Starting phenix.real_space_refine on Fri Mar 15 16:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzg_26910/03_2024/7uzg_26910_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzg_26910/03_2024/7uzg_26910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzg_26910/03_2024/7uzg_26910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzg_26910/03_2024/7uzg_26910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzg_26910/03_2024/7uzg_26910_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzg_26910/03_2024/7uzg_26910_updated.pdb" } resolution = 3.7 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= 1.329 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 388 5.16 5 C 44688 2.51 5 N 11744 2.21 5 O 12973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 502": "OE1" <-> "OE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 502": "OE1" <-> "OE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 41": "OE1" <-> "OE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "L PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 231": "OD1" <-> "OD2" Residue "R TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 427": "OE1" <-> "OE2" Residue "a GLU 438": "OE1" <-> "OE2" Residue "a TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 174": "OD1" <-> "OD2" Residue "d TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 82": "OD1" <-> "OD2" Residue "o PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69795 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4657 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 570} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4666 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain: "D" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3604 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3603 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "F" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3576 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 429} Chain breaks: 1 Chain: "G" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 9, 'TRANS': 348} Chain breaks: 1 Chain: "H" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1760 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 3, 'TRANS': 214} Chain: "I" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1808 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "J" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1808 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "K" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1808 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "M" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 920 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "N" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 935 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 935 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "Q" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2126 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "R" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2130 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain: "S" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2155 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain: "T" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1377 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain: "a" Number of atoms: 6164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6164 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 725} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1652 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain: "d" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2817 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 334} Chain: "e" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 623 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "f" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 652 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "g" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 423 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.38, per 1000 atoms: 0.38 Number of scatterers: 69795 At special positions: 0 Unit cell: (177.215, 189.117, 288.305, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 388 16.00 P 2 15.00 O 12973 8.00 N 11744 7.00 C 44688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.90 Conformation dependent library (CDL) restraints added in 10.2 seconds 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 305 helices and 48 sheets defined 59.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.68 Creating SS restraints... Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 281 through 293 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 320 through 339 removed outlier: 3.854A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.078A pdb=" N GLY A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU A 387 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 456 through 468 removed outlier: 4.100A pdb=" N ARG A 459 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 462 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 463 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 586 removed outlier: 4.885A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 removed outlier: 3.777A pdb=" N LEU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 281 through 293 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 320 through 340 removed outlier: 4.510A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 376 through 388 removed outlier: 4.289A pdb=" N GLY B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 382 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 383 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 384 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 387 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 457 through 468 removed outlier: 4.228A pdb=" N ASP B 462 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 465 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 496 removed outlier: 4.000A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 557 Processing helix chain 'B' and resid 567 through 586 removed outlier: 6.606A pdb=" N GLU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 613 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 281 through 290 removed outlier: 3.701A pdb=" N SER C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.839A pdb=" N ILE C 331 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 333 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 337 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 338 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 376 through 388 removed outlier: 4.178A pdb=" N GLY C 379 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 384 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C 387 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 458 through 468 removed outlier: 4.381A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 495 removed outlier: 4.268A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 527 through 530 No H-bonds generated for 'chain 'C' and resid 527 through 530' Processing helix chain 'C' and resid 534 through 558 Processing helix chain 'C' and resid 567 through 586 removed outlier: 6.417A pdb=" N GLU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 253 through 256 Processing helix chain 'D' and resid 268 through 287 removed outlier: 3.688A pdb=" N THR D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 3.578A pdb=" N LEU D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR D 287 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.777A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 325 through 335 removed outlier: 4.387A pdb=" N TYR D 328 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 331 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.038A pdb=" N ARG D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.785A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 268 through 287 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 325 through 335 removed outlier: 4.286A pdb=" N TYR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 331 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 removed outlier: 3.842A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.450A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.855A pdb=" N PHE F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 268 through 287 Proline residue: F 275 - end of helix removed outlier: 3.522A pdb=" N ALA F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 381 through 384 No H-bonds generated for 'chain 'F' and resid 381 through 384' Processing helix chain 'F' and resid 400 through 404 removed outlier: 4.092A pdb=" N LYS F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.733A pdb=" N ASN F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 461 Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.575A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'G' and resid 15 through 28 removed outlier: 3.795A pdb=" N TRP G 19 " --> pdb=" O CYS G 15 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 79 removed outlier: 4.271A pdb=" N ALA G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 90 removed outlier: 3.851A pdb=" N GLN G 88 " --> pdb=" O ASP G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 118 through 155 removed outlier: 4.051A pdb=" N ASN G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 193 through 203 removed outlier: 4.476A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TYR G 201 " --> pdb=" O ILE G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 4.877A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP G 236 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG G 238 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU G 243 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 309 Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 328 through 342 removed outlier: 6.209A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 379 No H-bonds generated for 'chain 'G' and resid 377 through 379' Processing helix chain 'H' and resid 13 through 76 removed outlier: 3.873A pdb=" N THR H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 128 through 174 Processing helix chain 'H' and resid 176 through 219 Processing helix chain 'I' and resid 5 through 107 Processing helix chain 'I' and resid 109 through 127 removed outlier: 3.653A pdb=" N LEU I 121 " --> pdb=" O ASP I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 158 Proline residue: I 142 - end of helix removed outlier: 4.274A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.682A pdb=" N ILE I 157 " --> pdb=" O MET I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 216 Proline residue: I 209 - end of helix removed outlier: 3.556A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 107 removed outlier: 3.542A pdb=" N ILE J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN J 66 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 126 removed outlier: 3.592A pdb=" N LEU J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 159 Proline residue: J 142 - end of helix removed outlier: 3.558A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.877A pdb=" N ILE J 157 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 215 removed outlier: 3.550A pdb=" N GLN J 205 " --> pdb=" O ASP J 201 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 5 through 107 removed outlier: 4.503A pdb=" N ALA K 17 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE K 18 " --> pdb=" O HIS K 14 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE K 19 " --> pdb=" O MET K 15 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS K 107 " --> pdb=" O SER K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 127 Processing helix chain 'K' and resid 138 through 159 Proline residue: K 142 - end of helix removed outlier: 3.774A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.676A pdb=" N ILE K 157 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 215 removed outlier: 3.581A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 45 through 57 Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 75 through 80 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'M' and resid 6 through 104 removed outlier: 3.534A pdb=" N GLN M 13 " --> pdb=" O GLN M 9 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN M 35 " --> pdb=" O ARG M 31 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN M 41 " --> pdb=" O LYS M 37 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA M 42 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU M 43 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 104 removed outlier: 4.014A pdb=" N VAL N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER N 71 " --> pdb=" O GLY N 67 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP N 93 " --> pdb=" O GLU N 89 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU N 94 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 104 removed outlier: 4.684A pdb=" N GLN O 9 " --> pdb=" O GLN O 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN O 13 " --> pdb=" O GLN O 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU O 24 " --> pdb=" O LYS O 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU O 39 " --> pdb=" O ALA O 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA O 40 " --> pdb=" O LYS O 37 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE O 44 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY O 64 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL O 73 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU O 76 " --> pdb=" O VAL O 73 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET O 81 " --> pdb=" O GLN O 78 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG O 92 " --> pdb=" O GLU O 89 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP O 93 " --> pdb=" O GLN O 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU O 99 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL O 103 " --> pdb=" O LEU O 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 36 Processing helix chain 'Q' and resid 43 through 57 removed outlier: 5.155A pdb=" N ASP Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP Q 55 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA Q 56 " --> pdb=" O VAL Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 70 Processing helix chain 'Q' and resid 78 through 97 Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 125 through 140 Processing helix chain 'Q' and resid 147 through 166 Processing helix chain 'Q' and resid 173 through 187 Processing helix chain 'Q' and resid 193 through 206 Processing helix chain 'Q' and resid 219 through 233 Processing helix chain 'Q' and resid 240 through 251 removed outlier: 3.771A pdb=" N SER Q 251 " --> pdb=" O SER Q 247 " (cutoff:3.500A) Processing helix chain 'Q' and resid 257 through 271 removed outlier: 3.604A pdb=" N ASN Q 270 " --> pdb=" O ILE Q 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 57 removed outlier: 3.508A pdb=" N ASP R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 78 through 97 Processing helix chain 'R' and resid 105 through 117 Processing helix chain 'R' and resid 121 through 123 No H-bonds generated for 'chain 'R' and resid 121 through 123' Processing helix chain 'R' and resid 125 through 140 Processing helix chain 'R' and resid 147 through 166 Processing helix chain 'R' and resid 173 through 187 Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 219 through 236 Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 240 through 251 removed outlier: 4.076A pdb=" N LEU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 272 Processing helix chain 'S' and resid 10 through 12 No H-bonds generated for 'chain 'S' and resid 10 through 12' Processing helix chain 'S' and resid 15 through 36 Processing helix chain 'S' and resid 43 through 57 removed outlier: 3.524A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL S 52 " --> pdb=" O ASP S 48 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TRP S 55 " --> pdb=" O ASP S 51 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA S 56 " --> pdb=" O VAL S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 70 Processing helix chain 'S' and resid 78 through 97 Processing helix chain 'S' and resid 99 through 101 No H-bonds generated for 'chain 'S' and resid 99 through 101' Processing helix chain 'S' and resid 105 through 116 Processing helix chain 'S' and resid 121 through 123 No H-bonds generated for 'chain 'S' and resid 121 through 123' Processing helix chain 'S' and resid 125 through 140 Processing helix chain 'S' and resid 147 through 166 Processing helix chain 'S' and resid 173 through 187 Processing helix chain 'S' and resid 193 through 206 Processing helix chain 'S' and resid 219 through 234 removed outlier: 3.562A pdb=" N TYR S 232 " --> pdb=" O THR S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 240 through 251 removed outlier: 3.711A pdb=" N SER S 251 " --> pdb=" O SER S 247 " (cutoff:3.500A) Processing helix chain 'S' and resid 257 through 273 Processing helix chain 'T' and resid 64 through 73 removed outlier: 4.290A pdb=" N ARG T 73 " --> pdb=" O GLN T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 104 Processing helix chain 'a' and resid 19 through 32 removed outlier: 4.362A pdb=" N TYR a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 74 Processing helix chain 'a' and resid 93 through 137 removed outlier: 3.500A pdb=" N GLU a 98 " --> pdb=" O ILE a 95 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU a 110 " --> pdb=" O GLU a 107 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN a 112 " --> pdb=" O LYS a 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN a 114 " --> pdb=" O ILE a 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN a 115 " --> pdb=" O ASN a 112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU a 118 " --> pdb=" O GLN a 115 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG a 120 " --> pdb=" O ALA a 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU a 125 " --> pdb=" O PHE a 122 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU a 127 " --> pdb=" O GLU a 124 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN a 136 " --> pdb=" O ARG a 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 190 Proline residue: a 181 - end of helix removed outlier: 3.827A pdb=" N GLU a 184 " --> pdb=" O PRO a 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 226 through 239 removed outlier: 3.520A pdb=" N LYS a 230 " --> pdb=" O GLY a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 309 removed outlier: 4.308A pdb=" N ARG a 291 " --> pdb=" O ALA a 287 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU a 309 " --> pdb=" O HIS a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 330 through 342 removed outlier: 3.527A pdb=" N GLN a 334 " --> pdb=" O LEU a 330 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 379 removed outlier: 3.563A pdb=" N VAL a 378 " --> pdb=" O PHE a 374 " (cutoff:3.500A) Processing helix chain 'a' and resid 392 through 406 removed outlier: 4.372A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 410 through 425 Processing helix chain 'a' and resid 427 through 432 removed outlier: 4.354A pdb=" N SER a 432 " --> pdb=" O SER a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 438 through 445 Processing helix chain 'a' and resid 447 through 463 Processing helix chain 'a' and resid 482 through 486 Processing helix chain 'a' and resid 491 through 498 removed outlier: 3.584A pdb=" N LEU a 496 " --> pdb=" O GLU a 493 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY a 497 " --> pdb=" O THR a 494 " (cutoff:3.500A) Processing helix chain 'a' and resid 521 through 525 Processing helix chain 'a' and resid 527 through 562 removed outlier: 4.593A pdb=" N LEU a 530 " --> pdb=" O THR a 527 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU a 533 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN a 534 " --> pdb=" O THR a 531 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET a 538 " --> pdb=" O SER a 535 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET a 540 " --> pdb=" O LYS a 537 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU a 544 " --> pdb=" O SER a 541 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL a 553 " --> pdb=" O LEU a 550 