 79} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1451 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 173} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "N" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1607 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Chain: "u" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1158 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1393 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain breaks: 1 Chain: "Q" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "R" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "r" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 579 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Chain: "S" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1425 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Chain: "U" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1814 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1100 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain breaks: 1 Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "y" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1712 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 219} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "z" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "1" Number of atoms: 57244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2676, 57244 Classifications: {'RNA': 2676} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 202, 'rna3p_pur': 1202, 'rna3p_pyr': 992} Link IDs: {'rna2p': 482, 'rna3p': 2193} Chain breaks: 13 Chain: "3" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 64, 'rna3p_pyr': 66} Link IDs: {'rna2p': 27, 'rna3p': 130} Chain: "K" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 244} Chain breaks: 1 Chain: "n" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3030 Classifications: {'peptide': 371} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 347} Chain breaks: 2 Chain: "o" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1046 Classifications: {'peptide': 125} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain breaks: 1 Chain: "q" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1178 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain breaks: 1 Chain: "t" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2306 Classifications: {'peptide': 287} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Chain: "6" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1370 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 17, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 24, 'rna3p': 40} Chain breaks: 1 Chain: "s" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} 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: "p" 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 24585 SG CYS j 19 112.336 103.704 132.251 1.00 30.37 S ATOM 24610 SG CYS j 22 112.713 106.504 135.558 1.00 35.35 S ATOM 24728 SG CYS j 37 109.159 105.413 132.932 1.00 30.01 S ATOM 28987 SG CYS p 39 123.860 39.908 117.257 1.00102.73 S ATOM 29010 SG CYS p 42 127.005 39.730 115.773 1.00103.62 S ATOM 29119 SG CYS p 57 126.388 41.328 119.233 1.00101.94 S ATOM 29137 SG CYS p 60 125.518 42.595 114.565 1.00 99.26 S ATOM 31059 SG CYS u 9 169.758 59.587 197.527 1.00 93.12 S ATOM 31244 SG CYS u 32 168.083 61.260 200.594 1.00 82.20 S ATOM 31276 SG CYS u 36 167.295 61.931 197.339 1.00 86.10 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 44.38, per 1000 atoms: 0.37 Number of scatterers: 120663 At special positions: 0 Unit cell: (215.716, 196.204, 320.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 126 16.00 P 2899 15.00 O 30637 8.00 N 22089 7.00 C 64909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.05 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.04 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.03 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 48.89 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb=" ZN p 501 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 39 " pdb=" ZN u 200 " pdb="ZN ZN u 200 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 200 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 200 " - pdb=" SG CYS u 36 " Number of angles added : 6 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB LEU B 17 " Number of C-beta restraints generated: 13860 Finding SS restraints... Secondary structure from input PDB file: 263 helices and 71 sheets defined 41.8% alpha, 12.2% beta 831 base pairs and 1385 stacking pairs defined. Time for finding SS restraints: 36.57 Creating SS restraints... Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.881A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 92 removed outlier: 4.389A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 142 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 141 through 154 removed outlier: 4.332A pdb=" N ILE B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'b' and resid 13 through 29 removed outlier: 3.823A pdb=" N THR b 29 " --> pdb=" O THR b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 68 removed outlier: 3.587A pdb=" N TYR b 46 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP b 63 " --> pdb=" O GLU b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 116 Processing helix chain 'b' and resid 117 through 119 No H-bonds generated for 'chain 'b' and resid 117 through 119' Processing helix chain 'b' and resid 121 through 143 removed outlier: 4.722A pdb=" N GLN b 127 " --> pdb=" O PHE b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 159 removed outlier: 4.324A pdb=" N ALA b 148 " --> pdb=" O ARG b 144 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS b 156 " --> pdb=" O GLN b 152 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 235 through 246 removed outlier: 4.425A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 274 removed outlier: 3.646A pdb=" N VAL b 268 " --> pdb=" O ILE b 264 " (cutoff:3.500A) Processing helix chain 'b' and resid 275 through 278 Processing helix chain 'b' and resid 294 through 298 removed outlier: 3.502A pdb=" N ASP b 297 " --> pdb=" O ARG b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 309 Processing helix chain 'b' and resid 325 through 343 Processing helix chain 'b' and resid 379 through 385 removed outlier: 4.174A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 405 removed outlier: 3.599A pdb=" N GLU b 405 " --> pdb=" O ASP b 401 " (cutoff:3.500A) Processing helix chain 'b' and resid 425 through 430 removed outlier: 4.165A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 444 removed outlier: 3.585A pdb=" N ASP b 443 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 466 removed outlier: 4.023A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU b 466 " --> pdb=" O LYS b 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 4.108A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 139 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: 3.617A pdb=" N LYS C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 194 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 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: 3.925A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.694A pdb=" N GLN C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.433A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'c' and resid 10 through 20 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.535A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 removed outlier: 3.551A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 44 removed outlier: 4.658A pdb=" N ALA d 29 " --> pdb=" O PHE d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix removed outlier: 3.688A pdb=" N VAL d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 61 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.749A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.724A pdb=" N ALA E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.736A pdb=" N VAL E 141 " --> pdb=" O ASP E 137 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.416A 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 'e' and resid 54 through 58 Processing helix chain 'e' and resid 60 through 64 removed outlier: 4.120A pdb=" N LYS e 64 " --> pdb=" O LYS e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.398A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 72 removed outlier: 3.808A pdb=" N GLU F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.810A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 174 removed outlier: 4.211A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.727A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.616A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 60 through 69 Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 119 removed outlier: 4.012A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 164 through 173 removed outlier: 4.601A pdb=" N ALA G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 223 removed outlier: 3.559A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 231 removed outlier: 4.197A pdb=" N GLU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 253 Processing helix chain 'g' and resid 59 through 64 Processing helix chain 'g' and resid 83 through 113 removed outlier: 3.689A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 removed outlier: 4.097A pdb=" N VAL I 6 " --> pdb=" O GLY I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 27 removed outlier: 3.547A pdb=" N TYR I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.138A pdb=" N VAL I 31 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN I 32 " --> pdb=" O LYS I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 69 removed outlier: 3.789A pdb=" N HIS I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 80 removed outlier: 3.610A pdb=" N LYS I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG I 75 " --> pdb=" O LYS I 71 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 93 removed outlier: 4.170A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 4.602A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.626A pdb=" N GLN H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 10 removed outlier: 3.617A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 38 removed outlier: 3.685A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 removed outlier: 4.088A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA h 52 " --> pdb=" O ARG h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 36 through 49 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 66 through 77 Processing helix chain 'i' and resid 82 through 98 removed outlier: 4.046A pdb=" N ARG i 98 " --> pdb=" O ILE i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 4.173A pdb=" N LYS j 54 " --> pdb=" O GLY j 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 76 Processing helix chain 'k' and resid 7 through 15 removed outlier: 4.953A pdb=" N GLU k 13 " --> pdb=" O LYS k 9 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU k 14 " --> pdb=" O GLN k 10 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR k 15 " --> pdb=" O PHE k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 69 Processing helix chain 'L' and resid 17 through 20 removed outlier: 4.020A pdb=" N GLU L 20 " --> pdb=" O HIS L 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 20' Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 62 through 66 Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.714A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.998A 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 'L' and resid 167 through 179 Processing helix chain 'L' and resid 179 through 192 Processing helix chain 'l' and resid 6 through 20 removed outlier: 3.635A pdb=" N LYS l 15 " --> pdb=" O GLN l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 3.736A pdb=" N LEU l 29 " --> pdb=" O TRP l 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 removed outlier: 3.523A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 112 removed outlier: 3.725A pdb=" N LYS M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.690A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) Processing helix chain 'p' and resid 8 through 12 removed outlier: 3.892A pdb=" N THR p 11 " --> pdb=" O VAL p 8 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY p 12 " --> pdb=" O GLY p 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 8 through 12' Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.886A pdb=" N GLN p 25 " --> pdb=" O SER p 21 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN p 32 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA p 35 " --> pdb=" O ILE p 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 removed outlier: 3.847A pdb=" N GLU p 88 " --> pdb=" O ARG p 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 12 removed outlier: 3.995A pdb=" N LEU N 10 " --> pdb=" O TYR N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.883A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 50 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.571A pdb=" N HIS N 156 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 186 through 195 Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 53 through 59 Processing helix chain 'u' and resid 66 through 71 Processing helix chain 'u' and resid 85 through 113 removed outlier: 4.884A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU u 97 " --> pdb=" O MET u 93 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 130 removed outlier: 4.009A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) Processing helix chain 'u' and resid 131 through 137 Processing helix chain 'O' and resid 15 through 30 removed outlier: 4.081A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.503A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 100 removed outlier: 3.713A pdb=" N LYS O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) 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 186 removed outlier: 3.720A pdb=" N VAL O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA O 154 " --> pdb=" O GLU O 150 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS O 170 " --> pdb=" O GLU O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 removed outlier: 3.995A pdb=" N LEU O 194 " --> pdb=" O VAL O 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 35 removed outlier: 3.864A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.660A pdb=" N LYS P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 74 removed outlier: 3.992A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 106 Processing helix chain 'P' and resid 169 through 183 removed outlier: 3.787A pdb=" N ARG P 175 " --> pdb=" O ARG P 171 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE P 176 " --> pdb=" O GLN P 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.593A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.184A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 107 through 118 removed outlier: 4.100A pdb=" N VAL Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 removed outlier: 3.687A pdb=" N LEU Q 127 " --> pdb=" O THR Q 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 22 removed outlier: 3.509A pdb=" N LYS R 21 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL R 22 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 22' Processing helix chain 'R' and resid 28 through 34 removed outlier: 3.615A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 47 removed outlier: 3.511A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 111 removed outlier: 4.339A pdb=" N ARG R 104 " --> pdb=" O ARG R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.584A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 Processing helix chain 'r' and resid 6 through 15 Processing helix chain 'r' and resid 20 through 41 removed outlier: 3.687A pdb=" N GLU r 28 " --> pdb=" O LYS r 24 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS r 41 " --> pdb=" O GLU r 37 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 67 removed outlier: 3.600A pdb=" N ALA r 51 " --> pdb=" O GLY r 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.605A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.671A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) 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 140 through 144 Processing helix chain 'T' and resid 102 through 122 removed outlier: 3.525A pdb=" N LYS T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 Processing helix chain 'U' and resid 29 through 41 removed outlier: 3.801A pdb=" N TYR U 33 " --> pdb=" O ASP U 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS U 40 " --> pdb=" O TYR U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 133 Processing