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 570 Processing helix chain 'a' and resid 573 through 597 removed outlier: 4.985A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 600 through 602 No H-bonds generated for 'chain 'a' and resid 600 through 602' Processing helix chain 'a' and resid 609 through 617 Processing helix chain 'a' and resid 633 through 652 Proline residue: a 649 - end of helix Processing helix chain 'a' and resid 654 through 665 Processing helix chain 'a' and resid 714 through 728 Processing helix chain 'a' and resid 730 through 758 removed outlier: 3.681A pdb=" N ALA a 737 " --> pdb=" O ILE a 733 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU a 740 " --> pdb=" O THR a 736 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG a 741 " --> pdb=" O ALA a 737 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU a 742 " --> pdb=" O SER a 738 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 764 Processing helix chain 'a' and resid 769 through 790 Processing helix chain 'a' and resid 794 through 808 Processing helix chain 'a' and resid 812 through 814 No H-bonds generated for 'chain 'a' and resid 812 through 814' Processing helix chain 'a' and resid 828 through 830 No H-bonds generated for 'chain 'a' and resid 828 through 830' Processing helix chain 'b' and resid 3 through 28 removed outlier: 3.512A pdb=" N THR b 27 " --> pdb=" O GLY b 23 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 43 Processing helix chain 'b' and resid 46 through 82 removed outlier: 3.614A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS b 82 " --> pdb=" O GLY b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 114 removed outlier: 3.706A pdb=" N LYS b 89 " --> pdb=" O ILE b 86 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN b 90 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE b 96 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE b 106 " --> pdb=" O TYR b 103 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE b 111 " --> pdb=" O ALA b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 168 removed outlier: 6.012A pdb=" N HIS b 128 " --> pdb=" O LYS b 124 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG b 129 " --> pdb=" O ALA b 125 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN b 130 " --> pdb=" O ILE b 126 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 200 removed outlier: 4.983A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE b 186 " --> pdb=" O PHE b 182 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 282 No H-bonds generated for 'chain 'c' and resid 280 through 282' Processing helix chain 'c' and resid 310 through 312 No H-bonds generated for 'chain 'c' and resid 310 through 312' Processing helix chain 'c' and resid 327 through 329 No H-bonds generated for 'chain 'c' and resid 327 through 329' Processing helix chain 'c' and resid 372 through 374 No H-bonds generated for 'chain 'c' and resid 372 through 374' Processing helix chain 'c' and resid 417 through 442 removed outlier: 3.922A pdb=" N PHE c 428 " --> pdb=" O LEU c 424 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE c 431 " --> pdb=" O LEU c 427 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 12 removed outlier: 4.510A pdb=" N ASN d 10 " --> pdb=" O GLU d 6 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL d 11 " --> pdb=" O LEU d 7 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 14 through 25 Processing helix chain 'd' and resid 30 through 38 removed outlier: 4.257A pdb=" N GLN d 38 " --> pdb=" O LEU d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 51 Processing helix chain 'd' and resid 67 through 88 removed outlier: 4.302A pdb=" N HIS d 88 " --> pdb=" O HIS d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 117 removed outlier: 3.887A pdb=" N SER d 103 " --> pdb=" O PHE d 99 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU d 111 " --> pdb=" O ASP d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 128 Proline residue: d 127 - end of helix Processing helix chain 'd' and resid 131 through 133 No H-bonds generated for 'chain 'd' and resid 131 through 133' Processing helix chain 'd' and resid 139 through 143 Processing helix chain 'd' and resid 147 through 157 Processing helix chain 'd' and resid 159 through 167 removed outlier: 4.130A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 174 Processing helix chain 'd' and resid 178 through 199 Processing helix chain 'd' and resid 203 through 229 Proline residue: d 210 - end of helix removed outlier: 3.703A pdb=" N PHE d 228 " --> pdb=" O THR d 224 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLY d 229 " --> pdb=" O ILE d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 240 Processing helix chain 'd' and resid 246 through 249 Proline residue: d 249 - end of helix No H-bonds generated for 'chain 'd' and resid 246 through 249' Processing helix chain 'd' and resid 251 through 257 Processing helix chain 'd' and resid 261 through 270 removed outlier: 4.099A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 272 through 279 Processing helix chain 'd' and resid 290 through 307 removed outlier: 4.049A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU d 307 " --> pdb=" O LYS d 303 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 337 Processing helix chain 'd' and resid 341 through 346 removed outlier: 5.100A pdb=" N ASP d 345 " --> pdb=" O ALA d 342 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 20 Processing helix chain 'e' and resid 23 through 27 Processing helix chain 'e' and resid 32 through 59 removed outlier: 3.983A pdb=" N GLY e 35 " --> pdb=" O PRO e 32 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE e 38 " --> pdb=" O GLY e 35 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA e 43 " --> pdb=" O MET e 40 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS e 48 " --> pdb=" O ALA e 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE e 51 " --> pdb=" O CYS e 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE e 54 " --> pdb=" O PHE e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 79 removed outlier: 4.469A pdb=" N ARG e 77 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 34 Processing helix chain 'f' and resid 38 through 40 No H-bonds generated for 'chain 'f' and resid 38 through 40' Processing helix chain 'f' and resid 56 through 89 removed outlier: 4.188A pdb=" N ARG f 88 " --> pdb=" O PHE f 84 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 45 removed outlier: 3.629A pdb=" N PHE g 14 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY g 15 " --> pdb=" O SER g 12 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER g 20 " --> pdb=" O MET g 17 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA g 22 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE g 25 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER g 26 " --> pdb=" O MET g 23 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET g 28 " --> pdb=" O PHE g 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY g 33 " --> pdb=" O ALA g 30 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS g 36 " --> pdb=" O GLY g 33 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER g 37 " --> pdb=" O THR g 34 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY g 38 " --> pdb=" O ALA g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 55 removed outlier: 4.281A pdb=" N MET g 53 " --> pdb=" O GLU g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 79 removed outlier: 3.926A pdb=" N ILE g 65 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE g 67 " --> pdb=" O GLY g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 123 removed outlier: 3.667A pdb=" N PHE g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG g 119 " --> pdb=" O ASP g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 154 removed outlier: 4.215A pdb=" N VAL g 129 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL g 140 " --> pdb=" O PHE g 137 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL g 148 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 3.698A pdb=" N PHE h 14 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER h 20 " --> pdb=" O MET h 17 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL h 24 " --> pdb=" O SER h 21 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE h 25 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY h 33 " --> pdb=" O ALA h 30 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS h 36 " --> pdb=" O GLY h 33 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER h 37 " --> pdb=" O THR h 34 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY h 38 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA h 43 " --> pdb=" O GLY h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 55 removed outlier: 4.230A pdb=" N MET h 53 " --> pdb=" O GLU h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 79 removed outlier: 3.661A pdb=" N ALA h 66 " --> pdb=" O ALA h 62 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER h 79 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 86 through 123 removed outlier: 3.512A pdb=" N GLN h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 125 through 154 removed outlier: 4.266A pdb=" N VAL h 129 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE h 132 " --> pdb=" O VAL h 129 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL h 140 " --> pdb=" O PHE h 137 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL h 148 " --> pdb=" O GLY h 145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU h 152 " --> pdb=" O ALA h 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 47 removed outlier: 4.401A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 55 removed outlier: 3.673A pdb=" N ILE i 52 " --> pdb=" O PRO i 49 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET i 53 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 79 removed outlier: 3.933A pdb=" N SER i 79 " --> pdb=" O LEU i 75 " (cutoff:3.500A) Processing helix chain 'i' and resid 86 through 123 removed outlier: 3.544A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 154 removed outlier: 3.936A pdb=" N VAL i 129 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE i 134 " --> pdb=" O MET i 131 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL i 140 " --> pdb=" O PHE i 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE i 151 " --> pdb=" O VAL i 148 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU i 152 " --> pdb=" O ALA i 149 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER i 153 " --> pdb=" O LEU i 150 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 45 removed outlier: 3.794A pdb=" N SER j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 55 removed outlier: 4.031A pdb=" N ILE j 52 " --> pdb=" O PRO j 49 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N MET j 53 " --> pdb=" O GLU j 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 57 through 79 removed outlier: 4.125A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 123 Processing helix chain 'j' and resid 125 through 154 removed outlier: 3.750A pdb=" N VAL j 129 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE j 132 " --> pdb=" O VAL j 129 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL j 140 " --> pdb=" O PHE j 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR j 144 " --> pdb=" O LEU j 141 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL j 148 " --> pdb=" O GLY j 145 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 46 removed outlier: 4.328A pdb=" N SER k 12 " --> pdb=" O GLU k 9 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE k 14 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY k 15 " --> pdb=" O SER k 12 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER k 20 " --> pdb=" O MET k 17 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL k 24 " --> pdb=" O SER k 21 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE k 25 " --> pdb=" O ALA k 22 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER k 26 " --> pdb=" O MET k 23 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS k 36 " --> pdb=" O GLY k 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER k 37 " --> pdb=" O THR k 34 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER k 45 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL k 46 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 79 removed outlier: 4.277A pdb=" N MET k 53 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE k 57 " --> pdb=" O LYS k 54 " (cutoff:3.500A) Proline residue: k 58 - end of helix removed outlier: 3.521A pdb=" N VAL k 71 " --> pdb=" O TYR k 68 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE k 76 " --> pdb=" O ALA k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 86 through 123 removed outlier: 3.574A pdb=" N SER k 102 " --> pdb=" O SER k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 125 through 152 removed outlier: 3.744A pdb=" N PHE k 128 " --> pdb=" O PRO k 125 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL k 129 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL k 140 " --> pdb=" O PHE k 137 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL k 148 " --> pdb=" O GLY k 145 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 45 removed outlier: 3.591A pdb=" N MET l 23 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER l 26 " --> pdb=" O ALA l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 79 removed outlier: 3.621A pdb=" N ILE l 52 " --> pdb=" O PRO l 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET l 53 " --> pdb=" O GLU l 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE l 57 " --> pdb=" O LYS l 54 " (cutoff:3.500A) Proline residue: l 58 - end of helix removed outlier: 3.863A pdb=" N VAL l 71 " --> pdb=" O TYR l 68 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL l 74 " --> pdb=" O VAL l 71 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE l 76 " --> pdb=" O ALA l 73 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN l 78 " --> pdb=" O LEU l 75 " (cutoff:3.500A) Processing helix chain 'l' and resid 86 through 123 removed outlier: 3.672A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 154 removed outlier: 3.699A pdb=" N VAL l 129 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL l 140 " --> pdb=" O PHE l 137 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL l 148 " --> pdb=" O GLY l 145 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU l 152 " --> pdb=" O ALA l 149 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER l 153 " --> pdb=" O LEU l 150 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 45 removed outlier: 4.454A pdb=" N GLY m 15 " --> pdb=" O SER m 11 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 55 removed outlier: 4.423A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 57 through 79 removed outlier: 4.231A pdb=" N ALA m 62 " --> pdb=" O PRO m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 123 removed outlier: 3.732A pdb=" N ARG m 119 " --> pdb=" O ASP m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 154 removed outlier: 3.973A pdb=" N VAL m 129 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL m 140 " --> pdb=" O PHE m 137 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL m 148 " --> pdb=" O GLY m 145 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU m 152 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER m 153 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 45 removed outlier: 4.239A pdb=" N SER n 12 " --> pdb=" O GLU n 9 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE n 14 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER n 20 " --> pdb=" O MET n 17 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA n 22 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL n 24 " --> pdb=" O SER n 21 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE n 25 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY n 33 " --> pdb=" O ALA n 30 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS n 36 " --> pdb=" O GLY n 33 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER n 37 " --> pdb=" O THR n 34 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY n 38 " --> pdb=" O ALA n 35 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE n 41 " --> pdb=" O GLY n 38 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET n 44 " --> pdb=" O ILE n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 55 removed outlier: 4.101A pdb=" N ILE n 52 " --> pdb=" O PRO n 49 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET n 53 " --> pdb=" O GLU n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 57 through 79 removed outlier: 3.822A pdb=" N ALA n 66 " --> pdb=" O ALA n 62 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 123 removed outlier: 3.976A pdb=" N VAL n 118 " --> pdb=" O GLY n 114 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN n 123 " --> pdb=" O ARG n 119 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 154 removed outlier: 3.608A pdb=" N VAL n 129 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE n 132 " --> pdb=" O VAL n 129 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL n 140 " --> pdb=" O PHE n 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE n 151 " --> pdb=" O VAL n 148 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU n 152 " --> pdb=" O ALA n 149 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER n 153 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 9 through 47 removed outlier: 4.471A pdb=" N SER o 12 " --> pdb=" O GLU o 9 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE o 14 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N MET o 23 " --> pdb=" O SER o 20 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL o 24 " --> pdb=" O SER o 21 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE o 25 " --> pdb=" O ALA o 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA o 30 " --> pdb=" O ALA o 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY o 33 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS o 36 " --> pdb=" O GLY o 33 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER o 37 " --> pdb=" O THR o 34 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY o 38 " --> pdb=" O ALA o 35 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE o 41 " --> pdb=" O GLY o 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET o 44 " --> pdb=" O ILE o 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL o 46 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 79 removed outlier: 4.103A pdb=" N ILE o 52 " --> pdb=" O PRO o 49 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET o 53 " --> pdb=" O GLU o 50 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE o 56 " --> pdb=" O MET o 53 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE o 57 " --> pdb=" O LYS o 54 " (cutoff:3.500A) Proline residue: o 58 - end of helix removed outlier: 3.533A pdb=" N MET o 61 " --> pdb=" O PRO o 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL o 72 " --> pdb=" O GLY o 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN o 78 " --> pdb=" O LEU o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 123 removed outlier: 3.927A pdb=" N GLN o 123 " --> pdb=" O ARG o 119 " (cutoff:3.500A) Processing helix chain 'o' and resid 125 through 154 removed outlier: 3.923A pdb=" N VAL o 129 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL o 140 " --> pdb=" O PHE o 137 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL o 148 " --> pdb=" O GLY o 145 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER o 153 " --> pdb=" O LEU o 150 " (cutoff:3.500A) Processing helix chain 'p' and resid 303 through 329 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.584A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 186 removed outlier: 7.148A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 245 through 248 removed outlier: 7.880A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= F, first strand: chain 'A' and resid 175 through 179 removed outlier: 6.444A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE A 179 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 191 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 203 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU A 193 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU A 201 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU A 195 