helix chain 'W' and resid 20 through 37 removed outlier: 3.821A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 96 removed outlier: 3.871A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 4.139A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS W 113 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE W 116 " --> pdb=" O VAL W 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 160 No H-bonds generated for 'chain 'W' and resid 158 through 160' Processing helix chain 'W' and resid 161 through 168 Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 4 through 17 removed outlier: 3.633A pdb=" N ALA X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA X 10 " --> pdb=" O LYS X 6 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL X 15 " --> pdb=" O LYS X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 71 through 80 Processing helix chain 'X' and resid 91 through 104 removed outlier: 3.682A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 140 Processing helix chain 'Y' and resid 11 through 21 removed outlier: 4.158A pdb=" N LYS Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 31 removed outlier: 4.460A 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 75 through 78 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 'y' and resid 33 through 42 removed outlier: 3.651A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 46 removed outlier: 4.177A pdb=" N ILE y 46 " --> pdb=" O GLY y 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 43 through 46' Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 134 removed outlier: 3.694A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.587A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'Z' and resid 58 through 66 Processing helix chain 'Z' and resid 89 through 93 removed outlier: 3.958A pdb=" N LYS Z 93 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 123 removed outlier: 3.725A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL Z 114 " --> pdb=" O ALA Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'z' and resid 7 through 20 removed outlier: 3.792A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 56 removed outlier: 3.607A pdb=" N LYS z 24 " --> pdb=" O GLY z 20 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS z 36 " --> pdb=" O ARG z 32 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 183 removed outlier: 4.365A pdb=" N LYS K 183 " --> pdb=" O LYS K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 210 Processing helix chain 'K' and resid 239 through 248 Processing helix chain 'K' and resid 269 through 281 removed outlier: 4.177A pdb=" N LEU K 273 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP K 278 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU K 280 " --> pdb=" O GLN K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 297 Processing helix chain 'K' and resid 299 through 310 removed outlier: 3.890A pdb=" N GLN K 309 " --> pdb=" O ALA K 305 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE K 310 " --> pdb=" O PHE K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 327 removed outlier: 4.055A pdb=" N LEU K 326 " --> pdb=" O SER K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 334 removed outlier: 3.860A pdb=" N TYR K 332 " --> pdb=" O GLY K 328 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS K 334 " --> pdb=" O LYS K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 352 through 365 removed outlier: 3.990A pdb=" N ASN K 358 " --> pdb=" O THR K 354 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 405 removed outlier: 4.366A pdb=" N ASP K 394 " --> pdb=" O GLU K 390 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS K 405 " --> pdb=" O GLU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 438 removed outlier: 3.888A pdb=" N LYS K 438 " --> pdb=" O LEU K 434 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 9 removed outlier: 3.696A pdb=" N THR n 8 " --> pdb=" O LYS n 5 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG n 9 " --> pdb=" O LYS n 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 5 through 9' Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 39 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 65 through 73 removed outlier: 4.424A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 97 removed outlier: 4.459A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS n 79 " --> pdb=" O PRO n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 132 Processing helix chain 'n' and resid 132 through 143 Processing helix chain 'n' and resid 153 through 173 Processing helix chain 'n' and resid 215 through 241 Processing helix chain 'n' and resid 249 through 254 Processing helix chain 'n' and resid 372 through 375 removed outlier: 3.790A pdb=" N ILE n 375 " --> pdb=" O PRO n 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 372 through 375' Processing helix chain 'n' and resid 376 through 383 Processing helix chain 'n' and resid 391 through 395 removed outlier: 4.333A pdb=" N GLN n 395 " --> pdb=" O ALA n 392 " (cutoff:3.500A) Processing helix chain 'n' and resid 428 through 439 removed outlier: 4.105A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 152 Processing helix chain 'o' and resid 193 through 214 removed outlier: 3.573A pdb=" N GLU o 205 " --> pdb=" O LYS o 201 " (cutoff:3.500A) Processing helix chain 'q' and resid 230 through 268 removed outlier: 3.594A pdb=" N GLU q 241 " --> pdb=" O LEU q 237 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU q 267 " --> pdb=" O ARG q 263 " (cutoff:3.500A) Processing helix chain 'q' and resid 405 through 409 Processing helix chain 'q' and resid 414 through 426 Processing helix chain 'q' and resid 448 through 454 Processing helix chain 't' and resid 16 through 53 removed outlier: 3.698A pdb=" N LEU t 20 " --> pdb=" O PRO t 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG t 23 " --> pdb=" O LEU t 19 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE t 31 " --> pdb=" O ASP t 27 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG t 49 " --> pdb=" O ILE t 45 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER t 50 " --> pdb=" O LYS t 46 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN t 53 " --> pdb=" O ARG t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 88 Processing helix chain 't' and resid 156 through 167 removed outlier: 5.211A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 183 through 191 Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 240 removed outlier: 3.871A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 261 through 268 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.962A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 321 removed outlier: 3.864A pdb=" N ALA t 319 " --> pdb=" O ASP t 315 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 35 removed outlier: 3.637A pdb=" N LYS s 35 " --> pdb=" O LYS s 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 6.650A pdb=" N LEU A 58 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 48 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ARG A 64 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG A 42 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.718A pdb=" N LEU A 102 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE A 136 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG A 149 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 72 through 74 removed outlier: 5.738A pdb=" N LEU a 73 " --> pdb=" O LEU a 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 99 through 100 Processing sheet with id=AA5, first strand: chain 'a' and resid 124 through 127 Processing sheet with id=AA6, first strand: chain 'B' and resid 356 through 359 removed outlier: 5.814A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP B 358 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 57 " --> pdb=" O TRP B 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 219 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 322 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 79 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 324 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 106 removed outlier: 6.490A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY B 88 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 157 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 179 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 106 removed outlier: 6.490A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 205 through 211 removed outlier: 3.605A pdb=" N TYR b 205 " --> pdb=" O ASP b 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU b 170 " --> pdb=" O ILE b 219 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU b 171 " --> pdb=" O LEU b 251 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE b 253 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS b 173 " --> pdb=" O PHE b 253 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET b 284 " --> pdb=" O VAL b 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.401A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 228 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB4, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.429A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 9 through 15 removed outlier: 3.794A pdb=" N ILE d 14 " --> pdb=" O LEU d 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.726A pdb=" N ARG E 77 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 65 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR E 62 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS E 57 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER E 66 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL E 53 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 74 through 76 removed outlier: 5.975A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 74 through 76 removed outlier: 3.639A pdb=" N VAL T 141 " --> pdb=" O TYR F 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 206 removed outlier: 5.161A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG F 88 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 117 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'f' and resid 8 through 18 removed outlier: 10.439A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER f 28 " --> pdb=" O ALA f 83 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR f 53 " --> pdb=" O ARG f 65 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS f 13 " --> pdb=" O ALA f 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 179 through 180 removed outlier: 6.901A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 21 through 23 removed outlier: 3.514A pdb=" N VAL g 23 " --> pdb=" O ARG g 31 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG g 31 " --> pdb=" O VAL g 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 50 through 51 removed outlier: 4.029A pdb=" N LYS I 56 " --> pdb=" O CYS I 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 11 removed outlier: 7.370A pdb=" N ILE H 4 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN H 8 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AC8, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.879A pdb=" N LYS H 87 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS H 184 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 180 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'h' and resid 116 through 118 removed outlier: 3.618A pdb=" N ILE L 124 " --> pdb=" O ALA h 117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AD3, first strand: chain 'k' and resid 52 through 56 Processing sheet with id=AD4, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.193A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'L' and resid 58 through 59 Processing sheet with id=AD6, first strand: chain 'M' and resid 56 through 59 removed outlier: 8.035A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'p' and resid 37 through 38 removed outlier: 3.706A pdb=" N GLY p 50 " --> pdb=" O ILE p 54 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 37 through 38 removed outlier: 3.612A pdb=" N VAL N 66 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'u' and resid 28 through 30 removed outlier: 3.575A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.068A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) 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 17 through 22 removed outlier: 3.573A pdb=" N LEU P 148 " --> pdb=" O ALA P 17 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN P 120 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.289A 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 'P' and resid 127 through 128 Processing sheet with id=AE6, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.380A pdb=" N VAL Q 62 " --> pdb=" O THR Q 88 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 11.429A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.380A pdb=" N VAL Q 62 " --> pdb=" O THR Q 88 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.790A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.709A pdb=" N ASP S 96 " --> pdb=" O LYS S 73 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 54 through 58 removed outlier: 8.345A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA U 106 " --> pdb=" O ARG U 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 22 through 24 removed outlier: 4.005A pdb=" N TYR V 35 " --> pdb=" O THR V 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR V 61 " --> pdb=" O TYR V 35 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 64 through 66 removed outlier: 4.055A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS W 216 " --> pdb=" O ILE W 233 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE W 233 " --> pdb=" O LYS W 216 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER W 218 " --> pdb=" O THR W 231 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP W 222 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR W 227 " --> pdb=" O ASP W 222 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 120 through 123 Processing sheet with id=AF5, first strand: chain 'W' and resid 136 through 137 removed outlier: 3.753A pdb=" N TYR W 186 " --> pdb=" O ILE W 137 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 174 through 175 removed outlier: 3.792A pdb=" N LYS W 174 " --> pdb=" O THR W 181 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR W 181 " --> pdb=" O LYS W 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'X' and resid 21 through 22 removed outlier: 3.620A pdb=" N THR q 446 " --> pdb=" O LYS X 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 63 through 65 removed outlier: 3.831A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS X 109 " --> pdb=" O ARG X 125 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 33 through 34 Processing sheet with id=AG1, first strand: chain 'Y' and resid 79 through 82 removed outlier: 7.179A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR Y 107 " --> pdb=" O GLU Y 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 87 through 88 Processing sheet with id=AG3, first strand: chain 'y' and resid 3 through 4 removed outlier: 6.789A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'y' and resid 17 through 19 removed outlier: 7.069A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.525A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'y' and resid 109 through 110 removed outlier: 3.669A pdb=" N CYS y 109 " --> pdb=" O LEU y 116 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'y' and resid 152 through 154 Processing sheet with id=AG8, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.415A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL Z 75 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL Z 12 " --> pdb=" O LEU Z 81 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU Z 81 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 376 through 383 removed outlier: 6.805A pdb=" N GLN K 212 " --> pdb=" O LEU K 381 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU K 213 " --> pdb=" O ILE K 414 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE K 414 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL K 215 " --> pdb=" O ILE K 412 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE K 412 " --> pdb=" O VAL K 215 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN K 217 " --> pdb=" O ARG K 410 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR K 425 " --> pdb=" O ILE K 412 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 233 through 234 Processing sheet with id=AH2, first strand: chain 'K' and resid 288 through 289 removed outlier: 8.751A pdb=" N ILE K 288 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU K 258 " --> pdb=" O ILE K 288 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'n' and resid 178 through 181 removed outlier: 3.665A pdb=" N VAL n 186 " --> pdb=" O VAL n 201 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'n' and resid 386 through 389 Processing sheet with id=AH5, first strand: chain 'o' and resid 119 through 124 removed outlier: 3.876A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU o 138 " --> pdb=" O GLU o 119 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY o 135 " --> pdb=" O VAL o 95 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU o 167 " --> pdb=" O ILE o 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN o 163 " --> pdb=" O SER o 96 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 't' and resid 132 through 133 Processing sheet with id=AH7, first strand: chain 't' and resid 194 through 197 removed outlier: 3.548A pdb=" N ARG t 146 " --> pdb=" O THR t 173 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 't' and resid 213 through 214 2282 hydrogen bonds defined for protein. 