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.623A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= I, first strand: chain 'B' and resid 183 through 185 removed outlier: 6.916A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 199 through 203 removed outlier: 5.996A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.260A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 246 through 248 removed outlier: 6.662A pdb=" N VAL B 431 " --> pdb=" O ALA B 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 295 through 298 Processing sheet with id= N, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.523A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLN C 65 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE C 54 " --> pdb=" O GLN C 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= P, first strand: chain 'C' and resid 183 through 185 removed outlier: 7.205A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 219 through 221 removed outlier: 4.123A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 245 through 247 removed outlier: 8.228A pdb=" N THR C 246 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 295 through 298 Processing sheet with id= T, first strand: chain 'C' and resid 175 through 179 removed outlier: 6.359A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 179 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL C 191 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU C 203 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU C 193 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU C 201 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 195 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.650A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= W, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.008A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE D 351 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 376 through 379 removed outlier: 7.484A pdb=" N VAL D 379 " --> pdb=" O PRO D 190 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE D 192 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 57 through 60 removed outlier: 3.566A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 120 through 123 removed outlier: 3.538A pdb=" N LEU E 151 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 149 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.667A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS E 292 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE E 351 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 376 through 378 Processing sheet with id= AC, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.551A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU F 88 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AE, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.746A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS F 292 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL F 230 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU F 294 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA F 232 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE F 296 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE F 351 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 376 through 379 removed outlier: 7.561A pdb=" N VAL F 379 " --> pdb=" O PRO F 190 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE F 192 " --> pdb=" O VAL F 379 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 370 through 375 removed outlier: 6.161A pdb=" N GLU G 3 " --> pdb=" O PRO G 323 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 9 " --> pdb=" O GLN G 317 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 182 through 190 removed outlier: 3.656A pdb=" N SER G 217 " --> pdb=" O LEU G 224 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR G 228 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER G 213 " --> pdb=" O THR G 228 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 92 through 99 Processing sheet with id= AJ, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= AK, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AL, first strand: chain 'K' and resid 164 through 167 Processing sheet with id= AM, first strand: chain 'L' and resid 36 through 38 removed outlier: 9.062A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA L 9 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE L 64 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE L 11 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE L 66 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA L 87 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE L 66 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU L 89 " --> pdb=" O ILE L 66 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 151 through 155 removed outlier: 4.254A pdb=" N ILE T 121 " --> pdb=" O PHE T 147 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR T 219 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU T 85 " --> pdb=" O THR T 219 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'T' and resid 164 through 166 Processing sheet with id= AP, first strand: chain 'T' and resid 190 through 192 Processing sheet with id= AQ, first strand: chain 'a' and resid 352 through 354 removed outlier: 4.299A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'a' and resid 243 through 245 removed outlier: 4.220A pdb=" N ALA a 172 " --> pdb=" O TYR a 245 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE a 196 " --> pdb=" O PHE a 223 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'c' and resid 408 through 410 removed outlier: 6.797A pdb=" N SER c 362 " --> pdb=" O SER c 409 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR c 254 " --> pdb=" O ARG c 260 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU c 262 " --> pdb=" O VAL c 252 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL c 252 " --> pdb=" O LEU c 262 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'c' and resid 275 through 278 removed outlier: 3.508A pdb=" N ASN c 267 " --> pdb=" O HIS c 391 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'c' and resid 295 through 297 removed outlier: 3.735A pdb=" N ARG c 338 " --> pdb=" O ILE c 320 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA c 322 " --> pdb=" O MET c 336 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N MET c 336 " --> pdb=" O ALA c 322 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG c 324 " --> pdb=" O PHE c 334 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE c 334 " --> pdb=" O ARG c 324 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'c' and resid 338 through 342 4095 hydrogen bonds defined for protein. 9990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.21 Time building geometry restraints manager: 23.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17998 1.33 - 1.46: 13327 1.46 - 1.58: 39085 1.58 - 1.70: 3 1.70 - 1.83: 686 Bond restraints: 71099 Sorted by residual: bond pdb=" C4 ADP C 801 " pdb=" C5 ADP C 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP C 801 " pdb=" C6 ADP C 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CA PRO c 250 " pdb=" C PRO c 250 " ideal model delta sigma weight residual 1.517 1.541 -0.024 6.70e-03 2.23e+04 1.31e+01 bond pdb=" CZ ARG C 212 " pdb=" NH2 ARG C 212 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" CA CYS a 729 " pdb=" C CYS a 729 " ideal model delta sigma weight residual 1.517 1.539 -0.021 6.30e-03 2.52e+04 1.15e+01 ... (remaining 71094 not shown) Histogram of bond angle deviations from ideal: 95.48 - 103.40: 816 103.40 - 111.32: 24220 111.32 - 119.25: 32680 119.25 - 127.17: 37751 127.17 - 135.09: 623 Bond angle restraints: 96090 Sorted by residual: angle pdb=" CB HIS c 364 " pdb=" CG HIS c 364 " pdb=" CD2 HIS c 364 " ideal model delta sigma weight residual 131.20 123.17 8.03 1.30e+00 5.92e-01 3.82e+01 angle pdb=" OE1 GLN F 288 " pdb=" CD GLN F 288 " pdb=" NE2 GLN F 288 " ideal model delta sigma weight residual 122.60 116.48 6.12 1.00e+00 1.00e+00 3.74e+01 angle pdb=" CA PHE c 268 " pdb=" CB PHE c 268 " pdb=" CG PHE c 268 " ideal model delta sigma weight residual 113.80 119.85 -6.05 1.00e+00 1.00e+00 3.67e+01 angle pdb=" CA ASP F 330 " pdb=" CB ASP F 330 " pdb=" CG ASP F 330 " ideal model delta sigma weight residual 112.60 106.79 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" OE1 GLN d 263 " pdb=" CD GLN d 263 " pdb=" NE2 GLN d 263 " ideal model delta sigma weight residual 122.60 117.12 5.48 1.00e+00 1.00e+00 3.00e+01 ... (remaining 96085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.65: 41442 22.65 - 45.30: 1252 45.30 - 67.95: 218 67.95 - 90.59: 95 90.59 - 113.24: 2 Dihedral angle restraints: 43009 sinusoidal: 17286 harmonic: 25723 Sorted by residual: dihedral pdb=" CA PRO D 318 " pdb=" C PRO D 318 " pdb=" N GLY D 319 " pdb=" CA GLY D 319 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" C5' ADP C 801 " pdb=" O5' ADP C 801 " pdb=" PA ADP C 801 " pdb=" O2A ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 -173.24 113.24 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" CA TYR c 367 " pdb=" C TYR c 367 " pdb=" N VAL c 368 " pdb=" CA VAL c 368 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 43006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 7490 0.080 - 0.159: 2872 0.159 - 0.239: 475 0.239 - 0.319: 61 0.319 - 0.398: 11 Chirality restraints: 10909 Sorted by residual: chirality pdb=" CA PRO B 398 " pdb=" N PRO B 398 " pdb=" C PRO B 398 " pdb=" CB PRO B 398 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ASP F 299 " pdb=" N ASP F 299 " pdb=" C ASP F 299 " pdb=" CB ASP F 299 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA TYR b 70 " pdb=" N TYR b 70 " pdb=" C TYR b 70 " pdb=" CB TYR b 70 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 10906 not shown) Planarity restraints: 12296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 371 " -0.181 2.00e-02 2.50e+03 1.08e-01 2.35e+02 pdb=" CG TYR E 371 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 371 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 TYR E 371 " 0.083 2.00e-02 2.50e+03 pdb=" CE1 TYR E 371 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR E 371 " 0.078 2.00e-02 2.50e+03 pdb=" CZ TYR E 371 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR E 371 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 389 " -0.182 2.00e-02 2.50e+03 9.41e-02 1.77e+02 pdb=" CG TYR D 389 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR D 389 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 TYR D 389 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 TYR D 389 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR D 389 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR D 389 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR D 389 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 389 " 0.181 2.00e-02 2.50e+03 9.35e-02 1.75e+02 pdb=" CG TYR E 389 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR E 389 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 TYR E 389 " -0.096 2.00e-02 2.50e+03 pdb=" CE1 TYR E 389 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR E 389 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR E 389 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR E 389 " 0.120 2.00e-02 2.50e+03 ... (remaining 12293 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 33900 2.98 - 3.46: 76724 3.46 - 3.94: 120095 3.94 - 4.42: 134617 4.42 - 4.90: 224701 Nonbonded interactions: 590037 Sorted by model distance: nonbonded pdb=" OE1 GLU C 53 " pdb=" OH TYR C 67 " model vdw 2.499 2.440 nonbonded pdb=" OH TYR D 303 " pdb=" OD1 ASP D 330 " model vdw 2.513 2.440 nonbonded pdb=" OH TYR F 303 " pdb=" OD2 ASP F 330 " model vdw 2.527 2.440 nonbonded pdb=" OG SER B 115 " pdb=" OD1 ASP J 226 " model vdw 2.530 2.440 nonbonded pdb=" OG SER T 133 " pdb=" O HIS T 135 " model vdw 2.532 2.440 ... (remaining 590032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 616) selection = chain 'B' selection = (chain 'C' and resid 17 through 616) } ncs_group { reference = (chain 'D' and (resid 39 through 213 or resid 226 through 506)) selection = (chain 'E' and (resid 39 through 213 or resid 226 through 506)) selection = (chain 'F' and resid 39 through 506) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = (chain 'N' and resid 5 through 116) selection = (chain 'O' and resid 5 through 116) } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 12 through 274) selection = (chain 'S' and resid 12 through 274) } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.040 Extract box with map and model: 10.380 Check model and map are aligned: 0.760 Set scattering table: 0.470 Process input model: 144.260 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.540 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.012 0.109 71099 Z= 0.796 Angle : 1.675 9.863 96090 Z= 1.142 Chirality : 0.082 0.398 10909 Planarity : 0.015 0.153 12296 Dihedral : 12.352 113.242 26495 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 0.11 % Allowed : 1.74 % Favored : 98.16 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 8831 helix: -0.30 (0.06), residues: 5219 sheet: -0.70 (0.20), residues: 662 loop : -0.39 (0.12), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.157 0.024 TRP b 67 HIS 0.023 0.003 HIS d 311 PHE 0.111 0.013 PHE m 137 TYR 0.188 0.021 TYR E 371 ARG 0.013 0.001 ARG F 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3100 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 3092 time to evaluate : 6.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.8548 (tp) cc_final: 0.8345 (tp) REVERT: A 61 MET cc_start: 0.8251 (mtt) cc_final: 0.8017 (mtm) REVERT: A 74 SER cc_start: 0.8320 (t) cc_final: 0.7904 (p) REVERT: A 77 ASP cc_start: 0.7985 (m-30) cc_final: 0.7722 (m-30) REVERT: A 80 LEU cc_start: 0.9048 (tp) cc_final: 0.8839 (tt) REVERT: A 148 THR cc_start: 0.9104 (t) cc_final: 0.8613 (t) REVERT: A 168 LEU cc_start: 0.9425 (tp) cc_final: 0.9209 (tp) REVERT: A 191 VAL cc_start: 0.8915 (m) cc_final: 0.8556 (m) REVERT: A 208 VAL cc_start: 0.9354 (t) cc_final: 0.9078 (m) REVERT: A 268 ASN cc_start: 0.7643 (m-40) cc_final: 0.7314 (t0) REVERT: A 288 LEU cc_start: 0.9294 (mt) cc_final: 0.9034 (mt) REVERT: A 387 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8122 (tp30) REVERT: A 477 THR cc_start: 0.8946 (p) cc_final: 0.8529 (t) REVERT: A 495 LEU cc_start: 0.8817 (mt) cc_final: 0.8183 (mt) REVERT: A 504 THR cc_start: 0.8773 (p) cc_final: 0.8389 (t) REVERT: A 510 GLU cc_start: 0.8012 (tt0) cc_final: 0.7800 (tt0) REVERT: A 550 MET cc_start: 0.8622 (mtm) cc_final: 0.8383 (mtp) REVERT: B 80 LEU cc_start: 0.8906 (tp) cc_final: 0.8587 (tt) REVERT: B 100 ASP cc_start: 0.8258 (p0) cc_final: 0.8027 (p0) REVERT: B 127 LEU cc_start: 0.9222 (mt) cc_final: 0.9015 (mm) REVERT: B 231 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7648 (mm-40) REVERT: B 235 ASP cc_start: 0.8281 (m-30) cc_final: 0.7926 (m-30) REVERT: B 268 ASN cc_start: 0.8068 (t0) cc_final: 0.7471 (t0) REVERT: B 275 VAL cc_start: 0.9132 (t) cc_final: 0.8897 (m) REVERT: B 279 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 328 TYR cc_start: 0.9120 (m-80) cc_final: 0.8875 (m-10) REVERT: B 340 MET cc_start: 0.8630 (mtt) cc_final: 0.8399 (mtt) REVERT: B 361 ILE cc_start: 0.9004 (mm) cc_final: 0.8668 (mm) REVERT: B 430 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7178 (mp10) REVERT: B 445 PHE cc_start: 0.8444 (m-80) cc_final: 0.8088 (m-80) REVERT: B 478 LYS cc_start: 0.8757 (mttt) cc_final: 0.8531 (mmmm) REVERT: B 513 LYS cc_start: 0.9059 (tttp) cc_final: 0.8701 (tppt) REVERT: B 523 ASN cc_start: 0.8124 (t0) cc_final: 0.7667 (t0) REVERT: B 525 TYR cc_start: 0.7755 (m-80) cc_final: 0.7412 (m-80) REVERT: B 550 MET cc_start: 0.8915 (mmm) cc_final: 0.8560 (mtm) REVERT: B 603 GLN cc_start: 0.8292 (tp40) cc_final: 0.7503 (tp-100) REVERT: C 39 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8595 (ttt) REVERT: C 80 LEU cc_start: 0.8812 (tp) cc_final: 0.8397 (mt) REVERT: C 208 VAL cc_start: 0.9482 (t) cc_final: 0.9277 (m) REVERT: C 264 SER cc_start: 0.9511 (m) cc_final: 0.9010 (p) REVERT: C 285 SER cc_start: 0.9332 (m) cc_final: 0.9004 (t) REVERT: C 307 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8299 (mttp) REVERT: C 316 SER cc_start: 0.9139 (p) cc_final: 0.8843 (m) REVERT: C 356 GLU cc_start: 0.8235 (tt0) cc_final: 0.7917 (tt0) REVERT: C 372 SER cc_start: 0.8474 (m) cc_final: 0.7581 (t) REVERT: C 393 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8828 (mttm) REVERT: C 401 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5782 (mt-10) REVERT: C 540 MET cc_start: 0.8726 (mtp) cc_final: 0.8438 (mtp) REVERT: C 574 MET cc_start: 0.8342 (mtp) cc_final: 0.8082 (mtm) REVERT: C 584 MET cc_start: 0.8684 (mtm) cc_final: 0.8411 (mtp) REVERT: D 51 SER cc_start: 0.8777 (p) cc_final: 0.8496 (t) REVERT: D 100 GLU cc_start: 0.7897 (mp0) cc_final: 0.7666 (mp0) REVERT: D 234 MET cc_start: 0.8305 (mpp) cc_final: 0.7926 (mtt) REVERT: D 254 MET cc_start: 0.9011 (tpt) cc_final: 0.8665 (tpt) REVERT: D 289 CYS cc_start: 0.8275 (m) cc_final: 0.7478 (t) REVERT: D 299 ASP cc_start: 0.8443 (t0) cc_final: 0.8212 (t0) REVERT: D 300 MET cc_start: 0.9229 (mmm) cc_final: 0.8920 (mmt) REVERT: D 367 ASP cc_start: 0.7929 (t0) cc_final: 0.7635 (t0) REVERT: D 451 TYR cc_start: 0.8802 (m-80) cc_final: 0.8202 (m-80) REVERT: D 455 LEU cc_start: 0.9090 (tt) cc_final: 0.8870 (tt) REVERT: E 60 LEU cc_start: 0.9664 (mm) cc_final: 0.9417 (mm) REVERT: E 87 LEU cc_start: 0.9382 (tp) cc_final: 0.9071 (tt) REVERT: E 113 GLU cc_start: 0.8133 (tt0) cc_final: 0.7771 (tt0) REVERT: E 118 ILE cc_start: 0.9560 (pp) cc_final: 0.9324 (pt) REVERT: E 127 MET cc_start: 0.8543 (mtp) cc_final: 0.8343 (mtp) REVERT: E 238 MET cc_start: 0.8314 (tpt) cc_final: 0.8044 (tpp) REVERT: E 266 ASP cc_start: 0.7704 (m-30) cc_final: 0.7499 (m-30) REVERT: E 345 ASN cc_start: 0.7935 (m-40) cc_final: 0.7735 (m110) REVERT: E 358 ASN cc_start: 0.8004 (t0) cc_final: 0.7667 (t0) REVERT: F 48 LYS cc_start: 0.8577 (mttt) cc_final: 0.8262 (mttp) REVERT: F 238 MET cc_start: 0.7683 (tpt) cc_final: 0.7423 (tpp) REVERT: F 302 SER cc_start: 0.9095 (m) cc_final: 0.8789 (t) REVERT: F 356 MET cc_start: 0.8000 (mtm) cc_final: 0.6925 (mtp) REVERT: F 389 TYR cc_start: 0.7763 (t80) cc_final: 0.7335 (t80) REVERT: F 395 LEU cc_start: 0.9018 (tp) cc_final: 0.8481 (tp) REVERT: F 425 CYS cc_start: 0.8493 (m) cc_final: 0.8004 (m) REVERT: F 448 ASP cc_start: 0.8305 (m-30) cc_final: 0.7973 (m-30) REVERT: G 68 VAL cc_start: 0.9085 (t) cc_final: 0.8226 (t) REVERT: G 125 ILE cc_start: 0.8078 (mt) cc_final: 0.7823 (mm) REVERT: H 28 THR cc_start: 0.8527 (m) cc_final: 0.8184 (p) REVERT: H 94 ILE cc_start: 0.8479 (pt) cc_final: 0.7759 (pt) REVERT: H 119 TYR cc_start: 0.8165 (m-80) cc_final: 0.7744 (m-80) REVERT: H 182 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7788 (mtm180) REVERT: H 193 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7815 (mm-30) REVERT: H 208 LYS cc_start: 0.8385 (mttm) cc_final: 0.8117 (mttp) REVERT: I 73 SER cc_start: 0.9166 (t) cc_final: 0.7755 (t) REVERT: I 77 ASN cc_start: 0.8778 (t0) cc_final: 0.8404 (t0) REVERT: I 89 ASP cc_start: 0.8407 (m-30) cc_final: 0.7932 (m-30) REVERT: I 106 VAL cc_start: 0.9068 (t) cc_final: 0.8745 (t) REVERT: I 112 TYR cc_start: 0.9018 (t80) cc_final: 0.8682 (t80) REVERT: I 133 ILE cc_start: 0.9235 (mt) cc_final: 0.8974 (mm) REVERT: I 159 THR cc_start: 0.8999 (p) cc_final: 0.8726 (m) REVERT: I 200 LEU cc_start: 0.8754 (tp) cc_final: 0.8385 (tp) REVERT: I 219 ASN cc_start: 0.8002 (t0) cc_final: 0.7113 (t0) REVERT: J 172 TYR cc_start: 0.8576 (m-80) cc_final: 0.8334 (m-10) REVERT: J 194 ASN cc_start: 0.8058 (t0) cc_final: 0.7839 (t0) REVERT: J 198 SER cc_start: 0.9264 (t) cc_final: 0.8906 (m) REVERT: J 207 MET cc_start: 0.8723 (mmm) cc_final: 0.8461 (mmm) REVERT: K 57 TYR cc_start: 0.8122 (m-80) cc_final: 0.7623 (m-80) REVERT: K 96 ASN cc_start: 0.9076 (m-40) cc_final: 0.8843 (m110) REVERT: K 110 THR cc_start: 0.8652 (m) cc_final: 0.8429 (p) REVERT: K 116 LEU cc_start: 0.8841 (mt) cc_final: 0.8581 (mt) REVERT: K 205 GLN cc_start: 0.8194 (tp40) cc_final: 0.7975 (mm-40) REVERT: K 207 MET cc_start: 0.7303 (mmm) cc_final: 0.6578 (mmm) REVERT: M 81 MET cc_start: 0.8379 (mtt) cc_final: 0.7808 (mtm) REVERT: M 82 THR cc_start: 0.8692 (m) cc_final: 0.8394 (m) REVERT: M 93 ASP cc_start: 0.7833 (m-30) cc_final: 