6561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2067 hydrogen bonds 3462 hydrogen bond angles 0 basepair planarities 831 basepair parallelities 1385 stacking parallelities Total time for adding SS restraints: 129.38 Time building geometry restraints manager: 52.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.51: 95258 1.51 - 1.82: 33759 1.82 - 2.13: 10 2.13 - 2.44: 3 2.44 - 2.75: 2 Bond restraints: 129032 Sorted by residual: bond pdb=" C2 A 11200 " pdb=" N3 A 11200 " ideal model delta sigma weight residual 1.331 2.751 -1.420 2.00e-02 2.50e+03 5.04e+03 bond pdb=" N3 A 11200 " pdb=" C4 A 11200 " ideal model delta sigma weight residual 1.344 2.627 -1.283 2.00e-02 2.50e+03 4.12e+03 bond pdb=" N LYS s 14 " pdb=" CA LYS s 14 " ideal model delta sigma weight residual 1.459 2.087 -0.628 1.20e-02 6.94e+03 2.74e+03 bond pdb=" N1 A 11200 " pdb=" C2 A 11200 " ideal model delta sigma weight residual 1.339 2.348 -1.009 2.00e-02 2.50e+03 2.54e+03 bond pdb=" C6 A 11200 " pdb=" N1 A 11200 " ideal model delta sigma weight residual 1.351 2.315 -0.964 2.00e-02 2.50e+03 2.32e+03 ... (remaining 129027 not shown) Histogram of bond angle deviations from ideal: 59.58 - 79.34: 2 79.34 - 99.10: 24 99.10 - 118.86: 122584 118.86 - 138.62: 65622 138.62 - 158.38: 13 Bond angle restraints: 188245 Sorted by residual: angle pdb=" C THR s 13 " pdb=" N LYS s 14 " pdb=" CA LYS s 14 " ideal model delta sigma weight residual 120.54 158.38 -37.84 1.35e+00 5.49e-01 7.86e+02 angle pdb=" C LYS s 16 " pdb=" N GLU s 17 " pdb=" CA GLU s 17 " ideal model delta sigma weight residual 120.28 155.38 -35.10 1.44e+00 4.82e-01 5.94e+02 angle pdb=" P C 11199 " pdb=" O5' C 11199 " pdb=" C5' C 11199 " ideal model delta sigma weight residual 120.90 155.08 -34.18 1.50e+00 4.44e-01 5.19e+02 angle pdb=" CA LYS s 16 " pdb=" CB LYS s 16 " pdb=" CG LYS s 16 " ideal model delta sigma weight residual 114.10 156.13 -42.03 2.00e+00 2.50e-01 4.42e+02 angle pdb=" CD1 LEU s 15 " pdb=" CG LEU s 15 " pdb=" CD2 LEU s 15 " ideal model delta sigma weight residual 110.80 70.26 40.54 2.20e+00 2.07e-01 3.40e+02 ... (remaining 188240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 73650 35.97 - 71.94: 7390 71.94 - 107.91: 710 107.91 - 143.89: 32 143.89 - 179.86: 58 Dihedral angle restraints: 81840 sinusoidal: 60440 harmonic: 21400 Sorted by residual: dihedral pdb=" CA PRO n 123 " pdb=" C PRO n 123 " pdb=" N SER n 124 " pdb=" CA SER n 124 " ideal model delta harmonic sigma weight residual -180.00 -66.62 -113.38 0 5.00e+00 4.00e-02 5.14e+02 dihedral pdb=" CA LYS n 54 " pdb=" C LYS n 54 " pdb=" N GLY n 55 " pdb=" CA GLY n 55 " ideal model delta harmonic sigma weight residual 180.00 109.37 70.63 0 5.00e+00 4.00e-02 2.00e+02 dihedral pdb=" CA LEU s 15 " pdb=" C LEU s 15 " pdb=" N LYS s 16 " pdb=" CA LYS s 16 " ideal model delta harmonic sigma weight residual 180.00 -110.66 -69.34 0 5.00e+00 4.00e-02 1.92e+02 ... (remaining 81837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.505: 23436 0.505 - 1.011: 3 1.011 - 1.516: 1 1.516 - 2.022: 2 2.022 - 2.527: 1 Chirality restraints: 23443 Sorted by residual: chirality pdb=" CA LEU B 17 " pdb=" N LEU B 17 " pdb=" C LEU B 17 " pdb=" CB LEU B 17 " both_signs ideal model delta sigma weight residual False 2.51 -0.02 2.53 2.00e-01 2.50e+01 1.60e+02 chirality pdb=" CG LEU n 25 " pdb=" CB LEU n 25 " pdb=" CD1 LEU n 25 " pdb=" CD2 LEU n 25 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.89e+01 chirality pdb=" CG LEU s 15 " pdb=" CB LEU s 15 " pdb=" CD1 LEU s 15 " pdb=" CD2 LEU s 15 " both_signs ideal model delta sigma weight residual False -2.59 -0.93 -1.66 2.00e-01 2.50e+01 6.90e+01 ... (remaining 23440 not shown) Planarity restraints: 13065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS s 14 " 0.062 2.00e-02 2.50e+03 1.34e-01 1.80e+02 pdb=" C LYS s 14 " -0.232 2.00e-02 2.50e+03 pdb=" O LYS s 14 " 0.096 2.00e-02 2.50e+03 pdb=" N LEU s 15 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11200 " -0.024 2.00e-02 2.50e+03 7.31e-02 1.47e+02 pdb=" N9 A 11200 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A 11200 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A 11200 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A 11200 " 0.010 2.00e-02 2.50e+03 pdb=" C6 A 11200 " 0.013 2.00e-02 2.50e+03 pdb=" N6 A 11200 " 0.000 2.00e-02 2.50e+03 pdb=" N1 A 11200 " 0.039 2.00e-02 2.50e+03 pdb=" C2 A 11200 " -0.150 2.00e-02 2.50e+03 pdb=" N3 A 11200 " 0.178 2.00e-02 2.50e+03 pdb=" C4 A 11200 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU s 15 " -0.051 2.00e-02 2.50e+03 1.08e-01 1.17e+02 pdb=" C LEU s 15 " 0.187 2.00e-02 2.50e+03 pdb=" O LEU s 15 " -0.071 2.00e-02 2.50e+03 pdb=" N LYS s 16 " -0.065 2.00e-02 2.50e+03 ... (remaining 13062 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 1334 2.54 - 3.13: 93722 3.13 - 3.72: 226521 3.72 - 4.31: 295244 4.31 - 4.90: 437805 Nonbonded interactions: 1054626 Sorted by model distance: nonbonded pdb=" N3 A 11200 " pdb=" N LYS s 14 " model vdw 1.952 2.600 nonbonded pdb=" O TRP B 106 " pdb=" OH TYR B 137 " model vdw 2.036 2.440 nonbonded pdb=" O2' C 1 69 " pdb=" O2' G 1 101 " model vdw 2.038 2.440 nonbonded pdb=" O ARG f 21 " pdb=" O2' C 1 633 " model vdw 2.040 2.440 nonbonded pdb=" SG CYS u 6 " pdb=" SG CYS u 32 " model vdw 2.048 3.760 ... (remaining 1054621 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 15.580 Check model and map are aligned: 1.350 Set scattering table: 0.810 Process input model: 362.220 Find NCS groups from input model: 2.560 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 387.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.013 1.420 129032 Z= 0.801 Angle : 1.196 48.420 188245 Z= 0.611 Chirality : 0.062 2.527 23443 Planarity : 0.007 0.134 13065 Dihedral : 23.007 179.858 67968 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Rotamer: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 3.24 % Twisted General : 0.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.08), residues: 7234 helix: -2.21 (0.07), residues: 2769 sheet: -3.31 (0.14), residues: 785 loop : -3.09 (0.08), residues: 3680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP V 85 HIS 0.021 0.002 HIS B 163 PHE 0.043 0.003 PHE F 229 TYR 0.042 0.003 TYR P 139 ARG 0.025 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1852 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1845 time to evaluate : 6.551 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: A 31 THR cc_start: 0.7269 (p) cc_final: 0.6946 (m) REVERT: A 46 LYS cc_start: 0.8825 (tppt) cc_final: 0.8615 (tttt) REVERT: A 88 ILE cc_start: 0.8522 (mm) cc_final: 0.8297 (mm) REVERT: a 84 GLU cc_start: 0.7011 (tt0) cc_final: 0.6787 (tt0) REVERT: a 85 ASP cc_start: 0.7590 (p0) cc_final: 0.7205 (p0) REVERT: a 90 TYR cc_start: 0.8632 (m-80) cc_final: 0.8324 (m-80) REVERT: a 120 ASN cc_start: 0.8135 (t0) cc_final: 0.7608 (t0) REVERT: a 132 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7931 (mtpp) REVERT: B 276 THR cc_start: 0.8075 (m) cc_final: 0.7873 (m) REVERT: b 59 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7921 (tm-30) REVERT: b 197 TYR cc_start: 0.7890 (p90) cc_final: 0.7438 (p90) REVERT: b 211 TYR cc_start: 0.5889 (t80) cc_final: 0.4879 (t80) REVERT: c 43 ILE cc_start: 0.8701 (tt) cc_final: 0.8033 (tt) REVERT: c 58 TYR cc_start: 0.8245 (t80) cc_final: 0.8016 (t80) REVERT: d 38 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8488 (tttt) REVERT: d 57 GLN cc_start: 0.7884 (mt0) cc_final: 0.7534 (mp10) REVERT: d 92 TYR cc_start: 0.8525 (t80) cc_final: 0.7528 (t80) REVERT: d 94 GLU cc_start: 0.7961 (pm20) cc_final: 0.7519 (pm20) REVERT: E 10 TYR cc_start: 0.7152 (m-80) cc_final: 0.6806 (m-80) REVERT: E 22 ARG cc_start: 0.8041 (mmt-90) cc_final: 0.7790 (mmt90) REVERT: E 28 GLN cc_start: 0.7176 (tt0) cc_final: 0.6570 (tt0) REVERT: E 29 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7833 (tttt) REVERT: E 61 ASN cc_start: 0.8935 (m-40) cc_final: 0.8433 (m-40) REVERT: E 137 ASP cc_start: 0.8077 (m-30) cc_final: 0.7771 (m-30) REVERT: e 60 ASN cc_start: 0.8736 (t0) cc_final: 0.8529 (m-40) REVERT: e 83 GLU cc_start: 0.7898 (mt-10) cc_final: 0.6815 (mt-10) REVERT: e 113 LYS cc_start: 0.9262 (ttmm) cc_final: 0.9058 (tptt) REVERT: F 33 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8238 (ttp-170) REVERT: F 169 ILE cc_start: 0.8138 (mm) cc_final: 0.7887 (mm) REVERT: F 182 ASP cc_start: 0.7227 (m-30) cc_final: 0.6778 (m-30) REVERT: F 183 ASP cc_start: 0.7105 (m-30) cc_final: 0.6818 (m-30) REVERT: G 89 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7176 (mm-30) REVERT: g 61 GLN cc_start: 0.8331 (tt0) cc_final: 0.8074 (mt0) REVERT: g 96 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7007 (tm-30) REVERT: g 97 GLU cc_start: 0.8232 (mm-30) cc_final: 0.6810 (mm-30) REVERT: H 1 MET cc_start: 0.7789 (ptm) cc_final: 0.7504 (ptt) REVERT: H 50 ASN cc_start: 0.8689 (m110) cc_final: 0.8088 (m110) REVERT: H 145 VAL cc_start: 0.8256 (t) cc_final: 0.7213 (t) REVERT: H 157 ASN cc_start: 0.7703 (t0) cc_final: 0.7272 (t0) REVERT: h 7 TYR cc_start: 0.8168 (p90) cc_final: 0.7927 (p90) REVERT: h 26 LYS cc_start: 0.8801 (mttt) cc_final: 0.8379 (mmtp) REVERT: i 20 MET cc_start: 0.6789 (mtp) cc_final: 0.6422 (mtp) REVERT: i 88 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7774 (mm-30) REVERT: k 9 LYS cc_start: 0.8974 (tppt) cc_final: 0.8585 (mtmt) REVERT: k 63 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8687 (mtmm) REVERT: L 53 LEU cc_start: 0.8714 (mt) cc_final: 0.8410 (mt) REVERT: L 89 TYR cc_start: 0.7684 (t80) cc_final: 0.7386 (t80) REVERT: L 106 GLN cc_start: 0.7917 (tp40) cc_final: 0.6756 (tp40) REVERT: L 160 GLN cc_start: 0.8302 (pp30) cc_final: 0.8039 (pp30) REVERT: L 184 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8554 (mt-10) REVERT: M 126 GLN cc_start: 0.8437 (mt0) cc_final: 0.8077 (mm-40) REVERT: p 47 VAL cc_start: 0.8283 (t) cc_final: 0.8019 (t) REVERT: u 29 PHE cc_start: 0.8739 (m-80) cc_final: 0.8483 (m-10) REVERT: u 43 ARG cc_start: 0.7397 (mmp80) cc_final: 0.7129 (mmt-90) REVERT: u 101 GLN cc_start: 0.9105 (mt0) cc_final: 0.8631 (mt0) REVERT: O 100 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6377 (mm-30) REVERT: O 114 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8491 (mmtt) REVERT: Q 122 ILE cc_start: 0.7568 (tt) cc_final: 0.7094 (tt) REVERT: Q 136 ASN cc_start: 0.6736 (t0) cc_final: 0.6334 (t0) REVERT: R 47 ASN cc_start: 0.7372 (p0) cc_final: 0.6685 (t0) REVERT: R 100 ARG cc_start: 0.7355 (mtm180) cc_final: 0.7025 (mtp180) REVERT: R 102 LEU cc_start: 0.9029 (mt) cc_final: 0.8768 (mt) REVERT: R 126 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8052 (mm-30) REVERT: S 57 GLU cc_start: 0.8077 (tp30) cc_final: 0.7867 (mp0) REVERT: S 82 ASP cc_start: 0.8644 (m-30) cc_final: 0.8154 (t0) REVERT: S 109 ASP cc_start: 0.7855 (t0) cc_final: 0.7633 (t0) REVERT: S 121 ILE cc_start: 0.9147 (tt) cc_final: 0.8480 (tt) REVERT: U 78 TYR cc_start: 0.8126 (t80) cc_final: 0.7862 (t80) REVERT: U 79 LEU cc_start: 0.9428 (mt) cc_final: 0.9036 (mt) REVERT: U 90 ARG cc_start: 0.6375 (mmm-85) cc_final: 0.5913 (tpt-90) REVERT: U 95 PHE cc_start: 0.8712 (t80) cc_final: 0.8504 (t80) REVERT: U 102 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7720 (tm-30) REVERT: U 103 TYR cc_start: 0.7730 (m-80) cc_final: 0.6912 (m-80) REVERT: V 81 GLN cc_start: 0.7683 (tt0) cc_final: 0.7426 (tt0) REVERT: V 106 LYS cc_start: 0.8881 (tptp) cc_final: 0.8565 (mmmt) REVERT: V 124 ASP cc_start: 0.8427 (t0) cc_final: 0.7968 (t0) REVERT: W 54 GLN cc_start: 0.8528 (mt0) cc_final: 0.7955 (mt0) REVERT: W 115 TYR cc_start: 0.8480 (t80) cc_final: 0.8078 (t80) REVERT: W 116 PHE cc_start: 0.7718 (m-80) cc_final: 0.7171 (m-80) REVERT: Y 56 VAL cc_start: 0.9155 (p) cc_final: 0.8940 (m) REVERT: Y 110 HIS cc_start: 0.7948 (t-90) cc_final: 0.7694 (t-90) REVERT: y 122 ASP cc_start: 0.8107 (p0) cc_final: 0.7494 (p0) REVERT: y 173 LEU cc_start: 0.9367 (mt) cc_final: 0.9114 (mt) REVERT: Z 18 TYR cc_start: 0.7236 (m-80) cc_final: 0.6679 (m-80) REVERT: Z 48 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7443 (mtm-85) REVERT: Z 68 ILE cc_start: 0.8694 (tt) cc_final: 0.8427 (mm) REVERT: Z 104 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7985 (Cg_endo) REVERT: Z 108 GLU cc_start: 0.8679 (pt0) cc_final: 0.8410 (pt0) REVERT: Z 122 HIS cc_start: 0.9021 (t70) cc_final: 0.8737 (t70) REVERT: Z 123 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8981 (mm-40) REVERT: Z 131 PHE cc_start: 0.8301 (m-80) cc_final: 0.8053 (m-10) REVERT: K 306 PHE cc_start: 0.8186 (t80) cc_final: 0.7984 (t80) REVERT: K 335 VAL cc_start: 0.9076 (m) cc_final: 0.8830 (p) REVERT: K 367 LEU cc_start: 0.8404 (mt) cc_final: 0.8026 (mt) REVERT: n 7 ASN cc_start: 0.7772 (t0) cc_final: 0.7470 (t0) REVERT: n 88 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7524 (mmp-170) REVERT: n 216 ARG cc_start: 0.5881 (mtt-85) cc_final: 0.5168 (mtm-85) REVERT: n 248 LEU cc_start: 0.7786 (pt) cc_final: 0.7396 (pt) REVERT: o 94 TYR cc_start: 0.7569 (t80) cc_final: 0.6902 (t80) REVERT: o 121 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7747 (mtm180) REVERT: o 134 TYR cc_start: 0.7971 (p90) cc_final: 0.7685 (p90) REVERT: o 149 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8793 (tm-30) REVERT: o 153 ASN cc_start: 0.7583 (p0) cc_final: 0.7207 (p0) REVERT: q 232 LYS cc_start: 0.8885 (tppt) cc_final: 0.8618 (tppt) REVERT: q 258 TYR cc_start: 0.7897 (t80) cc_final: 0.7601 (t80) REVERT: q 437 LYS cc_start: 0.4654 (pttm) cc_final: 0.3347 (mptt) REVERT: t 54 LYS cc_start: 0.2679 (tmtt) cc_final: 0.1848 (tmtt) REVERT: t 99 PHE cc_start: 0.5921 (m-80) cc_final: 0.5664 (m-80) REVERT: t 293 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7298 (tm-30) outliers start: 7 outliers final: 5 residues processed: 1849 average time/residue: 1.2415 time to fit residues: 3802.0117 Evaluate side-chains 1386 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1381 time to evaluate : 6.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain s residue 15 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 846 optimal weight: 10.0000 chunk 760 optimal weight: 10.0000 chunk 421 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 512 optimal weight: 10.0000 chunk 406 optimal weight: 0.8980 chunk 786 optimal weight: 50.0000 chunk 304 optimal weight: 1.9990 chunk 478 optimal weight: 4.9990 chunk 585 optimal weight: 10.0000 chunk 910 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 132 ASN A 139 HIS A 144 ASN A 187 HIS B 173 GLN B 177 HIS B 280 HIS b 26 GLN b 120 GLN ** b 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 365 GLN b 415 ASN C 9 HIS ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 HIS E 138 GLN e 31 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 HIS ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN G 95 ASN I 73 HIS H 51 GLN H 58 HIS H 100 ASN H 163 GLN H 183 HIS h 59 ASN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 GLN L 114 GLN L 120 GLN l 19 GLN l 50 ASN M 27 GLN M 119 GLN N 57 GLN N 70 ASN u 37 HIS ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN P 145 HIS Q 58 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 33 HIS S 8 GLN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN W 44 HIS ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN y 33 ASN y 83 HIS y 118 HIS ** K 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 GLN n 73 HIS ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 91 GLN t 265 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.633 129032 Z= 0.318 Angle : 0.775 45.680 188245 Z= 0.393 Chirality : 0.042 1.098 23443 Planarity : 0.006 0.131 13065 Dihedral : 23.580 179.826 52987 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 2.20 % Allowed : 15.61 % Favored : 82.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.44 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.09), residues: 7234 helix: -0.83 (0.09), residues: 2791 sheet: -2.42 (0.15), residues: 805 loop : -2.56 (0.09), residues: 3638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP n 431 HIS 0.010 0.001 HIS q 264 PHE 0.050 0.002 PHE K 413 TYR 0.031 0.002 TYR P 139 ARG 0.013 0.001 ARG K 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1788 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1650 time to evaluate : 6.559 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: A 46 LYS cc_start: 0.9047 (tppt) cc_final: 0.8623 (tttt) REVERT: A 67 TYR cc_start: 0.7797 (m-80) cc_final: 0.7529 (m-80) REVERT: A 140 ASN cc_start: 0.9125 (t0) cc_final: 0.8450 (t0) REVERT: A 144 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8804 (p0) REVERT: a 85 ASP cc_start: 0.7808 (p0) cc_final: 0.6841 (p0) REVERT: a 86 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8684 (mmtm) REVERT: a 90 TYR cc_start: 0.8897 (m-80) cc_final: 0.8230 (m-80) REVERT: a 120 ASN cc_start: 0.8022 (t0) cc_final: 0.7508 (t0) REVERT: B 33 PRO cc_start: 0.7339 (Cg_exo) cc_final: 0.7139 (Cg_endo) REVERT: B 58 ARG cc_start: 0.6963 (ttt-90) cc_final: 0.6697 (ttt90) REVERT: B 178 LEU cc_start: 0.8023 (mm) cc_final: 0.7783 (mm) REVERT: b 59 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7920 (tm-30) REVERT: b 156 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7191 (t-170) REVERT: b 197 TYR cc_start: 0.7872 (p90) cc_final: 0.7442 (p90) REVERT: b 232 MET cc_start: 0.1355 (mpp) cc_final: 0.0368 (mmm) REVERT: C 9 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8584 (m90) REVERT: C 33 ASP cc_start: 0.8331 (p0) cc_final: 0.8096 (p0) REVERT: C 188 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7325 (tpp80) REVERT: c 27 TYR cc_start: 0.7760 (t80) cc_final: 0.7377 (t80) REVERT: d 57 GLN cc_start: 0.7751 (mt0) cc_final: 0.7460 (mp10) REVERT: E 13 GLU cc_start: 0.7032 (mp0) cc_final: 0.6824 (mp0) REVERT: E 22 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.8015 (mmt90) REVERT: E 28 GLN cc_start: 0.7128 (tt0) cc_final: 0.6874 (tt0) REVERT: E 29 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7805 (tttt) REVERT: E 61 ASN cc_start: 0.8845 (m-40) cc_final: 0.8545 (m-40) REVERT: E 137 ASP cc_start: 0.8212 (m-30) cc_final: 0.7994 (m-30) REVERT: e 60 ASN cc_start: 0.8808 (t0) cc_final: 0.8440 (t0) REVERT: F 187 GLU cc_start: 0.7059 (tp30) cc_final: 0.6788 (tp30) REVERT: G 89 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7291 (mm-30) REVERT: G 112 GLU cc_start: 0.8202 (pp20) cc_final: 0.7838 (pp20) REVERT: g 93 PHE cc_start: 0.8413 (t80) cc_final: 0.8166 (t80) REVERT: g 97 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7154 (mm-30) REVERT: g 102 LYS cc_start: 0.8547 (mttp) cc_final: 0.8198 (tppt) REVERT: H 11 GLU cc_start: 0.7459 (tp30) cc_final: 0.7173 (tp30) REVERT: H 145 VAL cc_start: 0.8106 (t) cc_final: 0.7776 (t) REVERT: H 184 LYS cc_start: 0.8284 (mttt) cc_final: 0.7788 (mttt) REVERT: h 26 LYS cc_start: 0.8842 (mttt) cc_final: 0.8247 (mmtp) REVERT: i 38 LYS cc_start: 0.8152 (mttm) cc_final: 0.7923 (mptt) REVERT: i 90 MET cc_start: 0.8590 (mmm) cc_final: 0.8368 (mmt) REVERT: k 12 LEU cc_start: 0.8876 (mt) cc_final: 0.8544 (mt) REVERT: k 63 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8775 (mtmt) REVERT: l 27 ILE cc_start: 0.8602 (mt) cc_final: 0.8242 (tt) REVERT: M 27 GLN cc_start: 0.8338 (tp40) cc_final: 0.8095 (tp-100) REVERT: p 24 ARG cc_start: 0.8165 (ptp-110) cc_final: 0.7654 (mtm110) REVERT: u 25 ASP cc_start: 0.8080 (t0) cc_final: 0.7880 (t0) REVERT: u 27 LYS cc_start: 0.7984 (tptp) cc_final: 0.7480 (tptt) REVERT: u 41 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8473 (tttp) REVERT: u 101 GLN cc_start: 0.9310 (mt0) cc_final: 0.9065 (mt0) REVERT: u 107 PHE cc_start: 0.7681 (t80) cc_final: 0.7245 (t80) REVERT: O 100 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6932 (mm-30) REVERT: O 114 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8284 (mmtt) REVERT: P 144 SER cc_start: 0.9314 (OUTLIER) cc_final: 0.8946 (p) REVERT: P 179 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7243 (mm-40) REVERT: S 57 GLU cc_start: 0.8075 (tp30) cc_final: 0.7771 (mp0) REVERT: S 89 ASN cc_start: 0.8714 (m110) cc_final: 0.8260 (m-40) REVERT: S 109 ASP cc_start: 0.7763 (t0) cc_final: 0.7458 (t0) REVERT: U 78 TYR cc_start: 0.8137 (t80) cc_final: 0.7860 (t80) REVERT: U 102 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7458 (tm-30) REVERT: U 103 TYR cc_start: 0.8168 (m-80) cc_final: 0.7613 (m-80) REVERT: V 106 LYS cc_start: 0.8748 (tptp) cc_final: 0.8528 (tptt) REVERT: V 108 GLU cc_start: 0.8455 (mp0) cc_final: 0.8121 (mp0) REVERT: V 124 ASP cc_start: 0.8431 (t0) cc_final: 0.8150 (t0) REVERT: W 54 GLN cc_start: 0.8447 (mt0) cc_final: 0.8040 (mt0) REVERT: X 33 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8094 (mtp85) REVERT: Y 110 HIS cc_start: 0.8024 (t-90) cc_final: 0.7670 (t-90) REVERT: y 35 TYR cc_start: 0.7449 (t80) cc_final: 0.7113 (t80) REVERT: y 75 GLN cc_start: 0.8373 (mp10) cc_final: 0.7856 (mt0) REVERT: Z 54 THR cc_start: 0.8489 (t) cc_final: 0.8174 (t) REVERT: Z 106 GLN cc_start: 0.7667 (tt0) cc_final: 0.7425 (tt0) REVERT: Z 123 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8988 (mm110) REVERT: Z 131 PHE cc_start: 0.8367 (m-80) cc_final: 0.8052 (m-80) REVERT: K 335 VAL cc_start: 0.9100 (m) cc_final: 0.8875 (p) REVERT: K 413 PHE cc_start: 0.7733 (m-80) cc_final: 0.7103 (m-80) REVERT: n 88 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7718 (mmp-170) REVERT: n 216 ARG cc_start: 0.5846 (mtt-85) cc_final: 0.5277 (mtm180) REVERT: n 248 LEU cc_start: 0.7992 (pt) cc_final: 0.7701 (pt) REVERT: o 94 TYR cc_start: 0.7659 (t80) cc_final: 0.7008 (t80) REVERT: o 104 GLU cc_start: 0.7374 (tp30) cc_final: 0.6995 (mm-30) REVERT: o 134 TYR cc_start: 0.7923 (p90) cc_final: 0.7624 (p90) REVERT: o 136 PHE cc_start: 0.7852 (m-80) cc_final: 0.7644 (m-10) REVERT: o 155 TYR cc_start: 0.7979 (t80) cc_final: 0.7352 (t80) REVERT: o 163 GLN cc_start: 0.7606 (mp10) cc_final: 0.7348 (mp10) REVERT: q 232 LYS cc_start: 0.8974 (tppt) cc_final: 0.8732 (tppt) REVERT: q 437 LYS cc_start: 0.4509 (pttm) cc_final: 0.3118 (mptt) REVERT: t 30 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7560 (ttt180) REVERT: t 55 PHE cc_start: 0.6459 (t80) cc_final: 0.6247 (t80) REVERT: t 142 LEU cc_start: 0.8059 (mt) cc_final: 0.7760 (mt) REVERT: t 293 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7381 (tm-30) outliers start: 138 outliers final: 76 residues processed: 1713 average time/residue: 1.1077 time to fit residues: 3202.1910 Evaluate side-chains 1515 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1434 time to evaluate : 6.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain G residue 28 HIS Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain u residue 41 LYS Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 137 ASN Chi-restraints excluded: chain y residue 61 ARG Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 152 CYS Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 263 VAL Chi-restraints excluded: chain t residue 306 THR Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 19 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 506 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 758 optimal weight: 10.0000 chunk 620 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 912 optimal weight: 3.9990 chunk 985 optimal weight: 6.9990 chunk 812 optimal weight: 50.0000 chunk 904 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 732 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 74 ASN B 280 HIS ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN ** b 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 259 GLN ** b 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN ** e 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 HIS F 159 GLN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 162 GLN ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 113 GLN L 17 HIS ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 120 GLN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 ASN M 105 GLN N 57 GLN ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 37 HIS ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 GLN T 146 ASN U 9 GLN ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 GLN X 94 GLN Y 66 GLN Y 120 GLN y 50 HIS ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 118 HIS z 10 HIS z 55 GLN ** K 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 48 ASN ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 164 ASN ** o 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.584 129032 Z= 0.500 Angle : 0.861 45.060 188245 Z= 0.436 Chirality : 0.046 1.066 23443 Planarity : 0.006 0.115 13065 Dihedral : 23.540 179.686 52986 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.13 % Favored : 91.71 % Rotamer: Outliers : 4.24 % Allowed : 19.13 % Favored : 76.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.09), residues: 7234 helix: -0.49 (0.09), residues: 2789 sheet: -2.11 (0.16), residues: 830 loop : -2.40 (0.09), residues: 3615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 9 HIS 0.036 0.002 HIS y 118 PHE 0.037 0.003 PHE t 280 TYR 0.038 0.003 TYR P 139 ARG 0.014 0.001 ARG b 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1798 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1532 time to evaluate : 6.573 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: A 22 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 44 ILE cc_start: 0.8922 (mp) cc_final: 0.8667 (mm) REVERT: a 85 ASP cc_start: 0.7749 (p0) cc_final: 0.7101 (p0) REVERT: a 90 TYR cc_start: 0.8985 (m-80) cc_final: 0.8564 (m-80) REVERT: a 120 ASN cc_start: 0.8151 (t0) cc_final: 0.7817 (t0) REVERT: B 178 LEU cc_start: 0.8400 (mm) cc_final: 0.8051 (mm) REVERT: B 347 SER cc_start: 0.8721 (t) cc_final: 0.8511 (m) REVERT: b 59 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8094 (tm-30) REVERT: b 156 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7754 (t-170) REVERT: b 197 TYR cc_start: 0.8056 (p90) cc_final: 0.7685 (p90) REVERT: b 232 MET cc_start: 0.2056 (mpp) cc_final: -0.0106 (mmm) REVERT: b 284 MET cc_start: 0.4651 (OUTLIER) cc_final: 0.3237 (tpp) REVERT: C 234 ASN cc_start: 0.8723 (t0) cc_final: 0.8316 (t0) REVERT: c 70 PHE cc_start: 0.8713 (t80) cc_final: 0.8444 (t80) REVERT: d 55 LEU cc_start: 0.8497 (tp) cc_final: 0.8247 (tp) REVERT: E 28 GLN cc_start: 0.7184 (tt0) cc_final: 0.6732 (tt0) REVERT: E 61 ASN cc_start: 0.8861 (m-40) cc_final: 0.8468 (m-40) REVERT: e 83 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7473 (mt-10) REVERT: e 111 ARG cc_start: 0.8603 (tpt-90) cc_final: 0.8381 (tpt-90) REVERT: F 33 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8506 (ttp-170) REVERT: F 37 ASN cc_start: 0.8699 (m110) cc_final: 0.8478 (m-40) REVERT: F 51 TYR cc_start: 0.8149 (m-80) cc_final: 0.7677 (m-80) REVERT: F 187 GLU cc_start: 0.7223 (tp30) cc_final: 0.6987 (tp30) REVERT: G 107 GLU cc_start: 0.7619 (tp30) cc_final: 0.7362 (tp30) REVERT: G 112 GLU cc_start: 0.8262 (pp20) cc_final: 0.7804 (pp20) REVERT: g 102 LYS cc_start: 0.8469 (mttp) cc_final: 0.8264 (tppt) REVERT: H 23 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7798 (mpp80) REVERT: h 26 LYS cc_start: 0.8863 (mttt) cc_final: 0.8404 (mmtp) REVERT: h 116 TYR cc_start: 0.8690 (p90) cc_final: 0.8412 (p90) REVERT: i 38 LYS cc_start: 0.8333 (mttm) cc_final: 0.8091 (mptt) REVERT: i 82 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7130 (mtp85) REVERT: k 9 LYS cc_start: 0.9129 (tppt) cc_final: 0.8614 (mtmt) REVERT: k 63 LYS cc_start: 0.9002 (mtpp) cc_final: 0.8800 (mtmt) REVERT: L 93 ILE cc_start: 0.9039 (mm) cc_final: 0.8776 (tp) REVERT: L 112 ASN cc_start: 0.8935 (m-40) cc_final: 0.8678 (m110) REVERT: L 122 LYS cc_start: 0.8356 (mmmt) cc_final: 0.8150 (mmmt) REVERT: u 41 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8662 (ttpp) REVERT: u 101 GLN cc_start: 0.9260 (mt0) cc_final: 0.8916 (mt0) REVERT: O 150 GLU cc_start: 0.7194 (pm20) cc_final: 0.6864 (pm20) REVERT: O 193 GLN cc_start: 0.7162 (mt0) cc_final: 0.6877 (mt0) REVERT: O 199 TYR cc_start: 0.8286 (m-80) cc_final: 0.7969 (m-80) REVERT: P 144 SER cc_start: 0.9541 (OUTLIER) cc_final: 0.9137 (p) REVERT: P 154 GLU cc_start: 0.6180 (tp30) cc_final: 0.5976 (tp30) REVERT: Q 98 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: R 100 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7470 (mtp180) REVERT: R 120 TYR cc_start: 0.8267 (t80) cc_final: 0.8040 (t80) REVERT: S 57 GLU cc_start: 0.8190 (tp30) cc_final: 0.7825 (mp0) REVERT: S 89 ASN cc_start: 0.8737 (m110) cc_final: 0.8351 (m-40) REVERT: S 107 TYR cc_start: 0.8790 (m-80) cc_final: 0.8563 (m-10) REVERT: S 109 ASP cc_start: 0.7947 (t0) cc_final: 0.7672 (t0) REVERT: S 152 LEU cc_start: 0.8561 (mt) cc_final: 0.7827 (pt) REVERT: U 35 LYS cc_start: 0.8540 (tptp) cc_final: 0.8305 (tptp) REVERT: U 83 TYR cc_start: 0.7576 (t80) cc_final: 0.7188 (t80) REVERT: U 102 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7324 (tm-30) REVERT: V 54 LEU cc_start: 0.8053 (tp) cc_final: 0.7783 (tt) REVERT: V 63 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7551 (mmmt) REVERT: V 106 LYS cc_start: 0.8741 (tptp) cc_final: 0.8522 (tptt) REVERT: V 108 GLU cc_start: 0.8325 (mp0) cc_final: 0.7973 (mp0) REVERT: X 60 TYR cc_start: 0.8448 (m-80) cc_final: 0.7909 (m-80) REVERT: X 104 GLU cc_start: 0.8013 (mp0) cc_final: 0.7705 (mp0) REVERT: Y 112 ASP cc_start: 0.8259 (m-30) cc_final: 0.8049 (m-30) REVERT: y 34 PHE cc_start: 0.7171 (t80) cc_final: 0.6906 (t80) REVERT: y 35 TYR cc_start: 0.7404 (t80) cc_final: 0.7042 (t80) REVERT: Z 54 THR cc_start: 0.8678 (t) cc_final: 0.8390 (t) REVERT: Z 122 HIS cc_start: 0.8885 (t70) cc_final: 0.8666 (t70) REVERT: Z 123 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8963 (mm-40) REVERT: K 327 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7374 (ppp) REVERT: K 365 ASN cc_start: 0.7530 (p0) cc_final: 0.7160 (p0) REVERT: K 394 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7730 (p0) REVERT: K 413 PHE cc_start: 0.7914 (m-80) cc_final: 0.7340 (m-80) REVERT: n 88 ARG cc_start: 0.8533 (ttp80) cc_final: 0.7845 (mmp-170) REVERT: n 216 ARG cc_start: 0.6051 (mtt-85) cc_final: 0.5479 (mtm180) REVERT: n 248 LEU cc_start: 0.8000 (pt) cc_final: 0.7737 (pt) REVERT: o 104 GLU cc_start: 0.7359 (tp30) cc_final: 0.6674 (mm-30) REVERT: o 113 GLN cc_start: 0.7798 (mt0) cc_final: 0.7595 (mt0) REVERT: o 146 MET cc_start: 0.8549 (ttm) cc_final: 0.7906 (tpp) REVERT: o 155 TYR cc_start: 0.8180 (t80) cc_final: 0.7499 (t80) REVERT: q 232 LYS cc_start: 0.9024 (tppt) cc_final: 0.8784 (tppt) REVERT: q 242 TYR cc_start: 0.8134 (t80) cc_final: 0.7915 (t80) REVERT: q 258 TYR cc_start: 0.8090 (t80) cc_final: 0.7832 (t80) REVERT: q 421 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7527 (ttp80) REVERT: q 437 LYS cc_start: 0.4651 (pttm) cc_final: 0.3206 (mptt) REVERT: t 54 LYS cc_start: 0.2996 (tmtt) cc_final: 0.2627 (tmtt) REVERT: t 288 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7957 (ttpp) REVERT: t 293 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7541 (tm-30) outliers start: 266 outliers final: 170 residues processed: 1665 average time/residue: 1.0691 time to fit residues: 3037.9325 Evaluate side-chains 1571 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1391 time to evaluate : 6.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 117 ARG Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain p residue 33 GLN Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 41 LYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 111 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 98 LYS Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain y residue 152 CYS Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain Z residue 36 HIS Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 120 GLU Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain K residue 394 ASP Chi-restraints excluded: chain K residue 403 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain o residue 139 PHE Chi-restraints excluded: chain o residue 161 LEU Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 446 THR Chi-restraints excluded: chain t residue 165 LEU Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 263 VAL Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 306 THR Chi-restraints excluded: chain t residue 309 VAL Chi-restraints excluded: chain s residue 19 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 901 optimal weight: 30.0000 chunk 686 optimal weight: 20.0000 chunk 473 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 435 optimal weight: 9.9990 chunk 612 optimal weight: 20.0000 chunk 915 optimal weight: 2.9990 chunk 969 optimal weight: 7.9990 chunk 478 optimal weight: 0.9990 chunk 867 optimal weight: 1.9990 chunk 261 optimal weight: 40.