0.7423 (m-30) REVERT: N 50 GLN cc_start: 0.8919 (mt0) cc_final: 0.8428 (mt0) REVERT: N 82 THR cc_start: 0.8857 (m) cc_final: 0.8413 (m) REVERT: N 86 ASN cc_start: 0.8993 (m-40) cc_final: 0.8647 (m110) REVERT: N 92 ARG cc_start: 0.7954 (ptt90) cc_final: 0.7674 (ptt180) REVERT: O 55 PHE cc_start: 0.7368 (t80) cc_final: 0.7142 (t80) REVERT: Q 21 GLN cc_start: 0.8704 (mm-40) cc_final: 0.7629 (tp40) REVERT: Q 37 ASP cc_start: 0.6441 (t0) cc_final: 0.5775 (t0) REVERT: Q 54 ILE cc_start: 0.7803 (tp) cc_final: 0.5444 (tp) REVERT: Q 184 HIS cc_start: 0.7534 (t70) cc_final: 0.7120 (t70) REVERT: R 111 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7166 (mm110) REVERT: R 126 TYR cc_start: 0.5210 (t80) cc_final: 0.4974 (t80) REVERT: R 169 THR cc_start: 0.8507 (p) cc_final: 0.8155 (p) REVERT: R 197 TYR cc_start: 0.7683 (t80) cc_final: 0.6989 (t80) REVERT: R 200 PHE cc_start: 0.7118 (t80) cc_final: 0.6820 (t80) REVERT: R 204 VAL cc_start: 0.7740 (p) cc_final: 0.7312 (p) REVERT: S 10 MET cc_start: 0.7256 (mtm) cc_final: 0.7017 (mpp) REVERT: S 28 TYR cc_start: 0.7919 (t80) cc_final: 0.7697 (t80) REVERT: S 37 ASP cc_start: 0.7669 (t0) cc_final: 0.7414 (t0) REVERT: S 54 ILE cc_start: 0.8800 (tp) cc_final: 0.8250 (mt) REVERT: S 168 ILE cc_start: 0.8326 (mt) cc_final: 0.8024 (tp) REVERT: T 61 LEU cc_start: 0.8049 (mt) cc_final: 0.7517 (mt) REVERT: T 119 ASN cc_start: 0.8475 (m-40) cc_final: 0.8158 (m110) REVERT: T 143 PHE cc_start: 0.8161 (p90) cc_final: 0.7732 (p90) REVERT: T 164 ILE cc_start: 0.8139 (mm) cc_final: 0.7755 (mm) REVERT: T 213 GLN cc_start: 0.7918 (tt0) cc_final: 0.7078 (tm-30) REVERT: T 217 VAL cc_start: 0.8297 (t) cc_final: 0.7907 (p) REVERT: a 547 ILE cc_start: 0.8147 (mt) cc_final: 0.7777 (tp) REVERT: a 735 ASN cc_start: 0.8161 (m-40) cc_final: 0.7824 (m110) REVERT: a 794 MET cc_start: 0.8134 (tmm) cc_final: 0.7503 (tmm) REVERT: b 47 PHE cc_start: 0.6787 (m-80) cc_final: 0.6527 (m-80) REVERT: b 72 THR cc_start: 0.8404 (t) cc_final: 0.8168 (m) REVERT: b 103 TYR cc_start: 0.8976 (m-10) cc_final: 0.8630 (m-80) REVERT: b 136 SER cc_start: 0.9225 (t) cc_final: 0.8911 (m) REVERT: b 147 SER cc_start: 0.9405 (m) cc_final: 0.9192 (p) REVERT: c 254 TYR cc_start: 0.8571 (t80) cc_final: 0.8278 (t80) REVERT: c 266 GLN cc_start: 0.8125 (tt0) cc_final: 0.7833 (tt0) REVERT: c 318 LYS cc_start: 0.8596 (mttt) cc_final: 0.8297 (mttt) REVERT: c 341 ILE cc_start: 0.7416 (mt) cc_final: 0.6969 (mt) REVERT: c 367 TYR cc_start: 0.8791 (m-80) cc_final: 0.8517 (m-80) REVERT: c 386 TRP cc_start: 0.8094 (m100) cc_final: 0.7855 (m100) REVERT: d 217 ASP cc_start: 0.8047 (m-30) cc_final: 0.7846 (m-30) REVERT: d 263 GLN cc_start: 0.8429 (mt0) cc_final: 0.8139 (mt0) REVERT: d 275 LYS cc_start: 0.8494 (tttt) cc_final: 0.8004 (ttpp) REVERT: d 292 ASP cc_start: 0.8364 (m-30) cc_final: 0.8130 (m-30) REVERT: d 343 LYS cc_start: 0.8404 (mttt) cc_final: 0.8150 (mmmt) REVERT: d 350 ILE cc_start: 0.8459 (pt) cc_final: 0.8183 (pt) REVERT: f 59 TYR cc_start: 0.7681 (m-10) cc_final: 0.7439 (m-80) REVERT: g 26 SER cc_start: 0.8756 (p) cc_final: 0.8538 (p) REVERT: h 23 MET cc_start: 0.9042 (tpt) cc_final: 0.8737 (tpp) REVERT: h 54 LYS cc_start: 0.7621 (mttt) cc_final: 0.7303 (mmtt) REVERT: h 141 LEU cc_start: 0.8651 (mp) cc_final: 0.8251 (mp) REVERT: i 23 MET cc_start: 0.7244 (tpp) cc_final: 0.6857 (tpp) REVERT: i 61 MET cc_start: 0.8249 (mtt) cc_final: 0.7842 (mtt) REVERT: j 119 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7680 (mtt90) REVERT: j 124 GLN cc_start: 0.8272 (tp-100) cc_final: 0.8040 (tm-30) REVERT: k 23 MET cc_start: 0.8735 (tpt) cc_final: 0.8431 (mmm) REVERT: l 7 ASN cc_start: 0.8179 (m-40) cc_final: 0.7949 (m110) REVERT: l 10 TYR cc_start: 0.8667 (p90) cc_final: 0.8287 (p90) REVERT: l 54 LYS cc_start: 0.7886 (mttt) cc_final: 0.7518 (mmtt) REVERT: l 85 THR cc_start: 0.8886 (m) cc_final: 0.8667 (p) REVERT: l 89 SER cc_start: 0.9383 (m) cc_final: 0.9158 (t) REVERT: l 124 GLN cc_start: 0.8286 (tp-100) cc_final: 0.7918 (tm-30) REVERT: m 23 MET cc_start: 0.8725 (tpt) cc_final: 0.8511 (tpp) REVERT: m 28 MET cc_start: 0.8184 (mmt) cc_final: 0.7869 (mmm) REVERT: m 36 LYS cc_start: 0.8309 (mmmt) cc_final: 0.8028 (mptt) REVERT: n 28 MET cc_start: 0.8573 (mmt) cc_final: 0.8218 (mtp) REVERT: n 53 MET cc_start: 0.7050 (mmm) cc_final: 0.6843 (mmm) REVERT: n 54 LYS cc_start: 0.8382 (mttt) cc_final: 0.7790 (mtpp) REVERT: n 65 ILE cc_start: 0.9187 (mm) cc_final: 0.8949 (mm) REVERT: n 112 ILE cc_start: 0.9260 (mm) cc_final: 0.9053 (mm) REVERT: n 124 GLN cc_start: 0.8588 (tp-100) cc_final: 0.7960 (tm-30) REVERT: o 46 VAL cc_start: 0.9148 (t) cc_final: 0.8897 (p) REVERT: o 124 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7493 (tm-30) outliers start: 8 outliers final: 4 residues processed: 3094 average time/residue: 0.7331 time to fit residues: 3816.9765 Evaluate side-chains 2035 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2030 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain R residue 104 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 744 optimal weight: 0.7980 chunk 668 optimal weight: 0.6980 chunk 370 optimal weight: 0.6980 chunk 228 optimal weight: 0.0000 chunk 450 optimal weight: 30.0000 chunk 357 optimal weight: 0.8980 chunk 691 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 420 optimal weight: 7.9990 chunk 514 optimal weight: 0.8980 chunk 800 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 242 GLN A 573 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN B 609 GLN C 543 ASN ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN E 156 GLN E 209 GLN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 HIS G 90 ASN ** G 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN H 170 ASN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN M 66 HIS M 91 ASN M 113 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 46 GLN O 113 ASN Q 134 ASN Q 270 ASN ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 GLN R 198 HIS ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 GLN S 132 GLN ** S 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 391 HIS c 392 ASN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 ASN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 HIS ** d 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN m 123 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 71099 Z= 0.236 Angle : 0.691 11.705 96090 Z= 0.364 Chirality : 0.044 0.251 10909 Planarity : 0.005 0.057 12296 Dihedral : 5.695 103.757 9670 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.90 % Allowed : 13.31 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.09), residues: 8831 helix: 0.65 (0.07), residues: 5225 sheet: -0.76 (0.18), residues: 783 loop : 0.02 (0.12), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 52 HIS 0.012 0.001 HIS B 164 PHE 0.033 0.002 PHE Q 200 TYR 0.030 0.002 TYR S 232 ARG 0.015 0.001 ARG D 471 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2398 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 2179 time to evaluate : 6.015 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: A 25 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 39 MET cc_start: 0.8703 (tpt) cc_final: 0.8410 (tpt) REVERT: A 55 ILE cc_start: 0.8477 (tp) cc_final: 0.8274 (tp) REVERT: A 80 LEU cc_start: 0.9003 (tp) cc_final: 0.8377 (mt) REVERT: A 268 ASN cc_start: 0.7869 (m-40) cc_final: 0.7516 (t0) REVERT: A 284 MET cc_start: 0.9194 (mmm) cc_final: 0.8642 (tpp) REVERT: A 368 MET cc_start: 0.8764 (mmm) cc_final: 0.8329 (mmm) REVERT: A 387 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8298 (tp30) REVERT: A 494 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 550 MET cc_start: 0.8616 (mtm) cc_final: 0.8382 (mtp) REVERT: A 605 LEU cc_start: 0.9163 (tp) cc_final: 0.8960 (tt) REVERT: B 100 ASP cc_start: 0.8305 (p0) cc_final: 0.7837 (p0) REVERT: B 205 MET cc_start: 0.7879 (mtm) cc_final: 0.7616 (mtm) REVERT: B 268 ASN cc_start: 0.8268 (t0) cc_final: 0.7784 (t0) REVERT: B 279 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6932 (mm-30) REVERT: B 445 PHE cc_start: 0.8321 (m-80) cc_final: 0.7224 (m-80) REVERT: B 478 LYS cc_start: 0.8981 (mttt) cc_final: 0.8655 (mmmm) REVERT: B 513 LYS cc_start: 0.9029 (tttp) cc_final: 0.8374 (tppt) REVERT: B 523 ASN cc_start: 0.8259 (t0) cc_final: 0.8028 (t0) REVERT: B 525 TYR cc_start: 0.7992 (m-80) cc_final: 0.7671 (m-80) REVERT: B 550 MET cc_start: 0.8890 (mmm) cc_final: 0.8689 (mtm) REVERT: B 574 MET cc_start: 0.7592 (ppp) cc_final: 0.7290 (ppp) REVERT: B 582 SER cc_start: 0.9295 (m) cc_final: 0.8902 (p) REVERT: B 604 LEU cc_start: 0.9167 (tt) cc_final: 0.8874 (tt) REVERT: C 20 TYR cc_start: 0.7872 (m-80) cc_final: 0.6999 (m-10) REVERT: C 80 LEU cc_start: 0.8883 (tp) cc_final: 0.8441 (mt) REVERT: C 204 SER cc_start: 0.8621 (p) cc_final: 0.8102 (t) REVERT: C 264 SER cc_start: 0.9591 (m) cc_final: 0.9220 (p) REVERT: C 285 SER cc_start: 0.9338 (m) cc_final: 0.9022 (t) REVERT: C 307 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8397 (mttm) REVERT: C 346 MET cc_start: 0.9094 (ttt) cc_final: 0.8247 (ttt) REVERT: C 372 SER cc_start: 0.8480 (m) cc_final: 0.7661 (t) REVERT: C 416 ASP cc_start: 0.7787 (t0) cc_final: 0.7399 (p0) REVERT: C 441 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7089 (mm-40) REVERT: C 532 CYS cc_start: 0.9094 (t) cc_final: 0.8533 (t) REVERT: C 540 MET cc_start: 0.8668 (mtp) cc_final: 0.8451 (mtp) REVERT: C 543 ASN cc_start: 0.8161 (m-40) cc_final: 0.7954 (m110) REVERT: C 579 TYR cc_start: 0.9149 (t80) cc_final: 0.8879 (t80) REVERT: C 588 ASP cc_start: 0.7598 (t0) cc_final: 0.7092 (t0) REVERT: D 51 SER cc_start: 0.8640 (p) cc_final: 0.8393 (t) REVERT: D 96 VAL cc_start: 0.9653 (t) cc_final: 0.9273 (m) REVERT: D 127 MET cc_start: 0.8581 (mtp) cc_final: 0.8228 (mtp) REVERT: D 234 MET cc_start: 0.8407 (mpp) cc_final: 0.7901 (mtt) REVERT: D 249 GLU cc_start: 0.7376 (tp30) cc_final: 0.6996 (tp30) REVERT: D 254 MET cc_start: 0.8959 (tpt) cc_final: 0.8453 (tpp) REVERT: D 256 ASN cc_start: 0.8639 (t0) cc_final: 0.8404 (t0) REVERT: D 300 MET cc_start: 0.9182 (mmm) cc_final: 0.8898 (mmt) REVERT: D 389 TYR cc_start: 0.7938 (t80) cc_final: 0.7629 (t80) REVERT: D 491 MET cc_start: 0.8544 (mmp) cc_final: 0.8342 (tpp) REVERT: E 87 LEU cc_start: 0.9322 (tp) cc_final: 0.9034 (tt) REVERT: E 93 LYS cc_start: 0.8824 (mttt) cc_final: 0.8528 (mttm) REVERT: E 180 MET cc_start: 0.8835 (mmm) cc_final: 0.8427 (mmm) REVERT: E 238 MET cc_start: 0.8356 (tpt) cc_final: 0.7913 (tpp) REVERT: E 266 ASP cc_start: 0.7307 (m-30) cc_final: 0.7063 (m-30) REVERT: E 345 ASN cc_start: 0.8147 (m-40) cc_final: 0.7863 (m-40) REVERT: E 355 THR cc_start: 0.8771 (m) cc_final: 0.8277 (p) REVERT: E 358 ASN cc_start: 0.7813 (t0) cc_final: 0.7577 (t0) REVERT: E 406 ILE cc_start: 0.9435 (pp) cc_final: 0.8865 (pp) REVERT: E 435 MET cc_start: 0.7587 (ttp) cc_final: 0.7005 (tmm) REVERT: F 201 GLU cc_start: 0.8356 (mp0) cc_final: 0.8105 (mp0) REVERT: F 245 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8075 (tmtm) REVERT: F 255 ASP cc_start: 0.7648 (m-30) cc_final: 0.7219 (t0) REVERT: F 395 LEU cc_start: 0.9198 (tp) cc_final: 0.8273 (tp) REVERT: F 448 ASP cc_start: 0.8424 (m-30) cc_final: 0.8127 (m-30) REVERT: G 5 TRP cc_start: 0.5460 (m-10) cc_final: 0.4034 (m100) REVERT: G 85 ASP cc_start: 0.7675 (t0) cc_final: 0.7328 (t0) REVERT: G 100 THR cc_start: 0.8850 (m) cc_final: 0.8512 (p) REVERT: H 9 ILE cc_start: 0.9354 (mm) cc_final: 0.9137 (tp) REVERT: H 27 GLN cc_start: 0.8234 (mt0) cc_final: 0.7992 (mt0) REVERT: H 67 PHE cc_start: 0.8425 (t80) cc_final: 0.8090 (t80) REVERT: H 119 TYR cc_start: 0.8276 (m-80) cc_final: 0.8073 (m-80) REVERT: H 129 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7863 (mm-30) REVERT: I 73 SER cc_start: 0.8756 (t) cc_final: 0.8167 (t) REVERT: I 77 ASN cc_start: 0.8915 (t0) cc_final: 0.8587 (t0) REVERT: I 106 VAL cc_start: 0.9035 (t) cc_final: 0.8663 (t) REVERT: I 109 THR cc_start: 0.8619 (p) cc_final: 0.8263 (t) REVERT: I 112 TYR cc_start: 0.9031 (t80) cc_final: 0.8749 (t80) REVERT: I 133 ILE cc_start: 0.9296 (mt) cc_final: 0.9000 (mm) REVERT: I 159 THR cc_start: 0.8978 (p) cc_final: 0.8704 (t) REVERT: J 49 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8527 (tp-100) REVERT: J 136 CYS cc_start: 0.8110 (p) cc_final: 0.7674 (p) REVERT: J 172 TYR cc_start: 0.8518 (m-80) cc_final: 0.7560 (m-10) REVERT: J 198 SER cc_start: 0.9251 (t) cc_final: 0.8928 (m) REVERT: J 207 MET cc_start: 0.8353 (mmm) cc_final: 0.8125 (mmp) REVERT: K 184 TYR cc_start: 0.8444 (m-80) cc_final: 0.7970 (m-80) REVERT: M 75 LYS cc_start: 0.8819 (pttm) cc_final: 0.7752 (pptt) REVERT: M 77 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9107 (p) REVERT: M 100 LEU cc_start: 0.9237 (tp) cc_final: 0.8851 (mm) REVERT: N 41 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8716 (tp-100) REVERT: N 46 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8399 (tp-100) REVERT: N 49 LEU cc_start: 0.9360 (mt) cc_final: 0.9146 (pp) REVERT: N 86 ASN cc_start: 0.8880 (m-40) cc_final: 0.8626 (m-40) REVERT: N 92 ARG cc_start: 0.7790 (ptt90) cc_final: 0.7581 (ptt180) REVERT: O 86 ASN cc_start: 0.8446 (m-40) cc_final: 0.8093 (m110) REVERT: Q 21 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8521 (tp40) REVERT: Q 53 LEU cc_start: 0.8715 (pp) cc_final: 0.8143 (mp) REVERT: Q 54 ILE cc_start: 0.8311 (tp) cc_final: 0.7634 (pt) REVERT: Q 106 ASP cc_start: 0.8542 (p0) cc_final: 0.8271 (p0) REVERT: Q 134 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8255 (m110) REVERT: R 18 TYR cc_start: 0.8724 (t80) cc_final: 0.8373 (t80) REVERT: R 83 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7637 (ttt-90) REVERT: R 90 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7652 (pp20) REVERT: R 122 TRP cc_start: 0.8733 (m100) cc_final: 0.8459 (m100) REVERT: R 155 MET cc_start: 0.7941 (ttp) cc_final: 0.7666 (ttp) REVERT: R 229 MET cc_start: 0.8236 (tpt) cc_final: 0.7776 (mmm) REVERT: S 90 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7681 (tp30) REVERT: S 101 PHE cc_start: 0.8161 (m-80) cc_final: 0.7002 (m-10) REVERT: S 120 ASN cc_start: 0.7025 (t0) cc_final: 0.5250 (t0) REVERT: T 106 LEU cc_start: 0.7477 (mm) cc_final: 0.6802 (tp) REVERT: T 119 ASN cc_start: 0.8644 (m-40) cc_final: 0.8269 (m110) REVERT: T 143 PHE cc_start: 0.8210 (p90) cc_final: 0.7612 (p90) REVERT: T 145 TYR cc_start: 0.6778 (p90) cc_final: 0.6437 (p90) REVERT: T 163 PHE cc_start: 0.7768 (m-80) cc_final: 0.6926 (m-80) REVERT: T 216 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6054 (mt-10) REVERT: T 217 VAL cc_start: 0.8420 (t) cc_final: 0.8071 (p) REVERT: a 61 MET cc_start: 0.6422 (mtt) cc_final: 0.6168 (tpp) REVERT: a 300 MET cc_start: 0.7362 (mtm) cc_final: 0.7141 (mtm) REVERT: a 366 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7849 (tmtt) REVERT: a 451 LEU cc_start: 0.8450 (tp) cc_final: 0.8208 (mt) REVERT: a 540 MET cc_start: 0.7310 (ptm) cc_final: 0.7010 (ptm) REVERT: a 629 LEU cc_start: 0.4988 (mt) cc_final: 0.4670 (tp) REVERT: a 777 PHE cc_start: 0.7604 (t80) cc_final: 0.7202 (t80) REVERT: a 794 MET cc_start: 0.7954 (tmm) cc_final: 0.7687 (tmm) REVERT: b 6 LEU cc_start: 0.9260 (tp) cc_final: 0.9021 (tt) REVERT: b 166 ASP cc_start: 0.8373 (t0) cc_final: 0.8167 (t0) REVERT: c 318 LYS cc_start: 0.8204 (mttt) cc_final: 0.7750 (mttt) REVERT: d 17 GLU cc_start: 0.7944 (tp30) cc_final: 0.7713 (tt0) REVERT: d 93 LEU cc_start: 0.8897 (tp) cc_final: 0.8647 (tp) REVERT: d 145 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7735 (mm-40) REVERT: d 271 TYR cc_start: 0.8304 (m-80) cc_final: 0.8045 (m-80) REVERT: d 275 LYS cc_start: 0.8408 (tttt) cc_final: 0.7561 (ttpp) REVERT: d 292 ASP cc_start: 0.8487 (m-30) cc_final: 0.8152 (m-30) REVERT: d 308 ASN cc_start: 0.7557 (m-40) cc_final: 0.7265 (m-40) REVERT: d 309 GLN cc_start: 0.7982 (tt0) cc_final: 0.7561 (tt0) REVERT: d 310 PHE cc_start: 0.7984 (m-80) cc_final: 0.7758 (m-10) REVERT: d 343 LYS cc_start: 0.8452 (mttt) cc_final: 0.8141 (mtmt) REVERT: f 25 MET cc_start: 0.8553 (ppp) cc_final: 0.8161 (ppp) REVERT: f 59 TYR cc_start: 0.7608 (m-10) cc_final: 0.7049 (m-80) REVERT: g 26 SER cc_start: 0.8809 (p) cc_final: 0.8554 (p) REVERT: g 75 LEU cc_start: 0.8203 (mm) cc_final: 0.7965 (tt) REVERT: g 131 MET cc_start: 0.7929 (ttp) cc_final: 0.7728 (ttm) REVERT: h 54 LYS cc_start: 0.7874 (mttt) cc_final: 0.7446 (mmtt) REVERT: i 23 MET cc_start: 0.7459 (tpp) cc_final: 0.6970 (tpp) REVERT: i 47 MET cc_start: 0.7044 (mmm) cc_final: 0.6587 (mmm) REVERT: i 93 LEU cc_start: 0.8998 (tt) cc_final: 0.8765 (tt) REVERT: i 97 LEU cc_start: 0.8793 (mt) cc_final: 0.8353 (mp) REVERT: k 70 LEU cc_start: 0.9029 (tp) cc_final: 0.8763 (tp) REVERT: l 10 TYR cc_start: 0.8672 (p90) cc_final: 0.8472 (p90) REVERT: l 52 ILE cc_start: 0.9282 (pt) cc_final: 0.8983 (mt) REVERT: l 54 LYS cc_start: 0.8030 (mttt) cc_final: 0.7661 (mmtt) REVERT: l 78 ASN cc_start: 0.7977 (t0) cc_final: 0.7770 (t0) REVERT: l 89 SER cc_start: 0.9359 (m) cc_final: 0.9130 (t) REVERT: m 23 MET cc_start: 0.9081 (tpt) cc_final: 0.8875 (tpp) REVERT: m 36 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7899 (mptt) REVERT: n 47 MET cc_start: 0.7687 (mmm) cc_final: 0.7430 (mmt) REVERT: n 54 LYS cc_start: 0.8508 (mttt) cc_final: 0.7925 (mtpp) REVERT: p 294 ASN cc_start: 0.8162 (t0) cc_final: 0.7777 (t0) outliers start: 219 outliers final: 124 residues processed: 2280 average time/residue: 0.6509 time to fit residues: 2516.5023 Evaluate side-chains 2001 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1872 time to evaluate : 5.