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 322 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 71 HIS F 159 GLN F 172 ASN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN H 8 GLN H 156 GLN h 20 GLN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS L 28 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 120 GLN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 41 GLN p 33 GLN N 156 HIS u 37 HIS P 101 ASN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 234 ASN ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN y 50 HIS y 118 HIS K 333 ASN K 345 HIS ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 7 ASN n 48 ASN ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 149 GLN ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.572 129032 Z= 0.268 Angle : 0.700 42.220 188245 Z= 0.356 Chirality : 0.039 1.060 23443 Planarity : 0.005 0.105 13065 Dihedral : 23.391 179.859 52984 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.54 % Favored : 93.36 % Rotamer: Outliers : 3.25 % Allowed : 22.16 % Favored : 74.59 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 7234 helix: -0.14 (0.10), residues: 2787 sheet: -1.67 (0.16), residues: 840 loop : -2.13 (0.10), residues: 3607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 243 HIS 0.014 0.001 HIS q 264 PHE 0.041 0.002 PHE n 433 TYR 0.033 0.002 TYR P 139 ARG 0.017 0.001 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1805 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1601 time to evaluate : 6.550 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: A 22 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8097 (mp) REVERT: a 85 ASP cc_start: 0.7645 (p0) cc_final: 0.6794 (p0) REVERT: a 90 TYR cc_start: 0.8925 (m-80) cc_final: 0.8576 (m-80) REVERT: a 120 ASN cc_start: 0.8033 (t0) cc_final: 0.7660 (t0) REVERT: B 178 LEU cc_start: 0.8183 (mm) cc_final: 0.7821 (mm) REVERT: B 308 MET cc_start: 0.6705 (mtt) cc_final: 0.6416 (mtt) REVERT: b 59 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7804 (tm-30) REVERT: b 156 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.7644 (t-170) REVERT: b 197 TYR cc_start: 0.8147 (p90) cc_final: 0.7766 (p90) REVERT: b 211 TYR cc_start: 0.5617 (t80) cc_final: 0.4976 (t80) REVERT: b 232 MET cc_start: 0.1908 (mpp) cc_final: -0.0413 (mmm) REVERT: b 284 MET cc_start: 0.4273 (OUTLIER) cc_final: 0.2954 (mmm) REVERT: C 5 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7191 (tm-30) REVERT: c 41 LEU cc_start: 0.7601 (mt) cc_final: 0.7134 (mt) REVERT: c 52 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8524 (mtm180) REVERT: c 53 LYS cc_start: 0.9411 (mtpt) cc_final: 0.9089 (mmtp) REVERT: d 27 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8071 (mtmm) REVERT: E 28 GLN cc_start: 0.7422 (tt0) cc_final: 0.7091 (tt0) REVERT: E 61 ASN cc_start: 0.8794 (m-40) cc_final: 0.8416 (m-40) REVERT: E 137 ASP cc_start: 0.8305 (m-30) cc_final: 0.8052 (m-30) REVERT: e 111 ARG cc_start: 0.8616 (tpt-90) cc_final: 0.8344 (tpt-90) REVERT: F 33 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8473 (ttp-170) REVERT: F 37 ASN cc_start: 0.8806 (m110) cc_final: 0.8550 (m-40) REVERT: F 51 TYR cc_start: 0.8163 (m-80) cc_final: 0.7943 (m-80) REVERT: F 168 ILE cc_start: 0.9100 (mm) cc_final: 0.8834 (mt) REVERT: F 170 GLU cc_start: 0.7917 (pp20) cc_final: 0.7587 (pp20) REVERT: F 187 GLU cc_start: 0.7152 (tp30) cc_final: 0.6862 (tp30) REVERT: f 44 TYR cc_start: 0.7810 (m-80) cc_final: 0.7609 (m-80) REVERT: G 44 ARG cc_start: 0.8111 (mtt90) cc_final: 0.6608 (mtt180) REVERT: G 61 GLN cc_start: 0.8358 (mt0) cc_final: 0.8111 (mt0) REVERT: G 107 GLU cc_start: 0.7646 (tp30) cc_final: 0.7418 (tp30) REVERT: G 112 GLU cc_start: 0.8219 (pp20) cc_final: 0.8017 (pp20) REVERT: G 206 GLU cc_start: 0.7893 (pp20) cc_final: 0.7260 (pp20) REVERT: g 93 PHE cc_start: 0.8337 (t80) cc_final: 0.8091 (t80) REVERT: g 97 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7048 (mm-30) REVERT: g 102 LYS cc_start: 0.8532 (mttp) cc_final: 0.8211 (tppt) REVERT: H 5 GLN cc_start: 0.8976 (pm20) cc_final: 0.8765 (pm20) REVERT: H 23 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7554 (mpp80) REVERT: H 115 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7639 (ptp-170) REVERT: h 26 LYS cc_start: 0.8826 (mttt) cc_final: 0.8508 (mmtp) REVERT: i 20 MET cc_start: 0.7359 (mtp) cc_final: 0.6521 (mtp) REVERT: i 38 LYS cc_start: 0.8234 (mttm) cc_final: 0.7850 (mptt) REVERT: i 80 PHE cc_start: 0.7156 (t80) cc_final: 0.6142 (t80) REVERT: i 82 ARG cc_start: 0.7734 (mtt180) cc_final: 0.6960 (mtp85) REVERT: i 90 MET cc_start: 0.8649 (mmt) cc_final: 0.8432 (mmt) REVERT: j 68 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: L 106 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8081 (tp40) REVERT: L 112 ASN cc_start: 0.8686 (m-40) cc_final: 0.8379 (m110) REVERT: L 122 LYS cc_start: 0.8319 (mmmt) cc_final: 0.8057 (mmmt) REVERT: M 59 ASN cc_start: 0.8032 (t0) cc_final: 0.7791 (t0) REVERT: p 24 ARG cc_start: 0.8237 (ptp-110) cc_final: 0.7862 (mtm110) REVERT: p 44 LYS cc_start: 0.7551 (ptpt) cc_final: 0.7070 (pttp) REVERT: u 101 GLN cc_start: 0.9241 (mt0) cc_final: 0.9026 (mt0) REVERT: O 199 TYR cc_start: 0.8152 (m-80) cc_final: 0.7912 (m-10) REVERT: P 92 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7535 (tm-30) REVERT: P 112 LEU cc_start: 0.7797 (tp) cc_final: 0.7532 (tp) REVERT: Q 35 PHE cc_start: 0.8576 (t80) cc_final: 0.8335 (t80) REVERT: Q 120 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7682 (pp20) REVERT: R 92 GLN cc_start: 0.8198 (tt0) cc_final: 0.7903 (tt0) REVERT: R 100 ARG cc_start: 0.7676 (mtp180) cc_final: 0.6599 (mtp180) REVERT: r 4 ASN cc_start: 0.7283 (m110) cc_final: 0.6807 (m-40) REVERT: S 57 GLU cc_start: 0.8074 (tp30) cc_final: 0.7733 (mp0) REVERT: S 89 ASN cc_start: 0.8654 (m110) cc_final: 0.8157 (m-40) REVERT: S 152 LEU cc_start: 0.8498 (mt) cc_final: 0.7727 (pt) REVERT: T 156 TYR cc_start: 0.5264 (t80) cc_final: 0.5002 (t80) REVERT: U 28 PHE cc_start: 0.6373 (t80) cc_final: 0.6045 (t80) REVERT: U 102 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7316 (tm-30) REVERT: V 54 LEU cc_start: 0.8013 (tp) cc_final: 0.7565 (tt) REVERT: V 63 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7431 (mmmt) REVERT: V 108 GLU cc_start: 0.8356 (mp0) cc_final: 0.8015 (mp0) REVERT: V 124 ASP cc_start: 0.8449 (t0) cc_final: 0.8059 (t0) REVERT: W 234 ASN cc_start: 0.7295 (m-40) cc_final: 0.7094 (m-40) REVERT: X 60 TYR cc_start: 0.8334 (m-80) cc_final: 0.8041 (m-80) REVERT: Y 112 ASP cc_start: 0.8164 (m-30) cc_final: 0.7939 (m-30) REVERT: y 34 PHE cc_start: 0.7103 (t80) cc_final: 0.6742 (t80) REVERT: y 35 TYR cc_start: 0.7365 (t80) cc_final: 0.6999 (t80) REVERT: Z 18 TYR cc_start: 0.7308 (m-80) cc_final: 0.7093 (m-80) REVERT: Z 48 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.7882 (mtp85) REVERT: Z 118 PHE cc_start: 0.9119 (m-80) cc_final: 0.8917 (m-80) REVERT: Z 123 GLN cc_start: 0.9259 (mm-40) cc_final: 0.9017 (mm-40) REVERT: K 327 MET cc_start: 0.7867 (ppp) cc_final: 0.6544 (ppp) REVERT: K 365 ASN cc_start: 0.7402 (p0) cc_final: 0.7019 (p0) REVERT: K 413 PHE cc_start: 0.7943 (m-80) cc_final: 0.7378 (m-80) REVERT: n 88 ARG cc_start: 0.8410 (ttp80) cc_final: 0.7710 (mmp-170) REVERT: n 216 ARG cc_start: 0.5882 (mtt-85) cc_final: 0.5178 (mtm-85) REVERT: n 248 LEU cc_start: 0.7865 (pt) cc_final: 0.7613 (pt) REVERT: o 94 TYR cc_start: 0.7877 (t80) cc_final: 0.7586 (t80) REVERT: o 104 GLU cc_start: 0.7294 (tp30) cc_final: 0.6885 (mm-30) REVERT: o 134 TYR cc_start: 0.7970 (p90) cc_final: 0.7612 (p90) REVERT: o 136 PHE cc_start: 0.7568 (m-10) cc_final: 0.7304 (m-10) REVERT: o 146 MET cc_start: 0.8494 (ttm) cc_final: 0.8011 (tpp) REVERT: o 150 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7857 (mm-30) REVERT: o 155 TYR cc_start: 0.8210 (t80) cc_final: 0.7449 (t80) REVERT: o 179 TYR cc_start: 0.6706 (m-10) cc_final: 0.6421 (m-10) REVERT: q 232 LYS cc_start: 0.8981 (tppt) cc_final: 0.8772 (tppt) REVERT: q 242 TYR cc_start: 0.8039 (t80) cc_final: 0.7763 (t80) REVERT: q 253 ILE cc_start: 0.9097 (mm) cc_final: 0.8109 (mm) REVERT: q 258 TYR cc_start: 0.7982 (t80) cc_final: 0.7701 (t80) REVERT: q 264 HIS cc_start: 0.7558 (m-70) cc_final: 0.6812 (m90) REVERT: q 421 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.7413 (ttp80) REVERT: q 437 LYS cc_start: 0.4506 (pttm) cc_final: 0.3141 (mptt) REVERT: t 238 GLN cc_start: 0.8828 (mm110) cc_final: 0.8415 (mp10) outliers start: 204 outliers final: 119 residues processed: 1712 average time/residue: 1.0429 time to fit residues: 3049.4968 Evaluate side-chains 1536 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1412 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 59 ASN Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 145 PHE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 81 GLN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 120 GLU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 214 ASP Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain s residue 14 LYS Chi-restraints excluded: chain s residue 21 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 807 optimal weight: 50.0000 chunk 550 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 721 optimal weight: 6.9990 chunk 400 optimal weight: 0.9990 chunk 827 optimal weight: 10.0000 chunk 670 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 495 optimal weight: 2.9990 chunk 870 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 GLN F 172 ASN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN H 156 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN L 114 GLN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN u 37 HIS O 31 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 172 GLN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS T 122 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN ** y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 409 HIS ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.595 129032 Z= 0.410 Angle : 0.780 46.727 188245 Z= 0.394 Chirality : 0.042 0.970 23443 Planarity : 0.006 0.108 13065 Dihedral : 23.351 179.996 52984 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.58 % Rotamer: Outliers : 4.58 % Allowed : 23.50 % Favored : 71.93 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.09), residues: 7234 helix: -0.16 (0.10), residues: 2791 sheet: -1.65 (0.16), residues: 871 loop : -2.08 (0.10), residues: 3572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP n 431 HIS 0.014 0.001 HIS q 264 PHE 0.039 0.002 PHE t 280 TYR 0.032 0.002 TYR P 139 ARG 0.018 0.001 ARG G 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1774 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1487 time to evaluate : 6.615 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: A 22 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 190 ARG cc_start: 0.6974 (tmm-80) cc_final: 0.6676 (ptm-80) REVERT: a 85 ASP cc_start: 0.7616 (p0) cc_final: 0.7353 (p0) REVERT: a 90 TYR cc_start: 0.9021 (m-80) cc_final: 0.8592 (m-80) REVERT: a 120 ASN cc_start: 0.8206 (t0) cc_final: 0.7871 (t0) REVERT: a 132 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8685 (mmmm) REVERT: B 53 MET cc_start: 0.7553 (mtt) cc_final: 0.7282 (mtp) REVERT: B 196 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8227 (ttp80) REVERT: b 59 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8142 (tm-30) REVERT: b 156 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7567 (t-170) REVERT: b 232 MET cc_start: 0.2001 (mpp) cc_final: -0.0523 (mmm) REVERT: b 284 MET cc_start: 0.3425 (OUTLIER) cc_final: 0.2568 (mmm) REVERT: b 329 MET cc_start: 0.8675 (ppp) cc_final: 0.7324 (ppp) REVERT: C 308 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8239 (ttpt) REVERT: c 41 LEU cc_start: 0.7466 (mt) cc_final: 0.6923 (mt) REVERT: c 55 GLU cc_start: 0.8077 (pp20) cc_final: 0.7626 (pp20) REVERT: E 28 GLN cc_start: 0.7423 (tt0) cc_final: 0.6978 (tt0) REVERT: E 61 ASN cc_start: 0.8768 (m-40) cc_final: 0.8373 (m-40) REVERT: E 97 ASN cc_start: 0.8421 (p0) cc_final: 0.8182 (p0) REVERT: E 137 ASP cc_start: 0.8415 (m-30) cc_final: 0.8126 (m-30) REVERT: e 111 ARG cc_start: 0.8520 (tpt-90) cc_final: 0.8290 (tpt-90) REVERT: F 33 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8171 (ttp-170) REVERT: F 168 ILE cc_start: 0.9230 (mm) cc_final: 0.8938 (mt) REVERT: F 170 GLU cc_start: 0.8008 (pp20) cc_final: 0.7737 (pp20) REVERT: G 61 GLN cc_start: 0.8478 (mt0) cc_final: 0.8245 (mt0) REVERT: G 107 GLU cc_start: 0.7652 (tp30) cc_final: 0.7393 (tp30) REVERT: g 87 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: g 93 PHE cc_start: 0.8310 (t80) cc_final: 0.8009 (t80) REVERT: g 97 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7085 (mm-30) REVERT: H 5 GLN cc_start: 0.8999 (pm20) cc_final: 0.8726 (pm20) REVERT: H 23 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7658 (mpp80) REVERT: H 156 GLN cc_start: 0.8822 (mm110) cc_final: 0.8379 (mm-40) REVERT: h 26 LYS cc_start: 0.8850 (mttt) cc_final: 0.8439 (mmtp) REVERT: h 90 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6288 (mtm-85) REVERT: i 38 LYS cc_start: 0.8296 (mttm) cc_final: 0.8063 (mptt) REVERT: i 53 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7806 (p90) REVERT: j 68 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8183 (ttpt) REVERT: j 73 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8042 (mtm180) REVERT: k 63 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8790 (mtmm) REVERT: L 93 ILE cc_start: 0.9038 (mm) cc_final: 0.8678 (tp) REVERT: L 174 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8431 (ttm170) REVERT: p 41 PHE cc_start: 0.8130 (m-80) cc_final: 0.7917 (m-80) REVERT: u 23 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.7045 (mtm-85) REVERT: u 101 GLN cc_start: 0.9261 (mt0) cc_final: 0.9034 (mt0) REVERT: O 199 TYR cc_start: 0.8186 (m-80) cc_final: 0.7977 (m-10) REVERT: Q 35 PHE cc_start: 0.8800 (t80) cc_final: 0.8564 (t80) REVERT: Q 120 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7634 (pp20) REVERT: R 100 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7501 (mtp180) REVERT: R 104 ARG cc_start: 0.8458 (ptp90) cc_final: 0.8221 (ptp90) REVERT: R 120 TYR cc_start: 0.8149 (t80) cc_final: 0.7947 (t80) REVERT: r 4 ASN cc_start: 0.7246 (m110) cc_final: 0.6736 (m-40) REVERT: S 57 GLU cc_start: 0.8118 (tp30) cc_final: 0.7751 (mp0) REVERT: S 89 ASN cc_start: 0.8613 (m110) cc_final: 0.8180 (m110) REVERT: S 152 LEU cc_start: 0.8401 (mt) cc_final: 0.7647 (pt) REVERT: T 122 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: U 28 PHE cc_start: 0.6357 (t80) cc_final: 0.6073 (t80) REVERT: U 35 LYS cc_start: 0.8838 (tptp) cc_final: 0.8528 (tptp) REVERT: U 102 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7311 (tm-30) REVERT: V 54 LEU cc_start: 0.8034 (tp) cc_final: 0.7749 (tt) REVERT: V 63 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7412 (mmmt) REVERT: V 108 GLU cc_start: 0.8445 (mp0) cc_final: 0.7905 (mp0) REVERT: V 124 ASP cc_start: 0.8550 (t0) cc_final: 0.8090 (t0) REVERT: X 60 TYR cc_start: 0.8410 (m-80) cc_final: 0.8157 (m-80) REVERT: y 34 PHE cc_start: 0.7196 (t80) cc_final: 0.6880 (t80) REVERT: y 57 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.6748 (mtm-85) REVERT: y 101 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6716 (pp) REVERT: y 139 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7939 (ttm170) REVERT: Z 48 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.7988 (mtp85) REVERT: Z 65 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8513 (tpp80) REVERT: Z 77 TYR cc_start: 0.7294 (m-10) cc_final: 0.7068 (m-10) REVERT: Z 111 LYS cc_start: 0.8513 (mttm) cc_final: 0.8172 (mttm) REVERT: Z 123 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8940 (mm110) REVERT: K 292 ASP cc_start: 0.8306 (m-30) cc_final: 0.8023 (m-30) REVERT: K 314 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7357 (tt) REVERT: K 327 MET cc_start: 0.8029 (ppp) cc_final: 0.6742 (ppp) REVERT: K 365 ASN cc_start: 0.7586 (p0) cc_final: 0.7203 (p0) REVERT: n 88 ARG cc_start: 0.8534 (ttp80) cc_final: 0.7868 (mmp-170) REVERT: n 150 GLN cc_start: 0.8495 (mp10) cc_final: 0.8196 (mp10) REVERT: n 216 ARG cc_start: 0.6100 (mtt-85) cc_final: 0.5424 (mtm-85) REVERT: n 248 LEU cc_start: 0.7815 (pt) cc_final: 0.7538 (pt) REVERT: o 94 TYR cc_start: 0.7992 (t80) cc_final: 0.7706 (t80) REVERT: o 104 GLU