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 67 ASN Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 48 ASP Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain R residue 253 ASP Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 17 GLN Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 194 ASP Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 201 ASN Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain a residue 62 ASP Chi-restraints excluded: chain a residue 360 THR Chi-restraints excluded: chain a residue 366 LYS Chi-restraints excluded: chain a residue 646 LEU Chi-restraints excluded: chain a residue 736 THR Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 171 SER Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain d residue 4 PHE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 266 ASN Chi-restraints excluded: chain d residue 299 VAL Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 155 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 61 MET Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 78 ASN Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 132 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 445 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 666 optimal weight: 0.9990 chunk 545 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 802 optimal weight: 0.7980 chunk 866 optimal weight: 2.9990 chunk 714 optimal weight: 2.9990 chunk 795 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 643 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS F 251 ASN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN H 170 ASN H 206 GLN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 GLN ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN O 6 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 GLN ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS R 207 GLN S 127 HIS S 149 ASN a 489 ASN a 524 ASN ** a 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 391 HIS ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 GLN m 123 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 71099 Z= 0.367 Angle : 0.699 15.642 96090 Z= 0.364 Chirality : 0.045 0.264 10909 Planarity : 0.005 0.058 12296 Dihedral : 5.377 101.999 9657 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.46 % Favored : 97.53 % Rotamer: Outliers : 4.19 % Allowed : 15.67 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 8831 helix: 0.56 (0.07), residues: 5217 sheet: -0.94 (0.17), residues: 793 loop : -0.05 (0.12), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 122 HIS 0.024 0.001 HIS G 336 PHE 0.034 0.002 PHE S 200 TYR 0.029 0.002 TYR S 197 ARG 0.013 0.001 ARG O 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2227 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1911 time to evaluate : 6.127 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 25 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8084 (p) REVERT: A 39 MET cc_start: 0.8736 (tpt) cc_final: 0.8473 (tpt) REVERT: A 80 LEU cc_start: 0.9040 (tp) cc_final: 0.8571 (mt) REVERT: A 245 THR cc_start: 0.9294 (m) cc_final: 0.8786 (p) REVERT: A 268 ASN cc_start: 0.8008 (m-40) cc_final: 0.7516 (t0) REVERT: A 291 PHE cc_start: 0.7960 (m-80) cc_final: 0.7746 (m-80) REVERT: A 387 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8323 (tp30) REVERT: A 494 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 100 ASP cc_start: 0.8276 (p0) cc_final: 0.7989 (p0) REVERT: B 205 MET cc_start: 0.8391 (mtm) cc_final: 0.7860 (mtp) REVERT: B 268 ASN cc_start: 0.8348 (t0) cc_final: 0.7624 (t0) REVERT: B 279 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 320 VAL cc_start: 0.9548 (t) cc_final: 0.9098 (p) REVERT: B 445 PHE cc_start: 0.8641 (m-80) cc_final: 0.8201 (m-80) REVERT: B 478 LYS cc_start: 0.9011 (mttt) cc_final: 0.8675 (mmmm) REVERT: B 508 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 513 LYS cc_start: 0.9044 (tttp) cc_final: 0.8804 (ptpp) REVERT: B 517 ASP cc_start: 0.7930 (m-30) cc_final: 0.7640 (m-30) REVERT: B 518 ASP cc_start: 0.7815 (m-30) cc_final: 0.7462 (m-30) REVERT: B 523 ASN cc_start: 0.8247 (t0) cc_final: 0.7839 (t0) REVERT: B 525 TYR cc_start: 0.8063 (m-80) cc_final: 0.7739 (m-80) REVERT: B 550 MET cc_start: 0.8857 (mmm) cc_final: 0.8636 (mtm) REVERT: C 80 LEU cc_start: 0.9083 (tp) cc_final: 0.8660 (mt) REVERT: C 235 ASP cc_start: 0.7523 (m-30) cc_final: 0.7296 (m-30) REVERT: C 264 SER cc_start: 0.9697 (m) cc_final: 0.9104 (p) REVERT: C 285 SER cc_start: 0.9452 (m) cc_final: 0.9165 (t) REVERT: C 307 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8265 (mttm) REVERT: C 346 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8466 (ttt) REVERT: C 372 SER cc_start: 0.8661 (m) cc_final: 0.7837 (t) REVERT: C 441 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7461 (mm-40) REVERT: C 494 GLN cc_start: 0.8548 (tp40) cc_final: 0.8313 (tt0) REVERT: C 506 LYS cc_start: 0.8873 (mttt) cc_final: 0.8209 (mtmm) REVERT: C 510 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8357 (tt0) REVERT: C 532 CYS cc_start: 0.8915 (t) cc_final: 0.8358 (t) REVERT: C 540 MET cc_start: 0.8605 (mtp) cc_final: 0.8400 (mtp) REVERT: C 543 ASN cc_start: 0.8344 (m-40) cc_final: 0.7739 (m-40) REVERT: D 51 SER cc_start: 0.8747 (p) cc_final: 0.8486 (t) REVERT: D 127 MET cc_start: 0.8705 (mtp) cc_final: 0.8501 (mtp) REVERT: D 169 MET cc_start: 0.9328 (tmm) cc_final: 0.9046 (tmm) REVERT: D 254 MET cc_start: 0.9007 (tpt) cc_final: 0.8591 (tpp) REVERT: D 283 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7195 (tm-30) REVERT: D 300 MET cc_start: 0.9229 (mmm) cc_final: 0.8931 (mmt) REVERT: D 491 MET cc_start: 0.8597 (mmp) cc_final: 0.8395 (tpp) REVERT: E 87 LEU cc_start: 0.9408 (tp) cc_final: 0.9131 (tt) REVERT: E 238 MET cc_start: 0.8283 (tpt) cc_final: 0.7988 (tpp) REVERT: E 345 ASN cc_start: 0.8208 (m-40) cc_final: 0.7924 (m110) REVERT: E 355 THR cc_start: 0.8775 (m) cc_final: 0.8119 (p) REVERT: E 358 ASN cc_start: 0.7938 (t0) cc_final: 0.7738 (t0) REVERT: E 435 MET cc_start: 0.7413 (ttp) cc_final: 0.6995 (tmm) REVERT: F 238 MET cc_start: 0.8081 (tpp) cc_final: 0.7667 (tpp) REVERT: F 245 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8131 (tmtt) REVERT: F 255 ASP cc_start: 0.7663 (m-30) cc_final: 0.7350 (t0) REVERT: F 395 LEU cc_start: 0.9205 (tp) cc_final: 0.8456 (tt) REVERT: F 401 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8895 (mm) REVERT: G 85 ASP cc_start: 0.7599 (t0) cc_final: 0.7378 (t0) REVERT: G 100 THR cc_start: 0.8875 (m) cc_final: 0.8574 (p) REVERT: H 9 ILE cc_start: 0.9351 (mm) cc_final: 0.9129 (tp) REVERT: H 27 GLN cc_start: 0.8246 (mt0) cc_final: 0.8017 (mt0) REVERT: H 62 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7673 (tpp) REVERT: I 73 SER cc_start: 0.8811 (t) cc_final: 0.8574 (p) REVERT: I 77 ASN cc_start: 0.8961 (t0) cc_final: 0.8584 (t0) REVERT: I 106 VAL cc_start: 0.9017 (t) cc_final: 0.8692 (t) REVERT: I 109 THR cc_start: 0.8675 (p) cc_final: 0.8408 (t) REVERT: I 112 TYR cc_start: 0.9077 (t80) cc_final: 0.8779 (t80) REVERT: I 115 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8234 (mp) REVERT: I 133 ILE cc_start: 0.9274 (mt) cc_final: 0.8968 (mm) REVERT: I 159 THR cc_start: 0.9010 (p) cc_final: 0.8739 (t) REVERT: I 168 ASP cc_start: 0.7435 (t0) cc_final: 0.7178 (t0) REVERT: I 219 ASN cc_start: 0.8270 (t0) cc_final: 0.7590 (t0) REVERT: J 88 ASP cc_start: 0.8154 (m-30) cc_final: 0.7605 (m-30) REVERT: J 136 CYS cc_start: 0.8093 (p) cc_final: 0.7793 (p) REVERT: J 172 TYR cc_start: 0.8555 (m-80) cc_final: 0.7657 (m-10) REVERT: J 198 SER cc_start: 0.9282 (t) cc_final: 0.9055 (m) REVERT: K 72 MET cc_start: 0.8370 (ttm) cc_final: 0.8089 (tpp) REVERT: K 184 TYR cc_start: 0.8633 (m-80) cc_final: 0.8333 (m-80) REVERT: K 196 LEU cc_start: 0.9209 (mm) cc_final: 0.9002 (mm) REVERT: L 13 ASP cc_start: 0.8213 (p0) cc_final: 0.8011 (p0) REVERT: M 77 THR cc_start: 0.9187 (m) cc_final: 0.8943 (p) REVERT: M 80 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8790 (mmtm) REVERT: M 90 GLN cc_start: 0.8363 (tp40) cc_final: 0.7892 (tp40) REVERT: M 100 LEU cc_start: 0.9257 (tp) cc_final: 0.8809 (mm) REVERT: N 34 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8436 (mmtt) REVERT: N 86 ASN cc_start: 0.8896 (m-40) cc_final: 0.8661 (m-40) REVERT: N 102 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7990 (t80) REVERT: N 113 ASN cc_start: 0.9209 (m-40) cc_final: 0.8925 (m-40) REVERT: O 66 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7802 (t70) REVERT: O 86 ASN cc_start: 0.8543 (m-40) cc_final: 0.8221 (m110) REVERT: Q 98 ILE cc_start: 0.8249 (mm) cc_final: 0.7879 (mm) REVERT: R 90 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7844 (pp20) REVERT: R 155 MET cc_start: 0.8077 (ttp) cc_final: 0.7812 (ttp) REVERT: R 197 TYR cc_start: 0.7788 (t80) cc_final: 0.6887 (t80) REVERT: R 203 TYR cc_start: 0.7920 (t80) cc_final: 0.7711 (t80) REVERT: S 10 MET cc_start: 0.7529 (mpp) cc_final: 0.7307 (mpp) REVERT: S 28 TYR cc_start: 0.8301 (t80) cc_final: 0.7734 (t80) REVERT: S 113 GLU cc_start: 0.8190 (tp30) cc_final: 0.7981 (tp30) REVERT: S 120 ASN cc_start: 0.7025 (t0) cc_final: 0.6474 (t0) REVERT: S 151 PHE cc_start: 0.8084 (m-10) cc_final: 0.7573 (m-10) REVERT: S 200 PHE cc_start: 0.6776 (t80) cc_final: 0.6462 (t80) REVERT: T 61 LEU cc_start: 0.8202 (mt) cc_final: 0.7965 (mt) REVERT: T 119 ASN cc_start: 0.8680 (m-40) cc_final: 0.8349 (m110) REVERT: T 145 TYR cc_start: 0.6904 (p90) cc_final: 0.6439 (p90) REVERT: T 152 LYS cc_start: 0.8555 (mptt) cc_final: 0.8276 (mptt) REVERT: T 217 VAL cc_start: 0.8415 (t) cc_final: 0.8158 (p) REVERT: a 61 MET cc_start: 0.5782 (mtt) cc_final: 0.5338 (tpt) REVERT: a 300 MET cc_start: 0.7237 (mtm) cc_final: 0.7031 (mtm) REVERT: a 547 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.6951 (tp) REVERT: a 548 HIS cc_start: 0.6169 (OUTLIER) cc_final: 0.5868 (t-90) REVERT: a 584 PHE cc_start: 0.7348 (m-80) cc_final: 0.7071 (m-80) REVERT: a 777 PHE cc_start: 0.7750 (t80) cc_final: 0.7304 (t80) REVERT: b 6 LEU cc_start: 0.9306 (tp) cc_final: 0.9081 (tt) REVERT: c 318 LYS cc_start: 0.8245 (mttt) cc_final: 0.7824 (mtpt) REVERT: c 361 TYR cc_start: 0.8749 (m-10) cc_final: 0.8312 (m-10) REVERT: d 17 GLU cc_start: 0.8033 (tp30) cc_final: 0.7707 (tt0) REVERT: d 217 ASP cc_start: 0.7998 (m-30) cc_final: 0.7701 (m-30) REVERT: d 248 TYR cc_start: 0.7476 (t80) cc_final: 0.7242 (t80) REVERT: d 275 LYS cc_start: 0.8496 (tttt) cc_final: 0.8164 (ttpp) REVERT: d 292 ASP cc_start: 0.8557 (m-30) cc_final: 0.8206 (m-30) REVERT: d 308 ASN cc_start: 0.7921 (m-40) cc_final: 0.7563 (m-40) REVERT: d 309 GLN cc_start: 0.7998 (tt0) cc_final: 0.7694 (tt0) REVERT: d 343 LYS cc_start: 0.8523 (mttt) cc_final: 0.8126 (mtmt) REVERT: g 23 MET cc_start: 0.9110 (tpt) cc_final: 0.8872 (tpp) REVERT: g 26 SER cc_start: 0.8821 (p) cc_final: 0.8370 (t) REVERT: h 54 LYS cc_start: 0.7858 (mttt) cc_final: 0.7520 (mmtt) REVERT: h 131 MET cc_start: 0.8808 (ttp) cc_final: 0.8548 (ttp) REVERT: i 23 MET cc_start: 0.7834 (tpp) cc_final: 0.7286 (tpp) REVERT: i 85 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7471 (p) REVERT: i 88 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7670 (mmt-90) REVERT: i 93 LEU cc_start: 0.9144 (tt) cc_final: 0.8913 (tt) REVERT: i 97 LEU cc_start: 0.8767 (mt) cc_final: 0.8410 (mp) REVERT: i 123 GLN cc_start: 0.7841 (mp10) cc_final: 0.7626 (mp10) REVERT: j 51 LEU cc_start: 0.8581 (mp) cc_final: 0.8304 (mt) REVERT: j 54 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7763 (ttmt) REVERT: k 68 TYR cc_start: 0.8075 (m-10) cc_final: 0.7555 (m-10) REVERT: l 10 TYR cc_start: 0.8714 (p90) cc_final: 0.8450 (p90) REVERT: l 52 ILE cc_start: 0.9326 (pt) cc_final: 0.8990 (mt) REVERT: l 78 ASN cc_start: 0.8084 (t0) cc_final: 0.7792 (t0) REVERT: m 28 MET cc_start: 0.8140 (mmt) cc_final: 0.7655 (mmm) REVERT: m 36 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8026 (mptt) REVERT: m 53 MET cc_start: 0.6974 (tmm) cc_final: 0.5604 (tmm) REVERT: m 54 LYS cc_start: 0.7920 (mttt) cc_final: 0.7449 (mmtt) REVERT: n 21 SER cc_start: 0.9105 (m) cc_final: 0.8881 (p) REVERT: n 32 TYR cc_start: 0.8848 (t80) cc_final: 0.8609 (t80) REVERT: n 44 MET cc_start: 0.8120 (tmm) cc_final: 0.7883 (ptt) REVERT: n 50 GLU cc_start: 0.7541 (pm20) cc_final: 0.7338 (pm20) REVERT: n 54 LYS cc_start: 0.8775 (mttt) cc_final: 0.8241 (mtpp) REVERT: o 124 GLN cc_start: 0.7620 (tp-100) cc_final: 0.6875 (tm-30) REVERT: p 294 ASN cc_start: 0.8486 (t0) cc_final: 0.7957 (t0) outliers start: 316 outliers final: 195 residues processed: 2077 average time/residue: 0.6630 time to fit residues: 2328.4065 Evaluate side-chains 1947 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1739 time to evaluate : 6.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 48 ASP Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 272 LYS Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 194 ASP Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 201 ASN Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 547 ILE Chi-restraints excluded: chain a residue 548 HIS Chi-restraints excluded: chain a residue 646 LEU Chi-restraints excluded: chain a residue 736 THR Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 85 ARG Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 112 SER Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 155 VAL Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 298 ASP Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 114 THR Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 299 VAL Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 74 VAL Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 118 VAL Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 155 LYS Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 54 LYS Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 102 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 61 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain p residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 792 optimal weight: 0.6980 chunk 603 optimal weight: 50.0000 chunk 416 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 382 optimal weight: 0.9990 chunk 538 optimal weight: 10.0000 chunk 805 optimal weight: 2.9990 chunk 852 optimal weight: 0.6980 chunk 420 optimal weight: 40.0000 chunk 763 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 GLN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN G 17 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN Q 21 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN Q 207 GLN ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS S 17 GLN a 372 HIS ** a 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 266 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN d 118 HIS ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 ASN m 92 GLN m 123 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 71099 Z= 0.271 Angle : 0.654 13.218 96090 Z= 0.336 Chirality : 0.043 0.298 10909 Planarity : 0.005 0.071 12296 Dihedral : 5.210 99.347 9657 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.11 % Allowed : 16.89 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 8831 helix: 0.57 (0.07), residues: 5215 sheet: -0.94 (0.17), residues: 811 loop : -0.08 (0.12), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 122 HIS 0.010 0.001 HIS O 66 PHE 0.031 0.002 PHE a 551 TYR 0.031 0.002 TYR O 47 ARG 0.010 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2183 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1873 time to evaluate : 6.193 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 25 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8007 (p) REVERT: A 39 MET cc_start: 0.8753 (tpt) cc_final: 0.8473 (tpt) REVERT: A 80 LEU cc_start: 0.9015 (tp) cc_final: 0.8471 (mt) REVERT: A 268 ASN cc_start: 0.8048 (m-40) cc_final: 0.7249 (t0) REVERT: A 387 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8300 (tp30) REVERT: A 436 ASP cc_start: 0.8205 (t0) cc_final: 0.7707 (t0) REVERT: A 487 GLU cc_start: 0.8526 (tp30) cc_final: 0.8277 (tp30) REVERT: A 503 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 605 LEU cc_start: 0.9185 (tt) cc_final: 0.8747 (tt) REVERT: B 100 ASP cc_start: 0.8336 (p0) cc_final: 0.8034 (p0) REVERT: B 205 MET cc_start: 0.8433 (mtm) cc_final: 0.7841 (mtp) REVERT: B 268 ASN cc_start: 0.8290 (t0) cc_final: 0.7471 (t0) REVERT: B 279 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 296 MET cc_start: 0.8140 (pmm) cc_final: 0.7688 (pmm) REVERT: B 320 VAL cc_start: 0.9531 (t) cc_final: 0.9154 (p) REVERT: B 445 PHE cc_start: 0.8602 (m-80) cc_final: 0.8126 (m-80) REVERT: B 478 LYS cc_start: 0.8974 (mttt) cc_final: 0.8638 (mmmm) REVERT: B 517 ASP cc_start: 0.7926 (m-30) cc_final: 0.7676 (m-30) REVERT: B 518 ASP cc_start: 0.7763 (m-30) cc_final: 0.7354 (m-30) REVERT: B 523 ASN cc_start: 0.8323 (t0) cc_final: 0.8119 (t0) REVERT: B 525 TYR cc_start: 0.8073 (m-80) cc_final: 0.7719 (m-80) REVERT: B 550 MET cc_start: 0.8895 (mmm) cc_final: 0.8597 (mtm) REVERT: B 582 SER cc_start: 0.9170 (m) cc_final: 0.8662 (p) REVERT: C 80 LEU cc_start: 0.9096 (tp) cc_final: 0.8660 (mt) REVERT: C 139 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8326 (ptpp) REVERT: C 235 ASP cc_start: 0.7539 (m-30) cc_final: 0.7277 (m-30) REVERT: C 264 SER cc_start: 0.9651 (m) cc_final: 0.9122 (p) REVERT: C 283 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7375 (mt-10) REVERT: C 285 SER cc_start: 0.9494 (m) cc_final: 0.9181 (t) REVERT: C 307 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8473 (mttp) REVERT: C 346 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8536 (ttt) REVERT: C 372 SER cc_start: 0.8686 (m) cc_final: 0.7901 (t) REVERT: C 441 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7405 (mm-40) REVERT: C 494 GLN cc_start: 0.8784 (tp40) cc_final: 0.8494 (tt0) REVERT: C 506 LYS cc_start: 0.8885 (mttt) cc_final: 0.8236 (mtmm) REVERT: C 532 CYS cc_start: 0.8824 (t) cc_final: 0.8325 (t) REVERT: C 540 MET cc_start: 0.8572 (mtp) cc_final: 0.8341 (mtp) REVERT: C 543 ASN cc_start: 0.8435 (m-40) cc_final: 0.7977 (m-40) REVERT: C 553 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7514 (ttm110) REVERT: C 574 MET cc_start: 0.7823 (mtm) cc_final: 0.7485 (ptp) REVERT: D 169 MET cc_start: 0.9358 (tmm) cc_final: 0.8891 (tmm) REVERT: D 234 MET cc_start: 0.8248 (mpp) cc_final: 0.7799 (mtt) REVERT: D 254 MET cc_start: 0.9004 (tpt) cc_final: 0.8625 (tpp) REVERT: D 283 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7195 (tm-30) REVERT: D 300 MET cc_start: 0.9126 (mmm) cc_final: 0.8831 (mmt) REVERT: D 491 MET cc_start: 0.8585 (mmp) cc_final: 0.8378 (tpp) REVERT: E 87 LEU cc_start: 0.9373 (tp) cc_final: 0.9119 (tt) REVERT: E 345 ASN cc_start: 0.8162 (m-40) cc_final: 0.7844 (m110) REVERT: E 355 THR cc_start: 0.8733 (m) cc_final: 0.7928 (p) REVERT: E 435 MET cc_start: 0.7496 (ttp) cc_final: 0.7137 (tmm) REVERT: E 441 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7066 (pp20) REVERT: F 154 MET cc_start: 0.7981 (mmm) cc_final: 0.7700 (mtm) REVERT: F 201 GLU cc_start: 0.8372 (mp0) cc_final: 0.8142 (mp0) REVERT: F 238 MET cc_start: 0.8117 (tpp) cc_final: 0.7848 (tpp) REVERT: F 245 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8267 (tttm) REVERT: F 255 ASP cc_start: 0.7631 (m-30) cc_final: 0.7369 (t0) REVERT: F 395 LEU cc_start: 0.9296 (tp) cc_final: 0.8327 (tt) REVERT: F 401 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8810 (mm) REVERT: G 85 ASP cc_start: 0.7525 (t0) cc_final: 0.7288 (t0) REVERT: G 100 THR cc_start: 0.8804 (m) cc_final: 0.8548 (p) REVERT: G 336 HIS cc_start: 0.7730 (m90) cc_final: 0.7520 (m90) REVERT: H 8 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6898 (mm-30) REVERT: H 27 GLN cc_start: 0.8250 (mt0) cc_final: 0.8016 (mt0) REVERT: H 67 PHE cc_start: 0.8112 (t80) cc_final: 0.7863 (t80) REVERT: H 212 ILE cc_start: 0.9148 (tp) cc_final: 0.8920 (pt) REVERT: I 77 ASN cc_start: 0.8941 (t0) cc_final: 0.8595 (t0) REVERT: I 109 THR cc_start: 0.8584 (p) cc_final: 0.8285 (t) REVERT: I 115 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8156 (mp) REVERT: I 133 ILE cc_start: 0.9254 (mt) cc_final: 0.8960 (mm) REVERT: I 196 LEU cc_start: 0.9065 (mt) cc_final: 0.8749 (mt) REVERT: I 208 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (mmm) REVERT: J 88 ASP cc_start: 0.8346 (m-30) cc_final: 0.7702 (m-30) REVERT: J 89 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7931 (t0) REVERT: J 136 CYS cc_start: 0.8143 (p) cc_final: 0.7933 (p) REVERT: J 172 TYR cc_start: 0.8558 (m-80) cc_final: 0.7780 (m-10) REVERT: J 207 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7762 (mmm) REVERT: L 13 ASP cc_start: 0.8235 (p0) cc_final: 0.7951 (p0) REVERT: L 33 HIS cc_start: 0.7532 (m90) cc_final: 0.7281 (m170) REVERT: M 90 GLN cc_start: 0.8358 (tp40) cc_final: 0.7737 (tp40) REVERT: M 100 LEU cc_start: 0.9225 (tp) cc_final: 0.8793 (mm) REVERT: N 86 ASN cc_start: 0.8864 (m-40) cc_final: 0.8628 (m-40) REVERT: N 102 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8075 (t80) REVERT: O 66 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7976 (t70) REVERT: O 86 ASN cc_start: 0.8609 (m-40) cc_final: 0.8299 (m110) REVERT: Q 130 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8486 (mm) REVERT: Q 134 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8337 (m110) REVERT: Q 139 TYR cc_start: 0.8501 (t80) cc_final: 0.8284 (t80) REVERT: Q 151 PHE cc_start: 0.8284 (m-10) cc_final: 0.7956 (m-10) REVERT: Q 177 GLN cc_start: 0.8317 (pp30) cc_final: 0.8102 (pp30) REVERT: Q 213 PHE cc_start: 0.6384 (m-80) cc_final: 0.6019 (m-80) REVERT: R 155 MET cc_start: 0.8210 (ttp) cc_final: 0.7884 (ttp) REVERT: S 10 MET cc_start: 0.7491 (mpp) cc_final: 0.7217 (mpp) REVERT: S 17 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7781 (tp40) REVERT: S 28 TYR cc_start: 0.8252 (t80) cc_final: 0.7844 (t80) REVERT: S 113 GLU cc_start: 0.8268 (tp30) cc_final: 0.8056 (tp30) REVERT: S 120 ASN cc_start: 0.7057 (t0) cc_final: 0.6829 (t0) REVERT: S 126 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6741 (t80) REVERT: S 151 PHE cc_start: 0.8080 (m-10) cc_final: 0.7660 (m-10) REVERT: S 152 LEU cc_start: 0.8750 (tp) cc_final: 0.8522 (tp) REVERT: S 197 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6688 (m-80) REVERT: S 200 PHE cc_start: 0.7083 (t80) cc_final: 0.6763 (t80) REVERT: S 229 MET cc_start: 0.8689 (mmm) cc_final: 0.8447 (mmm) REVERT: T 119 ASN cc_start: 0.8672 (m-40) cc_final: 0.8406 (m110) REVERT: T 143 PHE cc_start: 0.8107 (p90) cc_final: 0.7184 (p90) REVERT: T 145 TYR cc_start: 0.6836 (p90) cc_final: 0.6385 (p90) REVERT: T 155 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8433 (tptp) REVERT: T 201 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6004 (p0) REVERT: a 61 MET cc_start: 0.5743 (mtt) cc_final: 0.5261 (tpt) REVERT: a 421 VAL cc_start: 0.8530 (m) cc_final: 0.8250 (p) REVERT: a 451 LEU cc_start: 0.7824 (mt) cc_final: 0.7459 (mt) REVERT: a 453 MET cc_start: 0.8939 (ppp) cc_final: 0.8158 (ppp) REVERT: a 484 MET cc_start: 0.3074 (mtp) cc_final: 0.1363 (ttp) REVERT: a 777 PHE cc_start: 0.7823 (t80) cc_final: 0.7612 (t80) REVERT: a 778 PHE cc_start: 0.7833 (m-80) cc_final: 0.7495 (m-80) REVERT: b 6 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9046 (tt) REVERT: b 82 LYS cc_start: 0.8395 (tppp) cc_final: 0.8036 (mttp) REVERT: c 277 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8073 (mmmm) REVERT: c 361 TYR cc_start: 0.8768 (m-10) cc_final: 0.8410 (m-10) REVERT: c 401 THR cc_start: 0.8654 (p) cc_final: 0.8405 (t) REVERT: d 17 GLU cc_start: 0.7867 (tp30) cc_final: 0.7625 (tt0) REVERT: d 217 ASP cc_start: 0.7977 (m-30) cc_final: 0.7722 (m-30) REVERT: d 291 GLU cc_start: 0.8248 (tp30) cc_final: 0.7875 (mm-30) REVERT: d 292 ASP cc_start: 0.8577 (m-30) cc_final: 0.8311 (m-30) REVERT: d 308 ASN cc_start: 0.7815 (m-40) cc_final: 0.7395 (m-40) REVERT: d 309 GLN cc_start: 0.7815 (tt0) cc_final: 0.7317 (tt0) REVERT: e 40 MET cc_start: 0.5343 (ptm) cc_final: 0.4750 (ppp) REVERT: g 17 MET cc_start: 0.9004 (tpp) cc_final: 0.8689 (mmt) REVERT: g 23 MET cc_start: 0.9123 (tpt) cc_final: 0.8896 (tpp) REVERT: g 26 SER cc_start: 0.8820 (p) cc_final: 0.8358 (t) REVERT: h 54 LYS cc_start: 0.7955 (mttt) cc_final: 0.7676 (mmtt) REVERT: h 97 LEU cc_start: 0.8745 (mt) cc_final: 0.8528 (tp) REVERT: h 131 MET cc_start: 0.8786 (ttp) cc_final: 0.8436 (ttp) REVERT: i 23 MET cc_start: 0.7844 (tpp) cc_final: 0.7398 (tpp) REVERT: i 54 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7768 (mmtt) REVERT: i 85 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7488 (p) REVERT: i 88 ARG cc_start: 0.8096 (mmt90) cc_final: 0.7763 (mmt-90) REVERT: i 97 LEU cc_start: 0.8635 (mt) cc_final: 0.8368 (mp) REVERT: k 68 TYR cc_start: 0.8090 (m-10) cc_final: 0.7384 (m-10) REVERT: k 143 LEU cc_start: 0.9055 (tp) cc_final: 0.8832 (tp) REVERT: l 10 TYR cc_start: 0.8595 (p90) cc_final: 0.8310 (p90) REVERT: l 52 ILE cc_start: 0.9275 (pt) cc_final: 0.8946 (mt) REVERT: l 78 ASN cc_start: 0.8082 (t0) cc_final: 0.7764 (t0) REVERT: m 28 MET cc_start: 0.8075 (mmt) cc_final: 0.7605 (mmm) REVERT: m 36 LYS cc_start: 0.8392 (mmmt) cc_final: 0.8004 (mptt) REVERT: m 53 MET cc_start: 0.6954 (tmm) cc_final: 0.6118 (tmm) REVERT: m 54 LYS cc_start: 0.7823 (mttt) cc_final: 0.7289 (mmtt) REVERT: m 124 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7920 (tm-30) REVERT: n 21 SER cc_start: 0.9008 (m) cc_final: 0.8807 (p) REVERT: n 54 LYS cc_start: 0.8751 (mttt) cc_final: 0.8225 (mtpp) REVERT: n 79 SER cc_start: 0.8368 (m) cc_final: 0.7866 (t) REVERT: n 91 LEU cc_start: 0.9291 (mt) cc_final: 0.9036 (mt) REVERT: p 294 ASN cc_start: 0.8643 (t0) cc_final: 0.8075 (t0) outliers start: 310 outliers final: 203 residues processed: 2021 average time/residue: 0.6519 time to fit residues: 2243.7983 Evaluate side-chains 1941 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1719 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 ASN Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain Q residue 48 ASP Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 130 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 17 GLN Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain T residue 201 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 646 LEU Chi-restraints excluded: chain a residue 736 THR Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 85 ARG Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 155 VAL Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 266 GLN Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 68 SER Chi-restraints excluded: chain d residue 114 THR Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain d residue 299 VAL Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain i residue 155 LYS Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 75 LEU Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 102 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 61 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 44 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain p residue 309 LEU Chi-restraints excluded: chain p residue 338 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 710 optimal weight: 3.9990 chunk 483 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 634 optimal weight: 20.0000 chunk 351 optimal weight: 50.0000 chunk 727 optimal weight: 8.9990 chunk 589 optimal weight: 50.0000 chunk 1 optimal weight: 0.8980 chunk 435 optimal weight: 0.9990 chunk 765 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN E 358 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN Q 184 HIS ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 GLN R 162 GLN R 198 HIS S 17 GLN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 812 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN d 60 ASN d 118 HIS ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 123 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 71099 Z= 0.389 Angle : 0.701 13.342 96090 Z= 0.361 Chirality : 0.045 0.339 10909 Planarity : 0.005 0.055 12296 Dihedral : 5.207 100.002 9657 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.81 % Allowed : 17.76 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.09), residues: 8831 helix: 0.50 (0.07), residues: 5227 sheet: -1.12 (0.17), residues: 831 loop : -0.18 (0.12), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP S 122 HIS 0.012 0.001 HIS B 164 PHE 0.035 0.002 PHE J 38 TYR 0.036 0.002 TYR a 728 ARG 0.011 0.001 ARG Q 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2148 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 1785 time to evaluate : 6.116 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: A 25 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 39 MET cc_start: 0.8722 (tpt) cc_final: 0.8477 (tpt) REVERT: A 80 LEU cc_start: 0.9082 (tp) cc_final: 0.8455 (mt) REVERT: A 245 THR cc_start: 0.9298 (m) cc_final: 0.8821 (p) REVERT: A 268 ASN cc_start: 0.8034 (m-40) cc_final: 0.7505 (t0) REVERT: A 387 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8350 (tp30) REVERT: A 436 ASP cc_start: 0.8138 (t0) cc_final: 0.7645 (t0) REVERT: A 487 GLU cc_start: 0.8547 (tp30) cc_final: 0.8251 (tp30) REVERT: A 548 TYR cc_start: 0.8621 (t80) cc_final: 0.8396 (t80) REVERT: B 100 ASP cc_start: 0.8350 (p0) cc_final: 0.8082 (p0) REVERT: B 117 TYR cc_start: 0.8876 (m-80) cc_final: 0.8098 (m-80) REVERT: B 140 ASN cc_start: 0.8030 (m-40) cc_final: 0.7814 (t0) REVERT: B 205 MET cc_start: 0.8568 (mtm) cc_final: 0.8299 (mtm) REVERT: B 268 ASN cc_start: 0.8272 (t0) cc_final: 0.7509 (t0) REVERT: B 296 MET cc_start: 0.7969 (pmm) cc_final: 0.7639 (pmm) REVERT: B 320 VAL cc_start: 0.9538 (t) cc_final: 0.9227 (p) REVERT: B 356 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: B 393 LYS cc_start: 0.8449 (mttt) cc_final: 0.8226 (ttmm) REVERT: B 445 PHE cc_start: 0.8535 (m-80) cc_final: 0.8127 (m-80) REVERT: B 478 LYS cc_start: 0.8993 (mttt) cc_final: 0.8667 (mmmm) REVERT: B 508 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8494 (p) REVERT: B 513 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8283 (ptpp) REVERT: B 517 ASP cc_start: 0.7889 (m-30) cc_final: 0.7644 (m-30) REVERT: B 518 ASP cc_start: 0.7668 (m-30) cc_final: 0.7323 (m-30) REVERT: B 523 ASN cc_start: 0.8441 (t0) cc_final: 0.8158 (t0) REVERT: B 525 TYR cc_start: 0.8095 (m-80) cc_final: 0.7699 (m-80) REVERT: B 550 MET cc_start: 0.8808 (mmm) cc_final: 0.8525 (mtm) REVERT: B 552 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7647 (mmm160) REVERT: B 582 SER cc_start: 0.9204 (m) cc_final: 0.8703 (p) REVERT: B 603 GLN cc_start: 0.8335 (tp40) cc_final: 0.7898 (tp-100) REVERT: C 80 LEU cc_start: 0.9137 (tp) cc_final: 0.8626 (mt) REVERT: C 139 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8364 (ptpp) REVERT: C 235 ASP cc_start: 0.7583 (m-30) cc_final: 0.7319 (m-30) REVERT: C 264 SER cc_start: 0.9585 (m) cc_final: 0.9083 (p) REVERT: C 279 GLU cc_start: 0.7746 (tp30) cc_final: 0.7238 (tp30) REVERT: C 283 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7516 (mt-10) REVERT: C 285 SER cc_start: 0.9503 (m) cc_final: 0.9169 (t) REVERT: C 307 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8569 (mttp) REVERT: C 346 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8391 (ttt) REVERT: C 347 MET cc_start: 0.8738 (mmt) cc_final: 0.8508 (mmt) REVERT: C 372 SER cc_start: 0.8704 (m) cc_final: 0.8091 (t) REVERT: C 441 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7545 (mm-40) REVERT: C 494 GLN cc_start: 0.8706 (tp40) cc_final: 0.8272 (tt0) REVERT: C 506 LYS cc_start: 0.8885 (mttt) cc_final: 0.8249 (mtmm) REVERT: C 532 CYS cc_start: 0.8787 (t) cc_final: 0.8291 (t) REVERT: C 540 MET cc_start: 0.8651 (mtp) cc_final: 0.8433 (mtp) REVERT: C 543 ASN cc_start: 0.8574 (m-40) cc_final: 0.8017 (m-40) REVERT: D 126 ASP cc_start: 0.8137 (m-30) cc_final: 0.7851 (p0) REVERT: D 127 MET cc_start: 0.8581 (mtp) cc_final: 0.8310 (mmm) REVERT: D 169 MET cc_start: 0.9395 (tmm) cc_final: 0.9012 (tmm) REVERT: D 234 MET cc_start: 0.8455 (mpp) cc_final: 0.7999 (mtt) REVERT: D 254 MET cc_start: 0.9074 (tpt) cc_final: 0.8698 (tpp) REVERT: D 283 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7321 (tm-30) REVERT: D 300 MET cc_start: 0.9191 (mmm) cc_final: 0.8859 (mmt) REVERT: D 435 MET cc_start: 0.8648 (ptm) cc_final: 0.8377 (ptm) REVERT: D 491 MET cc_start: 0.8639 (mmp) cc_final: 0.8395 (tpp) REVERT: E 254 MET cc_start: 0.8254 (mmt) cc_final: 0.7820 (mmt) REVERT: E 345 ASN cc_start: 0.8239 (m-40) cc_final: 0.7918 (m110) REVERT: E 355 THR cc_start: 0.8638 (m) cc_final: 0.7955 (p) REVERT: E 358 ASN cc_start: 0.7755 (t0) cc_final: 0.7543 (t0) REVERT: E 435 MET cc_start: 0.7546 (ttp) cc_final: 0.7196 (tmm) REVERT: F 148 GLU cc_start: 0.8349 (tp30) cc_final: 0.7731 (tp30) REVERT: F 154 MET cc_start: 0.8047 (mmm) cc_final: 0.7825 (mtm) REVERT: F 201 GLU cc_start: 0.8450 (mp0) cc_final: 0.8191 (mp0) REVERT: F 238 MET cc_start: 0.8269 (tpp) cc_final: 0.8002 (tpp) REVERT: F 255 ASP cc_start: 0.7651 (m-30) cc_final: 0.7449 (t0) REVERT: F 380 ASP cc_start: 0.8213 (t0) cc_final: 0.7991 (t0) REVERT: F 389 TYR cc_start: 0.7631 (t80) cc_final: 0.7268 (t80) REVERT: F 395 LEU cc_start: 0.9329 (tp) cc_final: 0.8115 (tp) REVERT: F 401 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8766 (mm) REVERT: F 435 MET cc_start: 0.8714 (mmp) cc_final: 0.8497 (tpp) REVERT: G 100 THR cc_start: 0.8772 (m) cc_final: 0.8510 (p) REVERT: H 7 ILE cc_start: 0.8649 (mm) cc_final: 0.8325 (mm) REVERT: H 27 GLN cc_start: 0.8293 (mt0) cc_final: 0.8083 (mt0) REVERT: H 51 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8402 (tp) REVERT: H 159 ASP cc_start: 0.8587 (t0) cc_final: 0.7035 (t70) REVERT: H 163 LYS cc_start: 0.8890 (mttt) cc_final: 0.8354 (mmtm) REVERT: I 109 THR cc_start: 0.8650 (p) cc_final: 0.8386 (t) REVERT: I 112 TYR cc_start: 0.9173 (t80) cc_final: 0.8908 (t80) REVERT: I 115 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8250 (mp) REVERT: I 133 ILE cc_start: 0.9275 (mt) cc_final: 0.8991 (mm) REVERT: I 196 LEU cc_start: 0.9213 (mt) cc_final: 0.8787 (mt) REVERT: I 208 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8704 (mmm) REVERT: J 88 ASP cc_start: 0.8298 (m-30) cc_final: 0.7723 (m-30) REVERT: J 89 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7447 (t0) REVERT: J 172 TYR cc_start: 0.8517 (m-80) cc_final: 0.7812 (m-10) REVERT: K 75 LEU cc_start: 0.9245 (tp) cc_final: 0.8728 (tt) REVERT: L 13 ASP cc_start: 0.8303 (p0) cc_final: 0.7953 (p0) REVERT: L 72 GLU cc_start: 0.8814 (mm-30) cc_final: 0.7494 (mm-30) REVERT: L 89 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8303 (mm) REVERT: M 80 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8794 (mmtm) REVERT: M 90 GLN cc_start: 0.8405 (tp40) cc_final: 0.7769 (tp40) REVERT: M 100 LEU cc_start: 0.9343 (tp) cc_final: 0.8905 (mm) REVERT: N 34 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8362 (mmtt) REVERT: N 86 ASN cc_start: 0.8853 (m-40) cc_final: 0.8647 (m-40) REVERT: N 92 ARG cc_start: 0.8417 (tmm-80) cc_final: 0.8175 (tmm-80) REVERT: N 102 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8167 (t80) REVERT: O 86 ASN cc_start: 0.8671 (m-40) cc_final: 0.8381 (m110) REVERT: Q 101 PHE cc_start: 0.7948 (m-10) cc_final: 0.5093 (m-10) REVERT: Q 130 LEU cc_start: 0.9046 (mm) cc_final: 0.8661 (mm) REVERT: Q 184 HIS cc_start: 0.7631 (t-90) cc_final: 0.7208 (t-90) REVERT: R 197 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7497 (t80) REVERT: S 10 MET cc_start: 0.7505 (mpp) cc_final: 0.7224 (mpp) REVERT: S 18 TYR cc_start: 0.8398 (t80) cc_final: 0.7959 (t80) REVERT: S 28 TYR cc_start: 0.8541 (t80) cc_final: 0.8083 (t80) REVERT: S 113 GLU cc_start: 0.8159 (tp30) cc_final: 0.7953 (tp30) REVERT: S 151 PHE cc_start: 0.7997 (m-10) cc_final: 0.7615 (m-10) REVERT: S 152 LEU cc_start: 0.8833 (tp) cc_final: 0.8536 (tp) REVERT: S 197 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6020 (m-80) REVERT: S 200 PHE cc_start: 0.7136 (t80) cc_final: 0.6768 (t80) REVERT: S 229 MET cc_start: 0.8679 (mmm) cc_final: 0.8447 (mmm) REVERT: T 62 LEU cc_start: 0.7957 (mm) cc_final: 0.7703 (tp) REVERT: T 143 PHE cc_start: 0.8184 (p90) cc_final: 0.7339 (p90) REVERT: T 155 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8513 (tptt) REVERT: T 201 ASN cc_start: 0.7121 (p0) cc_final: 0.6239 (p0) REVERT: a 10 MET cc_start: 0.3777 (pmm) cc_final: 0.3570 (pmm) REVERT: a 61 MET cc_start: 0.5762 (mtt) cc_final: 0.5299 (tpt) REVERT: a 417 THR cc_start: 0.7636 (m) cc_final: 0.7384 (p) REVERT: a 421 VAL cc_start: 0.8475 (m) cc_final: 0.8221 (p) REVERT: a 451 LEU cc_start: 0.7996 (mt) cc_final: 0.7612 (mt) REVERT: a 453 MET cc_start: 0.8850 (ppp) cc_final: 0.8130 (ppp) REVERT: a 466 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5294 (t0) REVERT: a 484 MET cc_start: 0.2795 (mtp) cc_final: 0.1181 (ttp) REVERT: a 759 MET cc_start: 0.4204 (mtt) cc_final: 0.3975 (mmt) REVERT: a 778 PHE cc_start: 0.7868 (m-80) cc_final: 0.7523 (m-80) REVERT: b 6 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9036 (tt) REVERT: b 82 LYS cc_start: 0.8356 (tppp) cc_final: 0.8075 (mttp) REVERT: b 180 GLU cc_start: 0.8041 (mp0) cc_final: 0.7772 (mp0) REVERT: c 277 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8068 (mmmm) REVERT: c 289 LEU cc_start: 0.7513 (tp) cc_final: 0.7308 (tp) REVERT: c 361 TYR cc_start: 0.8883 (m-10) cc_final: 0.8621 (m-10) REVERT: c 385 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8369 (tp) REVERT: c 404 GLN cc_start: 0.8441 (pm20) cc_final: 0.8208 (pm20) REVERT: d 17 GLU cc_start: 0.7919 (tp30) cc_final: 0.7645 (tt0) REVERT: d 239 LYS cc_start: 0.8821 (mttt) cc_final: 0.8368 (mtmm) REVERT: d 291 GLU cc_start: 0.8269 (tp30) cc_final: 0.8063 (mm-30) REVERT: d 292 ASP cc_start: 0.8577 (m-30) cc_final: 0.8318 (m-30) REVERT: d 308 ASN cc_start: 0.7888 (m-40) cc_final: 0.7479 (m-40) REVERT: d 309 GLN cc_start: 0.7994 (tt0) cc_final: 0.7599 (tt0) REVERT: d 343 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7979 (mtmt) REVERT: e 40 MET cc_start: 0.5427 (ptm) cc_final: 0.4976 (ppp) REVERT: g 17 MET cc_start: 0.8983 (tpp) cc_final: 0.8690 (mmt) REVERT: g 26 SER cc_start: 0.8718 (p) cc_final: 0.8221 (t) REVERT: g 144 TYR cc_start: 0.7851 (m-80) cc_final: 0.7382 (m-10) REVERT: h 97 LEU cc_start: 0.8798 (mt) cc_final: 0.8558 (tp) REVERT: h 131 MET cc_start: 0.8873 (ttp) cc_final: 0.8467 (ttp) REVERT: i 23 MET cc_start: 0.7736 (tpp) cc_final: 0.7266 (tpp) REVERT: j 51 LEU cc_start: 0.8569 (mp) cc_final: 0.8159 (mt) REVERT: j 123 GLN cc_start: 0.7212 (mt0) cc_final: 0.6258 (mt0) REVERT: k 68 TYR cc_start: 0.8073 (m-10) cc_final: 0.7646 (m-10) REVERT: l 10 TYR cc_start: 0.8685 (p90) cc_final: 0.8366 (p90) REVERT: l 52 ILE cc_start: 0.9303 (pt) cc_final: 0.8887 (mt) REVERT: l 78 ASN cc_start: 0.8167 (t0) cc_final: 0.7889 (t0) REVERT: l 87 TYR cc_start: 0.8612 (t80) cc_final: 0.8328 (t80) REVERT: m 28 MET cc_start: 0.8149 (mmt) cc_final: 0.7697 (mmm) REVERT: m 36 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8197 (mptt) REVERT: m 53 MET cc_start: 0.6945 (tmm) cc_final: 0.6036 (tmm) REVERT: m 54 LYS cc_start: 0.8001 (mttt) cc_final: 0.7415 (mmtt) REVERT: m 124 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8035 (tm-30) REVERT: n 26 SER cc_start: 0.8662 (p) cc_final: 0.8393 (p) REVERT: n 54 LYS cc_start: 0.8696 (mttt) cc_final: 0.8132 (mtpp) REVERT: n 79 SER cc_start: 0.8338 (m) cc_final: 0.7835 (t) REVERT: n 91 LEU cc_start: 0.9370 (mt) cc_final: 0.9099 (mt) outliers start: 363 outliers final: 250 residues processed: 1988 average time/residue: 0.6841 time to fit residues: 2333.2305 Evaluate side-chains 1952 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1685 time to evaluate : 6.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 75 ARG Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 48 ASP Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 135 HIS Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 646 LEU Chi-restraints excluded: chain a residue 736 THR Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 85 ARG Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain c residue 249 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 298 ASP Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 385 LEU Chi-restraints excluded: chain c residue 429 MET Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 68 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 114 THR Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain d residue 299 VAL Chi-restraints excluded: chain d residue 320 LYS Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 74 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 118 VAL Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 150 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 80 LEU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 121 THR Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 102 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 61 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 44 MET Chi-restraints excluded: chain o residue 47 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain p residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 286 optimal weight: 0.6980 chunk 767 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 500 optimal weight: 20.0000 chunk 210 optimal weight: 1.9990 chunk 853 optimal weight: 0.6980 chunk 708 optimal weight: 0.9990 chunk 395 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 448 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN H 206 GLN I 66 GLN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS S 17 GLN a 372 HIS a 807 HIS d 60 ASN d 118 HIS ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 123 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 71099 Z= 0.209 Angle : 0.647 13.947 96090 Z= 0.330 Chirality : 0.042 0.321 10909 Planarity : 0.005 0.116 12296 Dihedral : 5.081 95.432 9657 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.50 % Allowed : 19.92 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.09), residues: 8831 helix: 0.61 (0.07), residues: 5231 sheet: -1.08 (0.17), residues: 814 loop : -0.16 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP T 156 HIS 0.013 0.001 HIS a 372 PHE 0.047 0.002 PHE Q 101 TYR 0.035 0.002 TYR a 728 ARG 0.016 0.001 ARG Q 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2101 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1837 time to evaluate : 6.214 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: A 25 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 39 MET cc_start: 0.8661 (tpt) cc_final: 0.8424 (tpt) REVERT: A 80 LEU cc_start: 0.8948 (tp) cc_final: 0.8426 (mt) REVERT: A 268 ASN cc_start: 0.8017 (m-40) cc_final: 0.7247 (t0) REVERT: A 387 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8329 (tp30) REVERT: A 436 ASP cc_start: 0.8066 (t0) cc_final: 0.7627 (t0) REVERT: A 487 GLU cc_start: 0.8445 (tp30) cc_final: 0.8116 (tp30) REVERT: A 503 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 100 ASP cc_start: 0.8380 (p0) cc_final: 0.8020 (p0) REVERT: B 117 TYR cc_start: 0.8861 (m-80) cc_final: 0.7976 (m-80) REVERT: B 167 MET cc_start: 0.7821 (ptm) cc_final: 0.7614 (ptp) REVERT: B 205 MET cc_start: 0.8476 (mtm) cc_final: 0.8238 (mtm) REVERT: B 268 ASN cc_start: 0.8177 (t0) cc_final: 0.7352 (t0) REVERT: B 320 VAL cc_start: 0.9553 (t) cc_final: 0.9230 (p) REVERT: B 356 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: B 445 PHE cc_start: 0.8545 (m-80) cc_final: 0.8119 (m-80) REVERT: B 478 LYS cc_start: 0.8984 (mttt) cc_final: 0.8665 (mmmm) REVERT: B 508 THR cc_start: 0.9106 (m) cc_final: 0.8543 (p) REVERT: B 517 ASP cc_start: 0.7898 (m-30) cc_final: 0.7586 (m-30) REVERT: B 518 ASP cc_start: 0.7645 (m-30) cc_final: 0.7306 (m-30) REVERT: B 523 ASN cc_start: 