cc_start: 0.7370 (tp30) cc_final: 0.6779 (mm-30) REVERT: o 134 TYR cc_start: 0.8014 (p90) cc_final: 0.7644 (p90) REVERT: o 136 PHE cc_start: 0.7569 (m-10) cc_final: 0.7275 (m-10) REVERT: o 146 MET cc_start: 0.8593 (ttm) cc_final: 0.8099 (tpp) REVERT: o 150 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8086 (mm-30) REVERT: o 155 TYR cc_start: 0.8242 (t80) cc_final: 0.7598 (t80) REVERT: q 242 TYR cc_start: 0.8033 (t80) cc_final: 0.7762 (t80) REVERT: q 258 TYR cc_start: 0.8110 (t80) cc_final: 0.7778 (t80) REVERT: q 421 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7538 (ttp80) REVERT: q 437 LYS cc_start: 0.4546 (pttm) cc_final: 0.3185 (mptt) REVERT: t 238 GLN cc_start: 0.8711 (mm110) cc_final: 0.8158 (mm110) REVERT: t 276 GLU cc_start: 0.7556 (pm20) cc_final: 0.7318 (pm20) REVERT: t 288 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7959 (ttpp) outliers start: 287 outliers final: 209 residues processed: 1645 average time/residue: 1.0729 time to fit residues: 3029.0048 Evaluate side-chains 1606 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1384 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 63 ASP Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain b residue 156 HIS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 90 ARG Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 57 LEU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 73 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 58 ASP Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain T residue 122 GLN Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 103 TYR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 81 GLN Chi-restraints excluded: chain W residue 37 TYR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 148 VAL Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 120 GLU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain K residue 167 ARG Chi-restraints excluded: chain K residue 214 ILE Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain K residue 403 LEU Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 181 VAL Chi-restraints excluded: chain n residue 214 ASP Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain t residue 153 VAL Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 263 VAL Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain t residue 309 VAL Chi-restraints excluded: chain s residue 21 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 326 optimal weight: 0.6980 chunk 873 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 569 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 chunk 970 optimal weight: 0.0970 chunk 805 optimal weight: 20.0000 chunk 449 optimal weight: 3.9990 chunk 80 optimal weight: 50.0000 chunk 321 optimal weight: 5.9990 chunk 509 optimal weight: 30.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 237 GLN C 304 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 HIS ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN u 37 HIS ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 ASN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 GLN W 223 ASN ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 409 HIS o 113 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.591 129032 Z= 0.242 Angle : 0.683 44.643 188245 Z= 0.346 Chirality : 0.037 0.800 23443 Planarity : 0.005 0.103 13065 Dihedral : 23.295 179.800 52984 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 3.36 % Allowed : 25.86 % Favored : 70.78 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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: -1.64 (0.09), residues: 7234 helix: 0.04 (0.10), residues: 2783 sheet: -1.41 (0.16), residues: 867 loop : -1.94 (0.10), residues: 3584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 9 HIS 0.021 0.001 HIS q 264 PHE 0.031 0.002 PHE K 392 TYR 0.035 0.002 TYR U 75 ARG 0.022 0.001 ARG L 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1747 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1536 time to evaluate : 6.509 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: A 190 ARG cc_start: 0.6891 (tmm-80) cc_final: 0.6622 (ptm-80) REVERT: a 85 ASP cc_start: 0.8093 (p0) cc_final: 0.7528 (p0) REVERT: a 90 TYR cc_start: 0.8958 (m-80) cc_final: 0.8560 (m-80) REVERT: a 120 ASN cc_start: 0.8104 (t0) cc_final: 0.7689 (t0) REVERT: B 178 LEU cc_start: 0.8169 (mm) cc_final: 0.7741 (mm) REVERT: B 196 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.8204 (ttp80) REVERT: b 59 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7922 (tm-30) REVERT: b 197 TYR cc_start: 0.8111 (p90) cc_final: 0.7779 (p90) REVERT: b 211 TYR cc_start: 0.5680 (t80) cc_final: 0.5225 (t80) REVERT: b 232 MET cc_start: 0.1557 (mpp) cc_final: -0.1206 (mmm) REVERT: b 237 MET cc_start: 0.7688 (mmp) cc_final: 0.7073 (mmp) REVERT: b 284 MET cc_start: 0.3657 (OUTLIER) cc_final: 0.2686 (mmm) REVERT: C 5 GLN cc_start: 0.7602 (tp-100) cc_final: 0.7033 (tm-30) REVERT: c 53 LYS cc_start: 0.9425 (mtpt) cc_final: 0.9161 (mttp) REVERT: E 28 GLN cc_start: 0.7494 (tt0) cc_final: 0.7105 (tt0) REVERT: E 61 ASN cc_start: 0.8724 (m-40) cc_final: 0.8350 (m-40) REVERT: E 97 ASN cc_start: 0.8219 (p0) cc_final: 0.7979 (p0) REVERT: E 137 ASP cc_start: 0.8371 (m-30) cc_final: 0.8028 (m-30) REVERT: F 51 TYR cc_start: 0.8019 (m-80) cc_final: 0.7672 (m-80) REVERT: F 168 ILE cc_start: 0.9124 (mm) cc_final: 0.8885 (mt) REVERT: F 199 ASN cc_start: 0.8569 (t0) cc_final: 0.8021 (t0) REVERT: G 107 GLU cc_start: 0.7598 (tp30) cc_final: 0.7332 (tp30) REVERT: G 206 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: g 87 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: g 93 PHE cc_start: 0.8363 (t80) cc_final: 0.8015 (t80) REVERT: g 97 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7050 (mm-30) REVERT: H 5 GLN cc_start: 0.8933 (pm20) cc_final: 0.8711 (pm20) REVERT: H 23 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7391 (mpp80) REVERT: h 26 LYS cc_start: 0.8793 (mttt) cc_final: 0.8367 (mmtp) REVERT: i 38 LYS cc_start: 0.8178 (mttm) cc_final: 0.7876 (mptt) REVERT: i 82 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7175 (mtp85) REVERT: i 90 MET cc_start: 0.8597 (mmt) cc_final: 0.8393 (mmt) REVERT: k 19 ASP cc_start: 0.8254 (t0) cc_final: 0.8052 (t0) REVERT: k 63 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8861 (mtmm) REVERT: L 180 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7596 (ttp80) REVERT: l 13 MET cc_start: 0.7129 (mmm) cc_final: 0.6460 (mmt) REVERT: M 41 GLN cc_start: 0.8181 (mm110) cc_final: 0.7928 (mm-40) REVERT: M 114 ASP cc_start: 0.7182 (t70) cc_final: 0.6912 (t70) REVERT: u 25 ASP cc_start: 0.7708 (p0) cc_final: 0.7378 (p0) REVERT: u 101 GLN cc_start: 0.9232 (mt0) cc_final: 0.8968 (mt0) REVERT: O 199 TYR cc_start: 0.8127 (m-80) cc_final: 0.7924 (m-10) REVERT: P 92 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7725 (tm-30) REVERT: R 100 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7544 (mtp180) REVERT: R 120 TYR cc_start: 0.8093 (t80) cc_final: 0.7865 (t80) REVERT: r 12 LYS cc_start: 0.8927 (ptpt) cc_final: 0.8725 (pttp) REVERT: r 23 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8771 (tpp80) REVERT: S 57 GLU cc_start: 0.7981 (tp30) cc_final: 0.7751 (mp0) REVERT: S 89 ASN cc_start: 0.8503 (m110) cc_final: 0.8046 (m-40) REVERT: T 156 TYR cc_start: 0.5242 (t80) cc_final: 0.4782 (t80) REVERT: U 28 PHE cc_start: 0.6275 (t80) cc_final: 0.5993 (t80) REVERT: U 35 LYS cc_start: 0.8912 (tptp) cc_final: 0.8641 (tptp) REVERT: U 102 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7302 (tm-30) REVERT: V 54 LEU cc_start: 0.8109 (tp) cc_final: 0.7652 (tt) REVERT: V 57 MET cc_start: 0.7432 (ttt) cc_final: 0.7049 (mtm) REVERT: V 63 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7568 (mmmt) REVERT: V 108 GLU cc_start: 0.8346 (mp0) cc_final: 0.7901 (mp0) REVERT: V 124 ASP cc_start: 0.8565 (t0) cc_final: 0.8235 (t0) REVERT: X 60 TYR cc_start: 0.8276 (m-80) cc_final: 0.7929 (m-80) REVERT: Y 67 GLU cc_start: 0.8012 (pm20) cc_final: 0.7800 (pm20) REVERT: y 34 PHE cc_start: 0.7112 (t80) cc_final: 0.6793 (t80) REVERT: y 77 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7866 (m) REVERT: y 100 ARG cc_start: 0.6153 (ttp80) cc_final: 0.5856 (tmt170) REVERT: y 101 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7113 (pp) REVERT: y 139 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7591 (ttm170) REVERT: y 152 CYS cc_start: 0.6795 (m) cc_final: 0.6522 (m) REVERT: Z 48 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.7992 (mtp85) REVERT: Z 65 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8382 (ttt180) REVERT: Z 108 GLU cc_start: 0.7558 (pp20) cc_final: 0.6409 (pp20) REVERT: Z 109 GLU cc_start: 0.8561 (pm20) cc_final: 0.8074 (pm20) REVERT: Z 123 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8871 (mm110) REVERT: K 260 LEU cc_start: 0.7966 (mm) cc_final: 0.7758 (mm) REVERT: K 292 ASP cc_start: 0.8148 (m-30) cc_final: 0.7886 (m-30) REVERT: K 327 MET cc_start: 0.7967 (ppp) cc_final: 0.6874 (ppp) REVERT: K 365 ASN cc_start: 0.7489 (p0) cc_final: 0.7079 (p0) REVERT: n 88 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7685 (mmp-170) REVERT: n 150 GLN cc_start: 0.8480 (mp10) cc_final: 0.8262 (mp10) REVERT: n 160 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8563 (mm110) REVERT: n 216 ARG cc_start: 0.5941 (mtt-85) cc_final: 0.5347 (mtm-85) REVERT: n 248 LEU cc_start: 0.7777 (pt) cc_final: 0.7506 (pt) REVERT: o 94 TYR cc_start: 0.7953 (t80) cc_final: 0.7732 (t80) REVERT: o 134 TYR cc_start: 0.8004 (p90) cc_final: 0.7648 (p90) REVERT: o 136 PHE cc_start: 0.7509 (m-10) cc_final: 0.7249 (m-10) REVERT: o 146 MET cc_start: 0.8530 (ttm) cc_final: 0.7996 (tpp) REVERT: o 150 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8047 (mm-30) REVERT: o 155 TYR cc_start: 0.8221 (t80) cc_final: 0.7507 (t80) REVERT: q 246 LYS cc_start: 0.9077 (tppt) cc_final: 0.8870 (tppt) REVERT: q 258 TYR cc_start: 0.8094 (t80) cc_final: 0.7836 (t80) REVERT: q 400 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8796 (p0) REVERT: q 437 LYS cc_start: 0.4515 (pttm) cc_final: 0.3234 (mptt) REVERT: t 238 GLN cc_start: 0.8818 (mm110) cc_final: 0.8322 (mm110) REVERT: t 276 GLU cc_start: 0.7440 (pm20) cc_final: 0.7220 (pm20) REVERT: t 288 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7885 (ttpp) outliers start: 211 outliers final: 141 residues processed: 1660 average time/residue: 1.0597 time to fit residues: 3037.2454 Evaluate side-chains 1568 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1417 time to evaluate : 6.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 334 LYS Chi-restraints excluded: chain b residue 414 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 441 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 78 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 59 ASN Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 58 ASP Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 81 GLN Chi-restraints excluded: chain W residue 37 TYR Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 139 ARG Chi-restraints excluded: chain Z residue 65 ARG Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 120 GLU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain K residue 167 ARG Chi-restraints excluded: chain K residue 214 ILE Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 181 VAL Chi-restraints excluded: chain n residue 214 ASP Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain o residue 160 HIS Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 400 ASP Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 306 THR Chi-restraints excluded: chain t residue 309 VAL Chi-restraints excluded: chain s residue 21 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 935 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 552 optimal weight: 7.9990 chunk 708 optimal weight: 30.0000 chunk 549 optimal weight: 9.9990 chunk 816 optimal weight: 10.0000 chunk 541 optimal weight: 0.3980 chunk 966 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 589 optimal weight: 0.7980 chunk 446 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 237 GLN C 322 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 159 GLN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN H 156 GLN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN u 37 HIS ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 GLN O 182 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 ASN V 81 GLN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN y 187 ASN ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 113 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.546 129032 Z= 0.267 Angle : 0.683 39.676 188245 Z= 0.347 Chirality : 0.038 0.867 23443 Planarity : 0.005 0.104 13065 Dihedral : 23.201 179.899 52984 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 3.84 % Allowed : 26.59 % Favored : 69.57 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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: -1.54 (0.10), residues: 7234 helix: 0.10 (0.10), residues: 2786 sheet: -1.38 (0.16), residues: 871 loop : -1.85 (0.10), residues: 3577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 9 HIS 0.011 0.001 HIS C 311 PHE 0.028 0.002 PHE W 206 TYR 0.037 0.002 TYR W 115 ARG 0.012 0.001 ARG N 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1718 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1477 time to evaluate : 6.680 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: a 85 ASP cc_start: 0.8109 (p0) cc_final: 0.7558 (p0) REVERT: a 90 TYR cc_start: 0.8982 (m-80) cc_final: 0.8575 (m-80) REVERT: a 120 ASN cc_start: 0.8168 (t0) cc_final: 0.7775 (t0) REVERT: B 116 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7589 (ttp-170) REVERT: B 196 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.8248 (ttp80) REVERT: b 59 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8131 (tm-30) REVERT: b 211 TYR cc_start: 0.5989 (t80) cc_final: 0.5205 (t80) REVERT: b 232 MET cc_start: 0.1311 (mpp) cc_final: -0.1238 (mmm) REVERT: b 284 MET cc_start: 0.3346 (OUTLIER) cc_final: 0.2389 (mmm) REVERT: C 308 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8359 (ttpt) REVERT: c 41 LEU cc_start: 0.7317 (mt) cc_final: 0.6653 (mt) REVERT: d 27 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8306 (mtmm) REVERT: E 13 GLU cc_start: 0.7239 (mp0) cc_final: 0.6819 (mp0) REVERT: E 61 ASN cc_start: 0.8734 (m-40) cc_final: 0.8374 (m-40) REVERT: E 97 ASN cc_start: 0.8295 (p0) cc_final: 0.8026 (p0) REVERT: E 137 ASP cc_start: 0.8396 (m-30) cc_final: 0.8054 (m-30) REVERT: e 34 LYS cc_start: 0.8351 (mttm) cc_final: 0.8149 (mttm) REVERT: e 111 ARG cc_start: 0.8749 (tpt-90) cc_final: 0.8344 (tpt-90) REVERT: F 168 ILE cc_start: 0.9146 (mm) cc_final: 0.8888 (mt) REVERT: G 44 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7290 (mtt180) REVERT: G 107 GLU cc_start: 0.7684 (tp30) cc_final: 0.7445 (tp30) REVERT: G 206 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7303 (pp20) REVERT: g 87 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (tp30) REVERT: g 97 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7350 (mm-30) REVERT: H 5 GLN cc_start: 0.8906 (pm20) cc_final: 0.8688 (pm20) REVERT: H 23 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7162 (mpp80) REVERT: H 156 GLN cc_start: 0.8790 (mm110) cc_final: 0.7692 (mm-40) REVERT: h 26 LYS cc_start: 0.8841 (mttt) cc_final: 0.8385 (mmtp) REVERT: h 90 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.5905 (mtm-85) REVERT: i 38 LYS cc_start: 0.8178 (mttm) cc_final: 0.7871 (mptt) REVERT: i 53 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7661 (p90) REVERT: i 66 GLU cc_start: 0.8185 (pp20) cc_final: 0.7725 (pp20) REVERT: i 82 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7180 (mtp85) REVERT: j 73 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7889 (mtm180) REVERT: k 63 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8841 (mtmm) REVERT: L 129 ASN cc_start: 0.7752 (p0) cc_final: 0.7386 (p0) REVERT: l 13 MET cc_start: 0.7211 (mmm) cc_final: 0.6607 (mmt) REVERT: M 41 GLN cc_start: 0.8249 (mm110) cc_final: 0.7932 (mm-40) REVERT: M 114 ASP cc_start: 0.7233 (t70) cc_final: 0.6998 (t70) REVERT: M 121 MET cc_start: 0.8913 (ttm) cc_final: 0.8415 (ttt) REVERT: p 27 LYS cc_start: 0.8436 (ptpt) cc_final: 0.8209 (ptmt) REVERT: p 36 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7444 (mtp-110) REVERT: u 29 PHE cc_start: 0.8024 (m-10) cc_final: 0.7808 (m-10) REVERT: u 40 PHE cc_start: 0.8711 (t80) cc_final: 0.8510 (t80) REVERT: u 93 MET cc_start: 0.7360 (mpp) cc_final: 0.6953 (mpp) REVERT: u 101 GLN cc_start: 0.9200 (mt0) cc_final: 0.8925 (mt0) REVERT: u 107 PHE cc_start: 0.7962 (t80) cc_final: 