0.8345 (t0) cc_final: 0.8079 (t0) REVERT: B 525 TYR cc_start: 0.8095 (m-80) cc_final: 0.7707 (m-80) REVERT: B 550 MET cc_start: 0.8798 (mmm) cc_final: 0.8510 (mtm) REVERT: B 552 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7667 (mmm160) REVERT: B 582 SER cc_start: 0.9142 (m) cc_final: 0.8632 (p) REVERT: B 604 LEU cc_start: 0.9103 (tt) cc_final: 0.8829 (tt) REVERT: C 80 LEU cc_start: 0.8997 (tp) cc_final: 0.8586 (mt) REVERT: C 235 ASP cc_start: 0.7522 (m-30) cc_final: 0.7286 (m-30) REVERT: C 264 SER cc_start: 0.9614 (m) cc_final: 0.9185 (p) REVERT: C 283 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7390 (mt-10) REVERT: C 285 SER cc_start: 0.9491 (m) cc_final: 0.9122 (t) REVERT: C 307 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8582 (mmtp) REVERT: C 346 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8495 (ttt) REVERT: C 347 MET cc_start: 0.8674 (mmt) cc_final: 0.8425 (mmt) REVERT: C 372 SER cc_start: 0.8744 (m) cc_final: 0.8113 (t) REVERT: C 441 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7103 (mm-40) REVERT: C 494 GLN cc_start: 0.8684 (tp40) cc_final: 0.8267 (tt0) REVERT: C 506 LYS cc_start: 0.8827 (mttt) cc_final: 0.8189 (mtmm) REVERT: C 532 CYS cc_start: 0.8824 (t) cc_final: 0.8322 (t) REVERT: C 540 MET cc_start: 0.8689 (mtp) cc_final: 0.8444 (mtp) REVERT: C 543 ASN cc_start: 0.8500 (m-40) cc_final: 0.8086 (m110) REVERT: C 553 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7385 (mtm110) REVERT: D 127 MET cc_start: 0.8424 (mtp) cc_final: 0.8206 (mmm) REVERT: D 169 MET cc_start: 0.9414 (tmm) cc_final: 0.8927 (tmm) REVERT: D 234 MET cc_start: 0.8240 (mpp) cc_final: 0.7884 (mtt) REVERT: D 254 MET cc_start: 0.8914 (tpt) cc_final: 0.8652 (tpp) REVERT: D 283 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 300 MET cc_start: 0.9021 (mmm) cc_final: 0.8680 (mmt) REVERT: D 374 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7814 (mt-10) REVERT: D 389 TYR cc_start: 0.7916 (t80) cc_final: 0.7592 (t80) REVERT: D 435 MET cc_start: 0.8817 (ptm) cc_final: 0.8540 (ptm) REVERT: D 451 TYR cc_start: 0.8549 (m-80) cc_final: 0.8050 (m-80) REVERT: D 491 MET cc_start: 0.8625 (mmp) cc_final: 0.8310 (tpp) REVERT: E 254 MET cc_start: 0.8109 (mmt) cc_final: 0.7833 (mmt) REVERT: E 345 ASN cc_start: 0.8225 (m-40) cc_final: 0.7905 (m110) REVERT: E 355 THR cc_start: 0.8641 (m) cc_final: 0.7992 (p) REVERT: E 358 ASN cc_start: 0.7772 (t0) cc_final: 0.7429 (t0) REVERT: F 148 GLU cc_start: 0.8265 (tp30) cc_final: 0.7851 (tp30) REVERT: F 201 GLU cc_start: 0.8317 (mp0) cc_final: 0.8103 (mp0) REVERT: F 238 MET cc_start: 0.8186 (tpp) cc_final: 0.7930 (tpp) REVERT: F 367 ASP cc_start: 0.8794 (t70) cc_final: 0.8515 (t0) REVERT: F 389 TYR cc_start: 0.7399 (t80) cc_final: 0.7110 (t80) REVERT: F 395 LEU cc_start: 0.9236 (tp) cc_final: 0.7948 (tp) REVERT: F 401 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8766 (mm) REVERT: F 435 MET cc_start: 0.8697 (mmp) cc_final: 0.8417 (tpp) REVERT: G 19 TRP cc_start: 0.6462 (t-100) cc_final: 0.5930 (t-100) REVERT: G 100 THR cc_start: 0.8699 (m) cc_final: 0.8460 (p) REVERT: H 7 ILE cc_start: 0.8742 (mm) cc_final: 0.8397 (mm) REVERT: H 8 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6819 (mm-30) REVERT: H 27 GLN cc_start: 0.8261 (mt0) cc_final: 0.8032 (mt0) REVERT: H 51 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8502 (tp) REVERT: H 86 ASN cc_start: 0.8563 (m-40) cc_final: 0.8252 (m110) REVERT: H 163 LYS cc_start: 0.8845 (mttt) cc_final: 0.8494 (mmtm) REVERT: I 109 THR cc_start: 0.8608 (p) cc_final: 0.8377 (t) REVERT: I 112 TYR cc_start: 0.9127 (t80) cc_final: 0.8844 (t80) REVERT: I 115 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8253 (mp) REVERT: I 133 ILE cc_start: 0.9254 (mt) cc_final: 0.8952 (mm) REVERT: I 196 LEU cc_start: 0.9146 (mt) cc_final: 0.8934 (mt) REVERT: I 208 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8679 (mmm) REVERT: J 88 ASP cc_start: 0.8277 (m-30) cc_final: 0.7680 (m-30) REVERT: J 89 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7460 (t0) REVERT: J 117 ASP cc_start: 0.8525 (t0) cc_final: 0.8122 (t0) REVERT: J 172 TYR cc_start: 0.8518 (m-80) cc_final: 0.7783 (m-10) REVERT: K 72 MET cc_start: 0.8302 (tpp) cc_final: 0.8040 (tpp) REVERT: K 75 LEU cc_start: 0.9210 (tp) cc_final: 0.8700 (tt) REVERT: L 13 ASP cc_start: 0.8285 (p0) cc_final: 0.7900 (p0) REVERT: L 33 HIS cc_start: 0.7191 (m170) cc_final: 0.6912 (m170) REVERT: L 72 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8090 (tp30) REVERT: M 80 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8814 (mmtm) REVERT: M 90 GLN cc_start: 0.8390 (tp40) cc_final: 0.7714 (tp40) REVERT: M 100 LEU cc_start: 0.9295 (tp) cc_final: 0.8876 (mm) REVERT: M 113 ASN cc_start: 0.9247 (m-40) cc_final: 0.9004 (t0) REVERT: N 34 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8255 (mmtt) REVERT: N 102 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8213 (t80) REVERT: N 115 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7140 (mmt90) REVERT: O 86 ASN cc_start: 0.8651 (m-40) cc_final: 0.8381 (m110) REVERT: Q 130 LEU cc_start: 0.9091 (mm) cc_final: 0.8700 (mm) REVERT: Q 153 ARG cc_start: 0.7633 (mtm110) cc_final: 0.6913 (ptp-170) REVERT: Q 197 TYR cc_start: 0.7439 (t80) cc_final: 0.7172 (m-80) REVERT: Q 213 PHE cc_start: 0.6516 (m-80) cc_final: 0.6137 (m-80) REVERT: R 197 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7353 (t80) REVERT: S 10 MET cc_start: 0.7492 (mpp) cc_final: 0.7166 (mpp) REVERT: S 28 TYR cc_start: 0.8442 (t80) cc_final: 0.8012 (t80) REVERT: S 90 GLU cc_start: 0.8030 (tp30) cc_final: 0.7278 (tp30) REVERT: S 93 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7571 (ttp80) REVERT: S 113 GLU cc_start: 0.8131 (tp30) cc_final: 0.7918 (tp30) REVERT: S 150 ASN cc_start: 0.9141 (m-40) cc_final: 0.8851 (m110) REVERT: S 151 PHE cc_start: 0.7892 (m-10) cc_final: 0.7628 (m-10) REVERT: S 152 LEU cc_start: 0.8810 (tp) cc_final: 0.8417 (tp) REVERT: S 200 PHE cc_start: 0.7142 (t80) cc_final: 0.6781 (t80) REVERT: T 62 LEU cc_start: 0.7917 (mm) cc_final: 0.7546 (tp) REVERT: T 85 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7589 (tp) REVERT: T 122 PHE cc_start: 0.8502 (p90) cc_final: 0.8196 (p90) REVERT: T 155 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8398 (tptt) REVERT: T 218 TRP cc_start: 0.6983 (m100) cc_final: 0.5926 (m100) REVERT: a 80 MET cc_start: 0.4857 (pmm) cc_final: 0.4501 (pmm) REVERT: a 451 LEU cc_start: 0.8075 (mt) cc_final: 0.7721 (mt) REVERT: a 453 MET cc_start: 0.8811 (ppp) cc_final: 0.8100 (ppp) REVERT: a 484 MET cc_start: 0.2720 (mtp) cc_final: 0.1301 (ttp) REVERT: a 629 LEU cc_start: 0.4099 (mt) cc_final: 0.3295 (tp) REVERT: b 6 LEU cc_start: 0.9158 (tp) cc_final: 0.8879 (tt) REVERT: b 82 LYS cc_start: 0.8387 (tppp) cc_final: 0.8146 (mttp) REVERT: b 180 GLU cc_start: 0.7935 (mp0) cc_final: 0.7586 (mp0) REVERT: c 277 LYS cc_start: 0.8353 (mmmm) cc_final: 0.8067 (mmmm) REVERT: c 361 TYR cc_start: 0.8846 (m-10) cc_final: 0.8529 (m-10) REVERT: d 17 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: d 292 ASP cc_start: 0.8595 (m-30) cc_final: 0.8328 (m-30) REVERT: d 308 ASN cc_start: 0.7824 (m-40) cc_final: 0.7477 (m-40) REVERT: d 343 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7959 (mtmt) REVERT: e 40 MET cc_start: 0.5577 (ptm) cc_final: 0.5092 (ppp) REVERT: g 17 MET cc_start: 0.9090 (tpp) cc_final: 0.8761 (mmt) REVERT: g 131 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7912 (tmm) REVERT: g 144 TYR cc_start: 0.7777 (m-80) cc_final: 0.7489 (m-10) REVERT: h 26 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8621 (t) REVERT: h 97 LEU cc_start: 0.8672 (mt) cc_final: 0.8470 (tp) REVERT: i 23 MET cc_start: 0.7637 (tpp) cc_final: 0.7206 (tpp) REVERT: i 48 ARG cc_start: 0.7699 (mmp80) cc_final: 0.7463 (mmp80) REVERT: i 88 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7729 (mmt-90) REVERT: i 97 LEU cc_start: 0.8630 (mt) cc_final: 0.8346 (tp) REVERT: i 139 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7213 (tm-30) REVERT: i 154 THR cc_start: 0.8086 (p) cc_final: 0.7800 (m) REVERT: j 119 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7413 (mtt90) REVERT: k 68 TYR cc_start: 0.7957 (m-10) cc_final: 0.7386 (m-10) REVERT: k 143 LEU cc_start: 0.9030 (tp) cc_final: 0.8549 (tp) REVERT: l 10 TYR cc_start: 0.8571 (p90) cc_final: 0.8288 (p90) REVERT: l 52 ILE cc_start: 0.9246 (pt) cc_final: 0.8873 (mt) REVERT: l 78 ASN cc_start: 0.7983 (t0) cc_final: 0.7735 (t0) REVERT: l 90 PHE cc_start: 0.9311 (m-10) cc_final: 0.8983 (m-80) REVERT: m 28 MET cc_start: 0.7994 (mmt) cc_final: 0.7536 (mmm) REVERT: m 53 MET cc_start: 0.6826 (tmm) cc_final: 0.6273 (tmm) REVERT: m 54 LYS cc_start: 0.7900 (mttt) cc_final: 0.7242 (mmtt) REVERT: m 124 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7708 (tm-30) REVERT: n 54 LYS cc_start: 0.8640 (mttt) cc_final: 0.8131 (mtpp) REVERT: n 91 LEU cc_start: 0.9251 (mt) cc_final: 0.9003 (mt) REVERT: o 7 ASN cc_start: 0.7789 (p0) cc_final: 0.7518 (p0) REVERT: p 303 TYR cc_start: 0.8741 (t80) cc_final: 0.8534 (t80) REVERT: p 341 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7689 (mmm-85) outliers start: 264 outliers final: 180 residues processed: 1969 average time/residue: 0.6503 time to fit residues: 2177.8160 Evaluate side-chains 1928 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1734 time to evaluate : 6.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 ASN Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 197 TYR Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 17 GLN Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 135 HIS Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 290 ILE Chi-restraints excluded: chain a residue 308 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 429 MET Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 44 MET Chi-restraints excluded: chain o residue 47 MET Chi-restraints excluded: chain o residue 141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 822 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 486 optimal weight: 0.8980 chunk 623 optimal weight: 9.9990 chunk 482 optimal weight: 3.9990 chunk 718 optimal weight: 5.9990 chunk 476 optimal weight: 10.0000 chunk 850 optimal weight: 3.9990 chunk 532 optimal weight: 5.9990 chunk 518 optimal weight: 0.9990 chunk 392 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN E 205 GLN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 85 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN H 206 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 GLN Q 50 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 ASN R 198 HIS ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 GLN a 751 GLN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 288 ASN ** c 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN d 118 HIS ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 78 ASN m 123 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 71099 Z= 0.357 Angle : 0.694 13.985 96090 Z= 0.355 Chirality : 0.044 0.344 10909 Planarity : 0.005 0.092 12296 Dihedral : 5.105 95.125 9657 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.21 % Allowed : 20.08 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.09), residues: 8831 helix: 0.57 (0.07), residues: 5224 sheet: -1.16 (0.17), residues: 812 loop : -0.25 (0.12), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP T 156 HIS 0.014 0.001 HIS G 336 PHE 0.049 0.002 PHE R 151 TYR 0.043 0.002 TYR a 728 ARG 0.009 0.001 ARG O 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2085 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1767 time to evaluate : 6.166 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: A 25 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 39 MET cc_start: 0.8746 (tpt) cc_final: 0.8471 (tpt) REVERT: A 80 LEU cc_start: 0.9005 (tp) cc_final: 0.8360 (mt) REVERT: A 268 ASN cc_start: 0.8037 (m-40) cc_final: 0.7261 (t0) REVERT: A 387 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8373 (tp30) REVERT: A 405 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8988 (t) REVERT: A 436 ASP cc_start: 0.8231 (t0) cc_final: 0.7762 (t0) REVERT: A 487 GLU cc_start: 0.8478 (tp30) cc_final: 0.8114 (tp30) REVERT: B 117 TYR cc_start: 0.8959 (m-80) cc_final: 0.7912 (m-80) REVERT: B 140 ASN cc_start: 0.7715 (t0) cc_final: 0.7479 (t0) REVERT: B 167 MET cc_start: 0.7918 (ptm) cc_final: 0.7609 (ptp) REVERT: B 205 MET cc_start: 0.8573 (mtm) cc_final: 0.8327 (mtm) REVERT: B 268 ASN cc_start: 0.8272 (t0) cc_final: 0.7454 (t0) REVERT: B 320 VAL cc_start: 0.9530 (t) cc_final: 0.9206 (p) REVERT: B 356 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: B 393 LYS cc_start: 0.8510 (mttt) cc_final: 0.8252 (ttmt) REVERT: B 478 LYS cc_start: 0.9064 (mttt) cc_final: 0.8577 (mmmm) REVERT: B 508 THR cc_start: 0.9040 (m) cc_final: 0.8660 (p) REVERT: B 517 ASP cc_start: 0.7885 (m-30) cc_final: 0.7611 (m-30) REVERT: B 518 ASP cc_start: 0.7480 (m-30) cc_final: 0.7192 (m-30) REVERT: B 523 ASN cc_start: 0.8296 (t0) cc_final: 0.7926 (t0) REVERT: B 550 MET cc_start: 0.8805 (mmm) cc_final: 0.8496 (mtm) REVERT: B 582 SER cc_start: 0.9179 (m) cc_final: 0.8752 (p) REVERT: B 604 LEU cc_start: 0.9187 (tt) cc_final: 0.8542 (tt) REVERT: C 80 LEU cc_start: 0.9091 (tp) cc_final: 0.8635 (mt) REVERT: C 235 ASP cc_start: 0.7619 (m-30) cc_final: 0.7365 (m-30) REVERT: C 264 SER cc_start: 0.9666 (m) cc_final: 0.9237 (p) REVERT: C 285 SER cc_start: 0.9478 (m) cc_final: 0.9134 (t) REVERT: C 307 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8602 (mmtp) REVERT: C 346 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8409 (ttt) REVERT: C 372 SER cc_start: 0.8802 (m) cc_final: 0.8467 (t) REVERT: C 494 GLN cc_start: 0.8629 (tp40) cc_final: 0.8223 (tt0) REVERT: C 506 LYS cc_start: 0.8865 (mttt) cc_final: 0.8413 (mtmt) REVERT: C 532 CYS cc_start: 0.8736 (t) cc_final: 0.8183 (t) REVERT: C 552 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7655 (mmm-85) REVERT: C 553 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7343 (mtm110) REVERT: D 169 MET cc_start: 0.9378 (tmm) cc_final: 0.8984 (tmm) REVERT: D 234 MET cc_start: 0.8477 (mpp) cc_final: 0.8044 (mtt) REVERT: D 254 MET cc_start: 0.9035 (tpt) cc_final: 0.8764 (tpt) REVERT: D 283 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 300 MET cc_start: 0.9157 (mmm) cc_final: 0.8789 (mmt) REVERT: D 374 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: D 389 TYR cc_start: 0.8248 (t80) cc_final: 0.7909 (t80) REVERT: D 435 MET cc_start: 0.8862 (ptm) cc_final: 0.8589 (ptm) REVERT: D 491 MET cc_start: 0.8626 (mmp) cc_final: 0.8200 (tpp) REVERT: E 254 MET cc_start: 0.8257 (mmt) cc_final: 0.7893 (mmt) REVERT: E 345 ASN cc_start: 0.8264 (m-40) cc_final: 0.7954 (m110) REVERT: E 355 THR cc_start: 0.8651 (m) cc_final: 0.8008 (p) REVERT: E 358 ASN cc_start: 0.7779 (t0) cc_final: 0.7492 (t0) REVERT: E 435 MET cc_start: 0.7728 (tmm) cc_final: 0.7194 (tmm) REVERT: F 201 GLU cc_start: 0.8410 (mp0) cc_final: 0.8165 (mp0) REVERT: F 238 MET cc_start: 0.8293 (tpp) cc_final: 0.8080 (tpp) REVERT: F 367 ASP cc_start: 0.8858 (t70) cc_final: 0.8655 (t0) REVERT: F 389 TYR cc_start: 0.7663 (t80) cc_final: 0.7419 (t80) REVERT: F 401 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8775 (mm) REVERT: F 435 MET cc_start: 0.8592 (mmp) cc_final: 0.8083 (tpp) REVERT: G 19 TRP cc_start: 0.6519 (t-100) cc_final: 0.6174 (t-100) REVERT: G 100 THR cc_start: 0.8725 (m) cc_final: 0.8488 (p) REVERT: G 125 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7646 (mm) REVERT: H 7 ILE cc_start: 0.8641 (mm) cc_final: 0.8250 (mm) REVERT: H 27 GLN cc_start: 0.8298 (mt0) cc_final: 0.8085 (mt0) REVERT: H 51 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8477 (tp) REVERT: H 86 ASN cc_start: 0.8597 (m-40) cc_final: 0.8276 (m110) REVERT: H 163 LYS cc_start: 0.8798 (mttt) cc_final: 0.8454 (mmtm) REVERT: H 190 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7221 (mm-30) REVERT: I 112 TYR cc_start: 0.9150 (t80) cc_final: 0.8904 (t80) REVERT: I 115 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8277 (mp) REVERT: I 133 ILE cc_start: 0.9277 (mt) cc_final: 0.8993 (mm) REVERT: I 208 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8695 (mmm) REVERT: J 88 ASP cc_start: 0.8388 (m-30) cc_final: 0.7814 (m-30) REVERT: J 89 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7543 (t0) REVERT: J 117 ASP cc_start: 0.8571 (t0) cc_final: 0.8131 (t0) REVERT: J 172 TYR cc_start: 0.8581 (m-80) cc_final: 0.7821 (m-10) REVERT: K 72 MET cc_start: 0.8355 (tpp) cc_final: 0.8054 (tpp) REVERT: K 75 LEU cc_start: 0.9274 (tp) cc_final: 0.8742 (tt) REVERT: K 121 LEU cc_start: 0.8910 (tp) cc_final: 0.8529 (tp) REVERT: L 13 ASP cc_start: 0.8385 (p0) cc_final: 0.8070 (p0) REVERT: L 89 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8355 (mm) REVERT: M 80 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8810 (mmtm) REVERT: M 90 GLN cc_start: 0.8506 (tp40) cc_final: 0.7841 (tp40) REVERT: M 96 LEU cc_start: 0.8877 (tt) cc_final: 0.8667 (tp) REVERT: M 100 LEU cc_start: 0.9303 (tp) cc_final: 0.8889 (mm) REVERT: N 48 ARG cc_start: 0.9156 (ttt90) cc_final: 0.8892 (tpt-90) REVERT: N 102 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8243 (t80) REVERT: N 115 ARG cc_start: 0.7984 (tpp80) cc_final: 0.7146 (mmt90) REVERT: O 86 ASN cc_start: 0.8705 (m-40) cc_final: 0.8421 (m110) REVERT: Q 103 MET cc_start: 0.6794 (mmm) cc_final: 0.6480 (mmm) REVERT: Q 130 LEU cc_start: 0.9076 (mm) cc_final: 0.8705 (mm) REVERT: Q 178 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8035 (mm) REVERT: Q 184 HIS cc_start: 0.7686 (t-90) cc_final: 0.7218 (t-90) REVERT: Q 197 TYR cc_start: 0.7540 (t80) cc_final: 0.7310 (m-80) REVERT: Q 213 PHE cc_start: 0.6580 (m-80) cc_final: 0.6254 (m-80) REVERT: Q 229 MET cc_start: 0.9028 (mmm) cc_final: 0.8806 (mmm) REVERT: R 79 ASP cc_start: 0.8300 (t0) cc_final: 0.8093 (m-30) REVERT: R 134 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8237 (m110) REVERT: S 10 MET cc_start: 0.7556 (mpp) cc_final: 0.7238 (mpp) REVERT: S 28 TYR cc_start: 0.8574 (t80) cc_final: 0.8113 (t80) REVERT: S 54 ILE cc_start: 0.8789 (tp) cc_final: 0.8558 (mt) REVERT: S 90 GLU cc_start: 0.8109 (tp30) cc_final: 0.7461 (tp30) REVERT: S 93 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7802 (ttp80) REVERT: S 113 GLU cc_start: 0.8071 (tp30) cc_final: 0.7810 (tp30) REVERT: S 120 ASN cc_start: 0.6806 (t0) cc_final: 0.6552 (t0) REVERT: S 150 ASN cc_start: 0.9159 (m-40) cc_final: 0.8842 (m110) REVERT: S 151 PHE cc_start: 0.7996 (m-10) cc_final: 0.7611 (m-10) REVERT: S 152 LEU cc_start: 0.8788 (tp) cc_final: 0.8364 (tp) REVERT: S 200 PHE cc_start: 0.7111 (t80) cc_final: 0.6710 (t80) REVERT: T 62 LEU cc_start: 0.8026 (mm) cc_final: 0.7709 (tp) REVERT: T 155 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8418 (tptt) REVERT: T 201 ASN cc_start: 0.7600 (m110) cc_final: 0.6710 (p0) REVERT: T 207 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8392 (mmtm) REVERT: T 213 GLN cc_start: 0.7886 (tt0) cc_final: 0.6947 (tm-30) REVERT: a 80 MET cc_start: 0.5031 (pmm) cc_final: 0.4686 (pmm) REVERT: a 355 MET cc_start: 0.1447 (pmm) cc_final: 0.1132 (pmm) REVERT: a 451 LEU cc_start: 0.8203 (mt) cc_final: 0.7789 (mt) REVERT: a 453 MET cc_start: 0.8740 (ppp) cc_final: 0.8032 (ppp) REVERT: a 629 LEU cc_start: 0.4298 (mt) cc_final: 0.3370 (tp) REVERT: a 777 PHE cc_start: 0.7968 (t80) cc_final: 0.7676 (t80) REVERT: b 82 LYS cc_start: 0.8446 (tppp) cc_final: 0.8220 (mttp) REVERT: b 180 GLU cc_start: 0.7933 (mp0) cc_final: 0.7610 (mp0) REVERT: c 277 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8144 (mmmm) REVERT: c 361 TYR cc_start: 0.8896 (m-10) cc_final: 0.8626 (m-10) REVERT: d 10 ASN cc_start: 0.8539 (m-40) cc_final: 0.8328 (m110) REVERT: d 17 GLU cc_start: 0.7833 (tp30) cc_final: 0.7589 (tt0) REVERT: d 30 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8164 (tp-100) REVERT: d 292 ASP cc_start: 0.8556 (m-30) cc_final: 0.8298 (m-30) REVERT: d 343 LYS cc_start: 0.8500 (mmmt) cc_final: 0.7904 (mtmt) REVERT: e 40 MET cc_start: 0.5674 (ptm) cc_final: 0.5156 (ppp) REVERT: g 17 MET cc_start: 0.8998 (tpp) cc_final: 0.8663 (mmt) REVERT: g 26 SER cc_start: 0.8652 (p) cc_final: 0.8125 (t) REVERT: g 131 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8131 (tmm) REVERT: g 144 TYR cc_start: 0.7917 (m-10) cc_final: 0.7422 (m-10) REVERT: h 87 TYR cc_start: 0.8620 (t80) cc_final: 