0.7752 (t80) REVERT: P 92 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7785 (tm-30) REVERT: r 12 LYS cc_start: 0.8987 (ptpt) cc_final: 0.8782 (pttp) REVERT: r 23 ARG cc_start: 0.8983 (tpp80) cc_final: 0.8771 (tpp80) REVERT: S 89 ASN cc_start: 0.8502 (m110) cc_final: 0.8034 (m-40) REVERT: T 156 TYR cc_start: 0.5338 (t80) cc_final: 0.4971 (t80) REVERT: U 28 PHE cc_start: 0.6090 (t80) cc_final: 0.5873 (t80) REVERT: U 77 LYS cc_start: 0.8773 (tttt) cc_final: 0.8441 (ttmt) REVERT: U 99 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8838 (mtpp) REVERT: U 102 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7318 (tm-30) REVERT: V 54 LEU cc_start: 0.8171 (tp) cc_final: 0.7682 (tt) REVERT: V 57 MET cc_start: 0.7518 (ttt) cc_final: 0.7041 (mtm) REVERT: V 63 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7376 (mmmt) REVERT: V 108 GLU cc_start: 0.8319 (mp0) cc_final: 0.7798 (mp0) REVERT: V 124 ASP cc_start: 0.8524 (t0) cc_final: 0.8305 (t0) REVERT: X 12 LYS cc_start: 0.8668 (mttm) cc_final: 0.8465 (ttmm) REVERT: X 60 TYR cc_start: 0.8279 (m-80) cc_final: 0.7988 (m-80) REVERT: Y 67 GLU cc_start: 0.8022 (pm20) cc_final: 0.7801 (pm20) REVERT: y 7 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7788 (t80) REVERT: y 34 PHE cc_start: 0.7198 (t80) cc_final: 0.6719 (t80) REVERT: y 77 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (m) REVERT: y 101 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7120 (pp) REVERT: y 139 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: Z 48 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.7972 (mtp180) REVERT: Z 65 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8461 (ttt180) REVERT: Z 108 GLU cc_start: 0.7569 (pp20) cc_final: 0.6506 (pp20) REVERT: Z 109 GLU cc_start: 0.8447 (pm20) cc_final: 0.7769 (pm20) REVERT: Z 123 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8848 (mm110) REVERT: K 260 LEU cc_start: 0.8013 (mm) cc_final: 0.7769 (mm) REVERT: K 314 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7312 (tt) REVERT: K 327 MET cc_start: 0.8044 (ppp) cc_final: 0.7010 (ppp) REVERT: K 365 ASN cc_start: 0.7516 (p0) cc_final: 0.7118 (p0) REVERT: n 29 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7849 (mp) REVERT: n 150 GLN cc_start: 0.8451 (mp10) cc_final: 0.8241 (mp10) REVERT: n 216 ARG cc_start: 0.6007 (mtt-85) cc_final: 0.5406 (mtm-85) REVERT: n 248 LEU cc_start: 0.7868 (pt) cc_final: 0.7631 (pt) REVERT: o 134 TYR cc_start: 0.7987 (p90) cc_final: 0.7626 (p90) REVERT: o 136 PHE cc_start: 0.7484 (m-10) cc_final: 0.7239 (m-10) REVERT: o 146 MET cc_start: 0.8640 (ttm) cc_final: 0.8042 (tpp) REVERT: o 150 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8101 (mm-30) REVERT: o 155 TYR cc_start: 0.8196 (t80) cc_final: 0.7531 (t80) REVERT: q 258 TYR cc_start: 0.8098 (t80) cc_final: 0.7751 (t80) REVERT: q 400 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8800 (p0) REVERT: q 437 LYS cc_start: 0.4471 (pttm) cc_final: 0.3211 (mptt) REVERT: t 238 GLN cc_start: 0.8784 (mm110) cc_final: 0.8224 (mm110) REVERT: t 288 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7983 (ttpp) REVERT: s 33 MET cc_start: 0.8581 (tpp) cc_final: 0.8359 (ppp) outliers start: 241 outliers final: 181 residues processed: 1620 average time/residue: 1.0445 time to fit residues: 2913.2185 Evaluate side-chains 1599 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1401 time to evaluate : 6.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 414 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 90 ARG Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 73 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 58 ASP Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 145 PHE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain W residue 37 TYR Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain y residue 7 PHE Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 57 ARG Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 139 ARG Chi-restraints excluded: chain y residue 142 ILE Chi-restraints excluded: chain y residue 148 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 120 GLU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain K residue 167 ARG Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 29 LEU Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 181 VAL Chi-restraints excluded: chain n residue 214 ASP Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain o residue 161 LEU Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain q residue 400 ASP Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 263 VAL Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 306 THR Chi-restraints excluded: chain t residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 598 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 577 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 614 optimal weight: 10.0000 chunk 658 optimal weight: 6.9990 chunk 477 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 759 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN b 155 GLN C 175 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN H 8 GLN L 103 ASN L 114 GLN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 37 HIS ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 GLN P 55 GLN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 GLN S 68 HIS ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS U 87 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN y 50 HIS ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 165 GLN o 113 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 26 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.529 129032 Z= 0.470 Angle : 0.818 38.765 188245 Z= 0.413 Chirality : 0.044 0.467 23443 Planarity : 0.006 0.102 13065 Dihedral : 23.306 179.461 52984 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.71 % Favored : 91.19 % Rotamer: Outliers : 4.14 % Allowed : 27.05 % Favored : 68.80 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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: -1.74 (0.09), residues: 7234 helix: -0.07 (0.10), residues: 2785 sheet: -1.43 (0.16), residues: 864 loop : -1.98 (0.10), residues: 3585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 9 HIS 0.014 0.001 HIS C 311 PHE 0.036 0.002 PHE K 392 TYR 0.031 0.003 TYR F 51 ARG 0.015 0.001 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1461 time to evaluate : 6.608 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: a 85 ASP cc_start: 0.8157 (p0) cc_final: 0.7579 (p0) REVERT: a 90 TYR cc_start: 0.8962 (m-80) cc_final: 0.8550 (m-80) REVERT: a 120 ASN cc_start: 0.8251 (t0) cc_final: 0.7906 (t0) REVERT: B 196 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8341 (ttp80) REVERT: b 51 LYS cc_start: 0.9221 (tttt) cc_final: 0.8966 (tttm) REVERT: b 59 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8080 (tm-30) REVERT: b 232 MET cc_start: 0.1663 (mpp) cc_final: -0.0854 (mmm) REVERT: C 177 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: c 41 LEU cc_start: 0.7305 (mt) cc_final: 0.6613 (mt) REVERT: d 25 PHE cc_start: 0.8761 (m-10) cc_final: 0.8448 (m-10) REVERT: d 27 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8175 (mtmm) REVERT: E 13 GLU cc_start: 0.7474 (mp0) cc_final: 0.7120 (mp0) REVERT: E 33 SER cc_start: 0.8429 (p) cc_final: 0.8165 (t) REVERT: E 61 ASN cc_start: 0.8789 (m-40) cc_final: 0.8383 (m-40) REVERT: E 97 ASN cc_start: 0.8328 (p0) cc_final: 0.8019 (p0) REVERT: E 137 ASP cc_start: 0.8445 (m-30) cc_final: 0.8112 (m-30) REVERT: F 51 TYR cc_start: 0.8125 (m-80) cc_final: 0.7842 (m-80) REVERT: F 168 ILE cc_start: 0.9230 (mm) cc_final: 0.8897 (mt) REVERT: f 44 TYR cc_start: 0.8162 (m-80) cc_final: 0.7924 (m-80) REVERT: G 206 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7412 (pp20) REVERT: g 13 TYR cc_start: 0.8979 (m-80) cc_final: 0.7879 (m-80) REVERT: g 41 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8557 (mmm-85) REVERT: g 87 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8378 (tp30) REVERT: g 93 PHE cc_start: 0.8528 (t80) cc_final: 0.7944 (t80) REVERT: H 1 MET cc_start: 0.7991 (ptp) cc_final: 0.7390 (ptt) REVERT: H 23 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7821 (mpp80) REVERT: H 156 GLN cc_start: 0.8836 (mm110) cc_final: 0.7833 (mm-40) REVERT: h 26 LYS cc_start: 0.8899 (mttt) cc_final: 0.8331 (mmtp) REVERT: h 90 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6477 (mtm-85) REVERT: i 38 LYS cc_start: 0.8229 (mttm) cc_final: 0.7924 (mptt) REVERT: j 68 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8246 (ttpt) REVERT: j 73 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8192 (mtm180) REVERT: k 63 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8882 (mtmm) REVERT: L 93 ILE cc_start: 0.8895 (mm) cc_final: 0.8606 (tp) REVERT: L 129 ASN cc_start: 0.7818 (p0) cc_final: 0.7363 (p0) REVERT: l 13 MET cc_start: 0.7619 (mmm) cc_final: 0.7053 (mmt) REVERT: p 27 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8212 (ptmt) REVERT: u 101 GLN cc_start: 0.9082 (mt0) cc_final: 0.8807 (mt0) REVERT: u 107 PHE cc_start: 0.7923 (t80) cc_final: 0.7709 (t80) REVERT: P 112 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7973 (tp) REVERT: R 100 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7649 (mtp180) REVERT: r 12 LYS cc_start: 0.9025 (ptpt) cc_final: 0.8821 (pttp) REVERT: S 89 ASN cc_start: 0.8588 (m110) cc_final: 0.8124 (m-40) REVERT: S 139 TYR cc_start: 0.8655 (p90) cc_final: 0.8401 (p90) REVERT: U 44 GLU cc_start: 0.8225 (pm20) cc_final: 0.7884 (pm20) REVERT: U 102 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7361 (tm-30) REVERT: V 54 LEU cc_start: 0.8255 (tp) cc_final: 0.7886 (tt) REVERT: V 57 MET cc_start: 0.7559 (ttt) cc_final: 0.7140 (mtm) REVERT: V 63 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7706 (mmmt) REVERT: V 124 ASP cc_start: 0.8640 (t0) cc_final: 0.8359 (t0) REVERT: y 34 PHE cc_start: 0.7248 (t80) cc_final: 0.6790 (t80) REVERT: y 139 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7743 (ttm170) REVERT: Z 48 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8103 (mtp180) REVERT: Z 123 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8864 (mm110) REVERT: K 314 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7524 (tt) REVERT: K 327 MET cc_start: 0.8109 (ppp) cc_final: 0.7135 (ppp) REVERT: K 365 ASN cc_start: 0.7581 (p0) cc_final: 0.7152 (p0) REVERT: n 150 GLN cc_start: 0.8668 (mp10) cc_final: 0.8398 (mp10) REVERT: n 160 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8683 (mm-40) REVERT: n 216 ARG cc_start: 0.6134 (mtt-85) cc_final: 0.5429 (mtm-85) REVERT: n 248 LEU cc_start: 0.7932 (pt) cc_final: 0.7679 (pt) REVERT: o 94 TYR cc_start: 0.7806 (t80) cc_final: 0.7261 (t80) REVERT: o 134 TYR cc_start: 0.7999 (p90) cc_final: 0.7602 (p90) REVERT: o 146 MET cc_start: 0.8649 (ttm) cc_final: 0.8096 (tpp) REVERT: o 150 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8242 (mm-30) REVERT: o 155 TYR cc_start: 0.8231 (t80) cc_final: 0.7585 (t80) REVERT: o 179 TYR cc_start: 0.7543 (m-10) cc_final: 0.7285 (m-10) REVERT: q 258 TYR cc_start: 0.8145 (t80) cc_final: 0.7915 (t80) REVERT: q 262 ILE cc_start: 0.8976 (mm) cc_final: 0.6604 (mt) REVERT: q 266 MET cc_start: 0.7557 (mmm) cc_final: 0.7040 (mmt) REVERT: q 400 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.8871 (p0) REVERT: q 421 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7643 (ttp80) REVERT: q 437 LYS cc_start: 0.4244 (pttm) cc_final: 0.2982 (mptt) REVERT: t 288 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8138 (ttpp) outliers start: 260 outliers final: 195 residues processed: 1608 average time/residue: 1.0595 time to fit residues: 2934.6238 Evaluate side-chains 1611 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1404 time to evaluate : 6.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 414 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 441 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 59 ASN Chi-restraints excluded: chain h residue 90 ARG Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 57 LEU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 73 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 58 ASP Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 145 PHE Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain W residue 37 TYR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain y residue 15 VAL Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 57 ARG Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 139 ARG Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain z residue 18 ARG Chi-restraints excluded: chain K residue 167 ARG Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 64 TYR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 181 VAL Chi-restraints excluded: chain n residue 214 ASP Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain o residue 113 GLN Chi-restraints excluded: chain o residue 161 LEU Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain q residue 400 ASP Chi-restraints excluded: chain q residue 432 ARG Chi-restraints excluded: chain t residue 153 VAL Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 263 VAL Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 291 GLN Chi-restraints excluded: chain t residue 306 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 879 optimal weight: 6.9990 chunk 926 optimal weight: 4.9990 chunk 844 optimal weight: 10.0000 chunk 900 optimal weight: 0.9980 chunk 925 optimal weight: 1.9990 chunk 542 optimal weight: 0.9980 chunk 392 optimal weight: 30.0000 chunk 707 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 814 optimal weight: 50.0000 chunk 852 optimal weight: 20.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN b 177 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN L 120 GLN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 56 GLN N 175 ASN u 37 HIS ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN T 122 GLN U 87 ASN ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 232 ASN ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN y 50 HIS ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.524 129032 Z= 0.319 Angle : 0.732 36.968 188245 Z= 0.372 Chirality : 0.040 0.461 23443 Planarity : 0.005 0.104 13065 Dihedral : 23.290 179.926 52984 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.10 % Favored : 91.80 % Rotamer: Outliers : 3.60 % Allowed : 28.04 % Favored : 68.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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: -1.62 (0.10), residues: 7234 helix: 0.03 (0.10), residues: 2777 sheet: -1.48 (0.16), residues: 858 loop : -1.87 (0.10), residues: 3599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 9 HIS 0.012 0.001 HIS C 311 PHE 0.026 0.002 PHE n 433 TYR 0.033 0.002 TYR t 184 ARG 0.019 0.001 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1466 time to evaluate : 6.585 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: A 42 ARG cc_start: 0.7904 (tmm-80) cc_final: 0.7545 (tmm-80) REVERT: a 85 ASP cc_start: 0.8136 (p0) cc_final: 0.7590 (p0) REVERT: a 90 TYR cc_start: 0.8957 (m-80) cc_final: 0.8410 (m-80) REVERT: a 120 ASN cc_start: 0.8259 (t0) cc_final: 0.7905 (t0) REVERT: a 126 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8545 (mptt) REVERT: B 116 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7724 (ttp-170) REVERT: B 196 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.8288 (ttp80) REVERT: b 59 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8047 (tm-30) REVERT: b 211 TYR cc_start: 0.5978 (t80) cc_final: 0.5274 (t80) REVERT: b 232 MET cc_start: 0.1445 (mpp) cc_final: -0.0972 (mmm) REVERT: C 160 GLN cc_start: 0.8280 (mm110) cc_final: 0.8075 (mm110) REVERT: c 41 LEU cc_start: 0.7311 (mt) cc_final: 0.6648 (mt) REVERT: d 27 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8325 (mtmm) REVERT: E 13 GLU cc_start: 0.7508 (mp0) cc_final: 0.7123 (mp0) REVERT: E 28 GLN cc_start: 0.7480 (tt0) cc_final: 0.6943 (tt0) REVERT: E 61 ASN cc_start: 0.8740 (m-40) cc_final: 0.8309 (m-40) REVERT: E 97 ASN cc_start: 0.8308 (p0) cc_final: 0.7969 (p0) REVERT: E 137 ASP cc_start: 0.8392 (m-30) cc_final: 0.8044 (m-30) REVERT: F 51 TYR cc_start: 0.7984 (m-80) cc_final: 0.7465 (m-80) REVERT: F 168 ILE cc_start: 0.9191 (mm) cc_final: 0.8880 (mt) REVERT: F 179 LEU cc_start: 0.8756 (pt) cc_final: 0.8436 (tt) REVERT: G 107 GLU cc_start: 0.7524 (tp30) cc_final: 0.7139 (tp30) REVERT: G 206 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7370 (pp20) REVERT: G 222 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7167 (m-10) REVERT: g 13 TYR cc_start: 0.8891 (m-80) cc_final: 0.7741 (m-80) REVERT: g 87 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8359 (tp30) REVERT: g 97 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6934 (mm-30) REVERT: H 1 MET cc_start: 0.8074 (ptp) cc_final: 0.7483 (ptt) REVERT: H 23 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7625 (mpp80) REVERT: H 156 GLN cc_start: 0.8712 (mm110) cc_final: 0.7714 (mm-40) REVERT: h 26 LYS cc_start: 0.8819 (mttt) cc_final: 0.8426 (mmtp) REVERT: h 81 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8632 (mtp85) REVERT: h 116 TYR cc_start: 0.8602 (p90) cc_final: 0.8219 (p90) REVERT: i 38 LYS cc_start: 0.8177 (mttm) cc_final: 0.7882 (mptt) REVERT: i 66 GLU cc_start: 0.8129 (pp20) cc_final: 0.7774 (pp20) REVERT: j 73 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8101 (mtm180) REVERT: k 63 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8815 (mtmm) REVERT: L 129 ASN cc_start: 0.7787 (p0) cc_final: 0.7376 (p0) REVERT: l 13 MET cc_start: 0.7463 (mmm) cc_final: 0.6864 (mmt) REVERT: M 41 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7960 (mm-40) REVERT: p 24 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7538 (mtm-85) REVERT: p 27 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8185 (ptmt) REVERT: u 40 PHE cc_start: 0.8732 (t80) cc_final: 0.8504 (t80) REVERT: u 93 MET cc_start: 0.7413 (mpp) cc_final: 0.7106 (mtm) REVERT: u 101 GLN cc_start: 0.9057 (mt0) cc_final: 0.8769 (mt0) REVERT: O 89 SER cc_start: 0.8400 (p) cc_final: 0.8045 (p) REVERT: R 104 ARG cc_start: 0.8608 (ptp90) cc_final: 0.8193 (ptp90) REVERT: R 120 TYR cc_start: 0.8216 (t80) cc_final: 0.7998 (t80) REVERT: r 3 GLN cc_start: 0.6362 (mp10) cc_final: 0.5939 (mp10) REVERT: r 12 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8783 (pttp) REVERT: S 89 ASN cc_start: 0.8507 (m110) cc_final: 0.8125 (m110) REVERT: T 116 ARG cc_start: 0.8129 (ttm110) cc_final: 0.7780 (mtt-85) REVERT: T 122 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: T 156 TYR cc_start: 0.5441 (t80) cc_final: 0.5019 (t80) REVERT: U 44 GLU cc_start: 0.8171 (pm20) cc_final: 0.7794 (pm20) REVERT: U 102 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7336 (tm-30) REVERT: V 54 LEU cc_start: 0.8200 (tp) cc_final: 0.7861 (tt) REVERT: V 57 MET cc_start: 0.7563 (ttt) cc_final: 0.7142 (mtm) REVERT: V 108 GLU cc_start: 0.8464 (mp0) cc_final: 0.7935 (mp0) REVERT: V 124 ASP cc_start: 0.8869 (t0) cc_final: 0.8450 (t0) REVERT: y 34 PHE cc_start: 0.7314 (t80) cc_final: 0.6804 (t80) REVERT: Z 48 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8059 (mtp180) REVERT: Z 123 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8906 (mm-40) REVERT: K 260 LEU cc_start: 0.8136 (mm) cc_final: 0.7933 (tp) REVERT: K 327 MET cc_start: 0.8192 (ppp) cc_final: 0.7315 (ppp) REVERT: K 365 ASN cc_start: 0.7650 (p0) cc_final: 0.7219 (p0) REVERT: n 150 GLN cc_start: 0.8612 (mp10) cc_final: 0.8381 (mp10) REVERT: n 160 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8665 (mm-40) REVERT: n 216 ARG cc_start: 0.5956 (mtt-85) cc_final: 0.5350 (mtm-85) REVERT: n 248 LEU cc_start: 0.7814 (pt) cc_final: 0.7560 (pt) REVERT: o 94 TYR cc_start: 0.7795 (t80) cc_final: 0.7301 (t80) REVERT: o 134 TYR cc_start: 0.7986 (p90) cc_final: 0.7585 (p90) REVERT: o 146 MET cc_start: 0.8635 (ttm) cc_final: 0.7986 (tpp) REVERT: o 150 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8213 (mm-30) REVERT: o 155 TYR cc_start: 0.8230 (t80) cc_final: 0.7604 (t80) REVERT: q 258 TYR cc_start: 0.7982 (t80) cc_final: 0.7663 (t80) REVERT: q 400 ASP cc_start: 0.9269 (OUTLIER) cc_final: 0.8797 (p0) REVERT: q 421 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7492 (ttp80) REVERT: q 437 LYS cc_start: 0.4295 (pttm) cc_final: 0.3054 (mptt) REVERT: t 288 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8046 (ttpp) outliers start: 226 outliers final: 197 residues processed: 1603 average time/residue: 1.1580 time to fit residues: 3207.9416 Evaluate side-chains 1614 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1408 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain a residue 84 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 414 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 441 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 78 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 222 PHE Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 59 ASN Chi-restraints excluded: chain h residue 81 ARG Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 73 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 145 PHE Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain T residue 122 GLN Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain U residue 103 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 37 TYR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain y residue 15 VAL Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 57 ARG Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 142 ILE Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain K residue 167 ARG Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 64 TYR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 181 VAL Chi-restraints excluded: chain n residue 214 ASP Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain o residue 161 LEU Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain q residue 400 ASP Chi-restraints excluded: chain q residue 432 ARG Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 263 VAL Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 291 GLN Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain t residue 306 THR Chi-restraints excluded: chain t residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 897 optimal weight: 8.9990 chunk 591 optimal weight: 10.0000 chunk 952 optimal weight: 0.7980 chunk 581 optimal weight: 4.9990 chunk 451 optimal weight: 9.9990 chunk 662 optimal weight: 10.0000 chunk 999 optimal weight: 20.0000 chunk 919 optimal weight: 10.0000 chunk 795 optimal weight: 40.0000 chunk 82 optimal weight: 40.0000 chunk 614 optimal weight: 10.0000 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS C 9 HIS ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN g 14 ASN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN u 37 HIS ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS U 87 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 110 ASN ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN K 217 ASN ** K 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 191 ASN ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.522 129032 Z= 0.551 Angle : 0.883 36.059 188245 Z= 0.445 Chirality : 0.047 0.462 23443 Planarity : 0.006 0.111 13065 Dihedral : 23.381 179.945 52984 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.59 % Favored : 90.30 % Rotamer: Outliers : 3.89 % Allowed : 28.20 % Favored : 67.91 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.09), residues: 7234 helix: -0.22 (0.10), residues: 2770 sheet: -1.61 (0.16), residues: 878 loop : -2.05 (0.10), residues: 3586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 9 HIS 0.012 0.002 HIS C 311 PHE 0.055 0.003 PHE u 107 TYR 0.034 0.003 TYR c 23 ARG 0.018 0.001 ARG H 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14468 Ramachandran restraints generated. 7234 Oldfield, 0 Emsley, 7234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1452 time to evaluate : 6.613 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: a 85 ASP cc_start: 0.8127 (p0) cc_final: 0.7412 (p0) REVERT: a 120 ASN cc_start: 0.8359 (t0) cc_final: 0.7975 (t0) REVERT: a 128 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7763 (ttm110) REVERT: B 178 LEU cc_start: 0.8528 (mm) cc_final: 0.8088 (mm) REVERT: B 196 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8375 (ttp80) REVERT: B 226 PHE cc_start: 0.7278 (t80) cc_final: 0.6747 (t80) REVERT: B 261 MET cc_start: 0.7227 (mmm) cc_final: 0.7005 (tpp) REVERT: b 59 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8075 (tm-30) REVERT: b 193 ASP cc_start: 0.6250 (p0) cc_final: 0.5493 (m-30) REVERT: b 232 MET cc_start: 0.1611 (mpp) cc_final: -0.0424 (mmm) REVERT: C 160 GLN cc_start: 0.8381 (mm110) cc_final: 0.8166 (mm110) REVERT: c 41 LEU cc_start: 0.7325 (mt) cc_final: 0.6618 (mt) REVERT: d 25 PHE cc_start: 0.8702 (m-10) cc_final: 0.8384 (m-10) REVERT: E 13 GLU cc_start: 0.7497 (mp0) cc_final: 0.7147 (mp0) REVERT: E 28 GLN cc_start: 0.7468 (tt0) cc_final: 0.6821 (tt0) REVERT: E 61 ASN cc_start: 0.8745 (m-40) cc_final: 0.8301 (m-40) REVERT: E 97 ASN cc_start: 0.8329 (p0) cc_final: 0.7930 (p0) REVERT: E 137 ASP cc_start: 0.8434 (m-30) cc_final: 0.8094 (m-30) REVERT: e 123 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8008 (ttpt) REVERT: F 51 TYR cc_start: 0.8006 (m-80) cc_final: 0.7792 (m-80) REVERT: F 168 ILE cc_start: 0.9247 (mm) cc_final: 0.8934 (mt) REVERT: f 44 TYR cc_start: 0.8238 (m-80) cc_final: 0.8015 (m-80) REVERT: G 44 ARG cc_start: 0.8036 (mtt90) cc_final: 0.6806 (mtt180) REVERT: G 107 GLU cc_start: 0.7575 (tp30) cc_final: 0.7209 (tp30) REVERT: G 206 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: G 222 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: g 13 TYR cc_start: 0.9005 (m-80) cc_final: 0.7886 (m-80) REVERT: g 87 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: H 1 MET cc_start: 0.8029 (ptp) cc_final: 0.7555 (ptt) REVERT: H 23 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7964 (mpp80) REVERT: H 52 LEU cc_start: 0.8269 (tt) cc_final: 0.7959 (tp) REVERT: H 156 GLN cc_start: 0.8836 (mm110) cc_final: 0.8149 (mm-40) REVERT: h 26 LYS cc_start: 0.8849 (mttt) cc_final: 0.8631 (mmtp) REVERT: h 116 TYR cc_start: 0.8773 (p90) cc_final: 0.8488 (p90) REVERT: i 20 MET cc_start: 0.6970 (mtm) cc_final: 0.6680 (mpp) REVERT: i 38 LYS cc_start: 0.8334 (mttm) cc_final: 0.8010 (mptt) REVERT: j 68 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8109 (ttpt) REVERT: j 73 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8225 (mtm180) REVERT: k 63 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8818 (mtmm) REVERT: L 129 ASN cc_start: 0.7830 (p0) cc_final: 0.7375 (p0) REVERT: l 13 MET cc_start: 0.7639 (mmm) cc_final: 0.7017 (mmt) REVERT: l 36 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7228 (mmm160) REVERT: u 93 MET cc_start: 0.7425 (mpp) cc_final: 0.7202 (mtm) REVERT: u 101 GLN cc_start: 0.9052 (mt0) cc_final: 0.8751 (mt0) REVERT: O 48 PHE cc_start: 0.8091 (t80) cc_final: 0.7737 (t80) REVERT: P 39 TRP cc_start: 0.8407 (m100) cc_final: 0.8195 (m100) REVERT: R 104 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8184 (ptp90) REVERT: R 120 TYR cc_start: 0.8308 (t80) cc_final: 0.8074 (t80) REVERT: r 3 GLN cc_start: 0.6883 (mp10) cc_final: 0.6065 (mp10) REVERT: S 71 LYS cc_start: 0.9181 (tptt) cc_final: 0.8513 (tttt) REVERT: S 89 ASN cc_start: 0.8628 (m110) cc_final: 0.8239 (m-40) REVERT: S 139 TYR cc_start: 0.8726 (p90) cc_final: 0.8503 (p90) REVERT: T 116 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7781 (mtt-85) REVERT: U 44 GLU cc_start: 0.8345 (pm20) cc_final: 0.7931 (pm20) REVERT: U 102 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7269 (tm-30) REVERT: V 54 LEU cc_start: 0.8282 (tp) cc_final: 0.7904 (tt) REVERT: V 124 ASP cc_start: 0.8920 (t0) cc_final: 0.8569 (t0) REVERT: W 179 LYS cc_start: 0.4808 (tptt) cc_final: 0.4299 (tptt) REVERT: y 34 PHE cc_start: 0.7213 (t80) cc_final: 0.6815 (t80) REVERT: Z 40 HIS cc_start: 0.8126 (p-80) cc_final: 0.7652 (p-80) REVERT: Z 48 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8129 (mtp180) REVERT: K 259 ILE cc_start: 0.8980 (tp) cc_final: 0.8729 (tp) REVERT: K 327 MET cc_start: 0.8260 (ppp) cc_final: 0.7405 (ppp) REVERT: K 365 ASN cc_start: 0.7681 (p0) cc_final: 0.7245 (p0) REVERT: n 150 GLN cc_start: 0.8665 (mp10) cc_final: 0.8387 (mp10) REVERT: n 216 ARG cc_start: 0.6235 (mtt-85) cc_final: 0.5572 (mtm-85) REVERT: n 248 LEU cc_start: 0.7855 (pt) cc_final: 0.7630 (pt) REVERT: o 94 TYR cc_start: 0.7939 (t80) cc_final: 0.7401 (t80) REVERT: o 134 TYR cc_start: 0.7935 (p90) cc_final: 0.7476 (p90) REVERT: o 146 MET cc_start: 0.8734 (ttm) cc_final: 0.8454 (tpp) REVERT: o 155 TYR cc_start: 0.8343 (t80) cc_final: 0.7655 (t80) REVERT: q 400 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8768 (p0) REVERT: q 437 LYS cc_start: 0.4450 (pttm) cc_final: 0.3131 (mptt) REVERT: t 54 LYS cc_start: 0.3523 (tmtt) cc_final: 0.3183 (tmtt) REVERT: t 288 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8215 (ttpp) outliers start: 244 outliers final: 199 residues processed: 1594 average time/residue: 1.0353 time to fit residues: 2841.1610 Evaluate side-chains 1612 residues out of total 6282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1405 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain a residue 84 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 441 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 69 TYR Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 78 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 222 PHE Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 59 ASN Chi-restraints excluded: chain h residue 90 ARG Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 72 ARG Chi-restraints excluded: chain j residue 73 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 145 PHE Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 70 ASN Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 83 TYR Chi-restraints excluded: chain U residue 103 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain W residue 37 TYR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain y residue 15 VAL Chi-restraints excluded: chain y residue 38 PHE Chi-restraints excluded: chain y residue 57 ARG Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 120 GLU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain K residue 167 ARG Chi-restraints excluded: chain K residue 266 LYS Chi-restraints excluded: chain K residue 313 ILE Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 36 CYS Chi-restraints excluded: chain n residue 64 TYR Chi-restraints excluded: chain n residue 105 LEU Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 125 PHE Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 181 VAL Chi-restraints excluded: chain n residue 191 ASN Chi-restraints excluded: chain n residue 214 ASP Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 360 PHE Chi-restraints excluded: chain n residue 367 VAL Chi-restraints excluded: chain o residue 160 HIS Chi-restraints excluded: chain o residue 161 LEU Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 199 ASN Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain q residue 400 ASP Chi-restraints excluded: chain q residue 432 ARG Chi-restraints excluded: chain t residue 153 VAL Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 256 THR Chi-restraints excluded: chain t residue 263 VAL Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain t residue 306 THR Chi-restraints excluded: chain t residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1003 random chunks: chunk 487 optimal weight: 9.9990 chunk 632 optimal weight: 0.6980 chunk 847 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 733 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 796 optimal weight: 40.0000 chunk 333 optimal weight: 6.9990 chunk 818 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 14 ASN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 37 HIS ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 120 GLN ** Z 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 113 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.152856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112388 restraints weight = 251889.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110697 restraints weight = 229286.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113132 restraints weight = 142545.336| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.521 129032 Z= 0.422 Angle : 0.910 59.181 188245 Z= 0.472 Chirality : 0.044 1.088 23443 Planarity : 0.007 0.161 13065 Dihedral : 23.390 179.874 52984 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.57 % Favored : 90.30 % Rotamer: Outliers : 3.83 % Allowed : 28.58 % Favored : 67.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.07 % Twisted Proline : 1.08 % Twisted General : 0.13 % 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: -1.94 (0.09), residues: 7234 helix: -0.24 (0.10), residues: 2776 sheet: -1.63 (0.16), residues: 879 loop : -2.06 (0.10), residues: 3579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 9 HIS 0.046 0.002 HIS q 222 PHE 0.071 0.003 PHE W 27 TYR 0.090 0.003 TYR K 300 ARG 0.054 0.001 ARG z 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39098.75 seconds wall clock time: 680 minutes 5.31 seconds (40805.31 seconds total)