0.8260 (t80) REVERT: h 97 LEU cc_start: 0.8754 (mt) cc_final: 0.8501 (tp) REVERT: i 23 MET cc_start: 0.7736 (tpp) cc_final: 0.7308 (tpp) REVERT: j 139 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7984 (tm-30) REVERT: k 68 TYR cc_start: 0.8056 (m-10) cc_final: 0.7705 (m-10) REVERT: k 87 TYR cc_start: 0.9031 (t80) cc_final: 0.8682 (t80) REVERT: l 10 TYR cc_start: 0.8621 (p90) cc_final: 0.8348 (p90) REVERT: l 52 ILE cc_start: 0.9300 (pt) cc_final: 0.8874 (mt) REVERT: l 78 ASN cc_start: 0.8183 (t0) cc_final: 0.7886 (t0) REVERT: l 87 TYR cc_start: 0.8504 (t80) cc_final: 0.8270 (t80) REVERT: m 28 MET cc_start: 0.8116 (mmt) cc_final: 0.7640 (mmm) REVERT: m 53 MET cc_start: 0.6944 (tmm) cc_final: 0.6654 (tmm) REVERT: m 54 LYS cc_start: 0.8006 (mttt) cc_final: 0.7305 (mmtt) REVERT: m 123 GLN cc_start: 0.8172 (mt0) cc_final: 0.7805 (mt0) REVERT: m 124 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7789 (tm-30) REVERT: n 87 TYR cc_start: 0.8476 (t80) cc_final: 0.8196 (t80) REVERT: n 91 LEU cc_start: 0.9293 (mt) cc_final: 0.9062 (mt) outliers start: 318 outliers final: 235 residues processed: 1925 average time/residue: 0.6862 time to fit residues: 2266.7272 Evaluate side-chains 1966 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1715 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 199 PHE Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 308 ASN Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 85 ARG Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 249 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 298 ASP Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 429 MET Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 68 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 43 ASP Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain h residue 123 GLN Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 118 VAL Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 80 LEU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 11 SER Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 102 SER Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 153 SER Chi-restraints excluded: chain n residue 7 ASN Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 44 MET Chi-restraints excluded: chain o residue 47 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 135 LEU Chi-restraints excluded: chain o residue 141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 525 optimal weight: 20.0000 chunk 339 optimal weight: 40.0000 chunk 507 optimal weight: 30.0000 chunk 256 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 540 optimal weight: 0.6980 chunk 579 optimal weight: 50.0000 chunk 420 optimal weight: 40.0000 chunk 79 optimal weight: 1.9990 chunk 668 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 85 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN H 206 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN Q 17 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 ASN R 198 HIS T 120 GLN T 190 HIS ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN d 118 HIS ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 78 ASN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 71099 Z= 0.321 Angle : 0.691 13.382 96090 Z= 0.353 Chirality : 0.044 0.338 10909 Planarity : 0.005 0.102 12296 Dihedral : 5.094 92.279 9657 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.07 % Allowed : 20.80 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.09), residues: 8831 helix: 0.53 (0.07), residues: 5118 sheet: -1.15 (0.17), residues: 806 loop : -0.25 (0.12), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 122 HIS 0.014 0.001 HIS G 336 PHE 0.035 0.002 PHE T 132 TYR 0.057 0.002 TYR N 47 ARG 0.020 0.001 ARG Q 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2094 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1787 time to evaluate : 6.165 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 25 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8071 (p) REVERT: A 39 MET cc_start: 0.8734 (tpt) cc_final: 0.8502 (tpt) REVERT: A 80 LEU cc_start: 0.8993 (tp) cc_final: 0.8345 (mt) REVERT: A 245 THR cc_start: 0.9243 (m) cc_final: 0.8781 (p) REVERT: A 268 ASN cc_start: 0.8005 (m-40) cc_final: 0.7259 (t0) REVERT: A 387 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8388 (tp30) REVERT: A 405 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9051 (t) REVERT: A 436 ASP cc_start: 0.8228 (t0) cc_final: 0.7745 (t0) REVERT: A 487 GLU cc_start: 0.8461 (tp30) cc_final: 0.8104 (tp30) REVERT: A 552 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7644 (ttm-80) REVERT: B 117 TYR cc_start: 0.9013 (m-80) cc_final: 0.8016 (m-80) REVERT: B 205 MET cc_start: 0.8534 (mtm) cc_final: 0.8309 (mtm) REVERT: B 268 ASN cc_start: 0.8365 (t0) cc_final: 0.7502 (t0) REVERT: B 320 VAL cc_start: 0.9589 (t) cc_final: 0.9278 (p) REVERT: B 356 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: B 393 LYS cc_start: 0.8520 (mttt) cc_final: 0.8229 (ttmt) REVERT: B 445 PHE cc_start: 0.8479 (m-80) cc_final: 0.8126 (m-80) REVERT: B 478 LYS cc_start: 0.9004 (mttt) cc_final: 0.8692 (mmmm) REVERT: B 508 THR cc_start: 0.9083 (m) cc_final: 0.8627 (p) REVERT: B 517 ASP cc_start: 0.7870 (m-30) cc_final: 0.7589 (m-30) REVERT: B 518 ASP cc_start: 0.7484 (m-30) cc_final: 0.7192 (m-30) REVERT: B 523 ASN cc_start: 0.8247 (t0) cc_final: 0.7976 (t0) REVERT: B 525 TYR cc_start: 0.8193 (m-80) cc_final: 0.7902 (m-80) REVERT: B 550 MET cc_start: 0.8790 (mmm) cc_final: 0.8481 (mtm) REVERT: B 582 SER cc_start: 0.9240 (m) cc_final: 0.8813 (p) REVERT: B 604 LEU cc_start: 0.9140 (tt) cc_final: 0.8854 (tt) REVERT: C 80 LEU cc_start: 0.9096 (tp) cc_final: 0.8624 (mt) REVERT: C 235 ASP cc_start: 0.7621 (m-30) cc_final: 0.7339 (m-30) REVERT: C 264 SER cc_start: 0.9661 (m) cc_final: 0.9253 (p) REVERT: C 285 SER cc_start: 0.9499 (m) cc_final: 0.9170 (t) REVERT: C 293 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7148 (tm-30) REVERT: C 307 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8578 (mttp) REVERT: C 346 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8671 (ttt) REVERT: C 372 SER cc_start: 0.8798 (m) cc_final: 0.8490 (t) REVERT: C 441 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7242 (mm-40) REVERT: C 494 GLN cc_start: 0.8585 (tp40) cc_final: 0.8249 (tt0) REVERT: C 532 CYS cc_start: 0.8772 (t) cc_final: 0.8259 (t) REVERT: C 553 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7217 (mtm110) REVERT: D 169 MET cc_start: 0.9362 (tmm) cc_final: 0.8956 (tmm) REVERT: D 234 MET cc_start: 0.8332 (mpp) cc_final: 0.7949 (mtt) REVERT: D 254 MET cc_start: 0.9030 (tpt) cc_final: 0.8776 (tpt) REVERT: D 283 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 300 MET cc_start: 0.9110 (mmm) cc_final: 0.8792 (mmt) REVERT: D 374 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: D 389 TYR cc_start: 0.8273 (t80) cc_final: 0.7914 (t80) REVERT: D 435 MET cc_start: 0.8865 (ptm) cc_final: 0.8578 (ptm) REVERT: D 491 MET cc_start: 0.8613 (mmp) cc_final: 0.8340 (tpp) REVERT: E 254 MET cc_start: 0.8273 (mmt) cc_final: 0.7965 (mmt) REVERT: E 345 ASN cc_start: 0.8257 (m-40) cc_final: 0.7955 (m110) REVERT: E 355 THR cc_start: 0.8658 (m) cc_final: 0.7966 (p) REVERT: E 358 ASN cc_start: 0.7781 (t0) cc_final: 0.7511 (t0) REVERT: E 435 MET cc_start: 0.7628 (tmm) cc_final: 0.7131 (tmm) REVERT: F 148 GLU cc_start: 0.8275 (tp30) cc_final: 0.7946 (tp30) REVERT: F 201 GLU cc_start: 0.8374 (mp0) cc_final: 0.8150 (mp0) REVERT: F 238 MET cc_start: 0.8317 (tpp) cc_final: 0.8101 (tpp) REVERT: F 380 ASP cc_start: 0.8230 (t0) cc_final: 0.7973 (t0) REVERT: F 401 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8728 (mm) REVERT: F 435 MET cc_start: 0.8578 (mmp) cc_final: 0.8166 (mmt) REVERT: G 100 THR cc_start: 0.8705 (m) cc_final: 0.8471 (p) REVERT: G 131 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7655 (tm-30) REVERT: H 7 ILE cc_start: 0.8679 (mm) cc_final: 0.8302 (mm) REVERT: H 27 GLN cc_start: 0.8303 (mt0) cc_final: 0.8094 (mt0) REVERT: H 51 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8517 (tp) REVERT: H 86 ASN cc_start: 0.8512 (m-40) cc_final: 0.8209 (m110) REVERT: H 163 LYS cc_start: 0.8783 (mttt) cc_final: 0.8476 (mmtm) REVERT: H 190 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7218 (mm-30) REVERT: I 112 TYR cc_start: 0.9152 (t80) cc_final: 0.8841 (t80) REVERT: I 115 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8347 (mp) REVERT: I 133 ILE cc_start: 0.9273 (mt) cc_final: 0.8987 (mm) REVERT: I 168 ASP cc_start: 0.7327 (t0) cc_final: 0.6850 (t0) REVERT: J 88 ASP cc_start: 0.8357 (m-30) cc_final: 0.7787 (m-30) REVERT: J 89 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7590 (t0) REVERT: J 172 TYR cc_start: 0.8626 (m-80) cc_final: 0.7940 (m-10) REVERT: K 72 MET cc_start: 0.8367 (tpp) cc_final: 0.8071 (tpp) REVERT: K 75 LEU cc_start: 0.9259 (tp) cc_final: 0.8700 (tt) REVERT: K 89 ASP cc_start: 0.8429 (m-30) cc_final: 0.8213 (p0) REVERT: L 13 ASP cc_start: 0.8409 (p0) cc_final: 0.8097 (p0) REVERT: L 89 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8343 (mm) REVERT: M 80 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8832 (mmtm) REVERT: M 90 GLN cc_start: 0.8542 (tp40) cc_final: 0.7883 (tp40) REVERT: M 100 LEU cc_start: 0.9299 (tp) cc_final: 0.8896 (mm) REVERT: N 48 ARG cc_start: 0.9174 (ttt90) cc_final: 0.8900 (tpt-90) REVERT: N 102 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8290 (t80) REVERT: O 86 ASN cc_start: 0.8636 (m-40) cc_final: 0.8325 (m110) REVERT: Q 103 MET cc_start: 0.6771 (mmm) cc_final: 0.6428 (mmm) REVERT: Q 130 LEU cc_start: 0.9080 (mm) cc_final: 0.8698 (mm) REVERT: Q 157 SER cc_start: 0.8726 (m) cc_final: 0.8522 (p) REVERT: Q 178 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7997 (mm) REVERT: Q 213 PHE cc_start: 0.6520 (m-80) cc_final: 0.6202 (m-80) REVERT: R 134 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8188 (m110) REVERT: S 10 MET cc_start: 0.7643 (mpp) cc_final: 0.7295 (mpp) REVERT: S 17 GLN cc_start: 0.8149 (tt0) cc_final: 0.7836 (tp40) REVERT: S 28 TYR cc_start: 0.8578 (t80) cc_final: 0.8113 (t80) REVERT: S 46 ARG cc_start: 0.8787 (ttm110) cc_final: 0.8167 (tpp80) REVERT: S 54 ILE cc_start: 0.8733 (tp) cc_final: 0.8519 (mt) REVERT: S 90 GLU cc_start: 0.8134 (tp30) cc_final: 0.7438 (tp30) REVERT: S 93 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7901 (ttp80) REVERT: S 120 ASN cc_start: 0.7037 (t0) cc_final: 0.6834 (t0) REVERT: S 150 ASN cc_start: 0.9164 (m-40) cc_final: 0.8843 (m110) REVERT: S 151 PHE cc_start: 0.7955 (m-10) cc_final: 0.7565 (m-10) REVERT: S 152 LEU cc_start: 0.8789 (tp) cc_final: 0.8361 (tp) REVERT: S 200 PHE cc_start: 0.7166 (t80) cc_final: 0.6757 (t80) REVERT: T 147 PHE cc_start: 0.7686 (m-10) cc_final: 0.7231 (m-10) REVERT: T 155 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8457 (tptt) REVERT: a 80 MET cc_start: 0.4995 (pmm) cc_final: 0.4719 (pmm) REVERT: a 355 MET cc_start: 0.1114 (pmm) cc_final: 0.0863 (pmm) REVERT: a 451 LEU cc_start: 0.8258 (mt) cc_final: 0.7773 (mt) REVERT: a 453 MET cc_start: 0.8684 (ppp) cc_final: 0.7926 (ppp) REVERT: a 484 MET cc_start: 0.2608 (mtp) cc_final: 0.1180 (ttp) REVERT: a 629 LEU cc_start: 0.4211 (mt) cc_final: 0.3253 (tp) REVERT: a 777 PHE cc_start: 0.8057 (t80) cc_final: 0.7799 (t80) REVERT: a 804 LEU cc_start: 0.9003 (mt) cc_final: 0.8589 (tp) REVERT: b 6 LEU cc_start: 0.9206 (tp) cc_final: 0.8989 (tt) REVERT: b 82 LYS cc_start: 0.8393 (tppp) cc_final: 0.8189 (mttp) REVERT: b 180 GLU cc_start: 0.7889 (mp0) cc_final: 0.7573 (mp0) REVERT: c 277 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8069 (mmmm) REVERT: c 361 TYR cc_start: 0.8877 (m-10) cc_final: 0.8609 (m-10) REVERT: d 10 ASN cc_start: 0.8518 (m-40) cc_final: 0.8316 (m110) REVERT: d 17 GLU cc_start: 0.7828 (tp30) cc_final: 0.7479 (tt0) REVERT: d 30 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8169 (tp-100) REVERT: d 186 TYR cc_start: 0.8948 (t80) cc_final: 0.8473 (t80) REVERT: d 292 ASP cc_start: 0.8539 (m-30) cc_final: 0.8307 (m-30) REVERT: d 343 LYS cc_start: 0.8460 (mmmt) cc_final: 0.7868 (mtmt) REVERT: e 40 MET cc_start: 0.5732 (ptm) cc_final: 0.5239 (ppp) REVERT: g 17 MET cc_start: 0.9090 (tpp) cc_final: 0.8758 (mmt) REVERT: g 23 MET cc_start: 0.9207 (tpt) cc_final: 0.8941 (tpp) REVERT: g 26 SER cc_start: 0.8664 (p) cc_final: 0.8118 (t) REVERT: g 131 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8129 (tmm) REVERT: g 144 TYR cc_start: 0.7970 (m-10) cc_final: 0.7414 (m-10) REVERT: h 26 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8661 (t) REVERT: h 97 LEU cc_start: 0.8729 (mt) cc_final: 0.8485 (tp) REVERT: i 23 MET cc_start: 0.7719 (tpp) cc_final: 0.7327 (tpp) REVERT: j 139 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7931 (tm-30) REVERT: k 68 TYR cc_start: 0.8049 (m-10) cc_final: 0.7662 (m-10) REVERT: k 87 TYR cc_start: 0.9060 (t80) cc_final: 0.8685 (t80) REVERT: l 10 TYR cc_start: 0.8621 (p90) cc_final: 0.8350 (p90) REVERT: l 52 ILE cc_start: 0.9271 (pt) cc_final: 0.8833 (mt) REVERT: l 78 ASN cc_start: 0.8183 (t0) cc_final: 0.7831 (t0) REVERT: l 87 TYR cc_start: 0.8482 (t80) cc_final: 0.8240 (t80) REVERT: l 124 GLN cc_start: 0.8789 (tm-30) cc_final: 0.7057 (tm-30) REVERT: m 28 MET cc_start: 0.8140 (mmt) cc_final: 0.7668 (mmm) REVERT: m 53 MET cc_start: 0.6910 (tmm) cc_final: 0.6641 (tmm) REVERT: m 54 LYS cc_start: 0.7993 (mttt) cc_final: 0.7281 (mmtt) REVERT: m 124 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7633 (tm-30) REVERT: n 87 TYR cc_start: 0.8518 (t80) cc_final: 0.8198 (t80) REVERT: n 91 LEU cc_start: 0.9290 (mt) cc_final: 0.9073 (mt) REVERT: p 294 ASN cc_start: 0.8718 (t0) cc_final: 0.8413 (t0) REVERT: p 303 TYR cc_start: 0.8734 (t80) cc_final: 0.8509 (t80) outliers start: 307 outliers final: 242 residues processed: 1942 average time/residue: 0.6571 time to fit residues: 2178.6898 Evaluate side-chains 1971 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1714 time to evaluate : 6.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 196 CYS Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 94 MET Chi-restraints excluded: chain a residue 308 ASN Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 85 ARG Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 249 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 385 LEU Chi-restraints excluded: chain c residue 429 MET Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 68 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 267 VAL Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain h residue 123 GLN Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 80 LEU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 81 THR Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 153 SER Chi-restraints excluded: chain n residue 7 ASN Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 61 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 44 MET Chi-restraints excluded: chain o residue 47 MET Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 141 LEU Chi-restraints excluded: chain p residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 773 optimal weight: 1.9990 chunk 814 optimal weight: 1.9990 chunk 743 optimal weight: 0.5980 chunk 792 optimal weight: 0.9990 chunk 476 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 622 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 715 optimal weight: 0.0170 chunk 749 optimal weight: 0.9980 chunk 789 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN H 85 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN I 77 ASN I 78 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 HIS Q 17 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN d 118 HIS d 263 GLN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 ASN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 78 ASN ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 123 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 71099 Z= 0.219 Angle : 0.690 13.810 96090 Z= 0.349 Chirality : 0.043 0.303 10909 Planarity : 0.005 0.071 12296 Dihedral : 5.022 91.259 9657 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.41 % Allowed : 22.11 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.09), residues: 8831 helix: 0.63 (0.07), residues: 5211 sheet: -1.07 (0.17), residues: 821 loop : -0.25 (0.12), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP S 122 HIS 0.013 0.001 HIS G 336 PHE 0.034 0.002 PHE T 132 TYR 0.042 0.002 TYR a 728 ARG 0.013 0.001 ARG Q 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2070 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1813 time to evaluate : 6.230 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 25 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.8013 (p) REVERT: A 80 LEU cc_start: 0.8942 (tp) cc_final: 0.8397 (mt) REVERT: A 268 ASN cc_start: 0.7980 (m-40) cc_final: 0.7229 (t0) REVERT: A 296 MET cc_start: 0.7544 (ptt) cc_final: 0.7330 (ptt) REVERT: A 387 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8387 (tp30) REVERT: A 436 ASP cc_start: 0.8064 (t0) cc_final: 0.7583 (t0) REVERT: A 487 GLU cc_start: 0.8411 (tp30) cc_final: 0.8057 (tp30) REVERT: B 117 TYR cc_start: 0.8947 (m-80) cc_final: 0.7957 (m-80) REVERT: B 205 MET cc_start: 0.8422 (mtm) cc_final: 0.8199 (mtm) REVERT: B 268 ASN cc_start: 0.8343 (t0) cc_final: 0.7478 (t0) REVERT: B 320 VAL cc_start: 0.9497 (t) cc_final: 0.9208 (p) REVERT: B 356 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: B 393 LYS cc_start: 0.8434 (mttt) cc_final: 0.8206 (ttmt) REVERT: B 445 PHE cc_start: 0.8461 (m-80) cc_final: 0.8149 (m-80) REVERT: B 508 THR cc_start: 0.9058 (m) cc_final: 0.8833 (p) REVERT: B 517 ASP cc_start: 0.7845 (m-30) cc_final: 0.7533 (m-30) REVERT: B 518 ASP cc_start: 0.7387 (m-30) cc_final: 0.7111 (m-30) REVERT: B 523 ASN cc_start: 0.8125 (t0) cc_final: 0.7857 (t0) REVERT: B 525 TYR cc_start: 0.8153 (m-80) cc_final: 0.7880 (m-80) REVERT: B 550 MET cc_start: 0.8833 (mmm) cc_final: 0.8610 (mtt) REVERT: B 582 SER cc_start: 0.9257 (m) cc_final: 0.8905 (p) REVERT: B 584 MET cc_start: 0.7899 (ptp) cc_final: 0.7536 (ptp) REVERT: B 604 LEU cc_start: 0.9129 (tt) cc_final: 0.8909 (tt) REVERT: C 80 LEU cc_start: 0.9055 (tp) cc_final: 0.8598 (mt) REVERT: C 235 ASP cc_start: 0.7623 (m-30) cc_final: 0.7329 (m-30) REVERT: C 263 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 264 SER cc_start: 0.9635 (m) cc_final: 0.9189 (p) REVERT: C 285 SER cc_start: 0.9502 (m) cc_final: 0.9132 (t) REVERT: C 307 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8281 (mttt) REVERT: C 346 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8626 (ttt) REVERT: C 372 SER cc_start: 0.8750 (m) cc_final: 0.8451 (t) REVERT: C 441 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7153 (mm-40) REVERT: C 494 GLN cc_start: 0.8551 (tp40) cc_final: 0.8315 (tt0) REVERT: C 532 CYS cc_start: 0.8726 (t) cc_final: 0.8223 (t) REVERT: C 553 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7205 (mtm110) REVERT: D 169 MET cc_start: 0.9430 (tmm) cc_final: 0.8904 (tmm) REVERT: D 254 MET cc_start: 0.8977 (tpt) cc_final: 0.8718 (tpp) REVERT: D 283 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7243 (tm-30) REVERT: D 300 MET cc_start: 0.9009 (mmm) cc_final: 0.8540 (tpp) REVERT: D 374 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: D 389 TYR cc_start: 0.8246 (t80) cc_final: 0.7919 (t80) REVERT: D 435 MET cc_start: 0.8844 (ptm) cc_final: 0.8608 (ptm) REVERT: D 451 TYR cc_start: 0.8491 (m-80) cc_final: 0.8124 (m-80) REVERT: D 491 MET cc_start: 0.8572 (mmp) cc_final: 0.8352 (tpp) REVERT: E 254 MET cc_start: 0.8165 (mmt) cc_final: 0.7904 (mmt) REVERT: E 345 ASN cc_start: 0.8257 (m-40) cc_final: 0.7945 (m110) REVERT: E 355 THR cc_start: 0.8678 (m) cc_final: 0.7969 (p) REVERT: E 435 MET cc_start: 0.7711 (tmm) cc_final: 0.7140 (tmm) REVERT: F 145 VAL cc_start: 0.9358 (t) cc_final: 0.9047 (m) REVERT: F 182 SER cc_start: 0.7998 (t) cc_final: 0.7283 (p) REVERT: F 201 GLU cc_start: 0.8410 (mp0) cc_final: 0.8162 (mp0) REVERT: F 238 MET cc_start: 0.8285 (tpp) cc_final: 0.8044 (tpp) REVERT: F 367 ASP cc_start: 0.8517 (t0) cc_final: 0.8241 (t0) REVERT: F 380 ASP cc_start: 0.8132 (t0) cc_final: 0.7876 (t0) REVERT: F 395 LEU cc_start: 0.9275 (tt) cc_final: 0.8041 (tp) REVERT: F 401 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8705 (mm) REVERT: F 493 LYS cc_start: 0.9263 (ttmm) cc_final: 0.8789 (mtpp) REVERT: G 100 THR cc_start: 0.8639 (m) cc_final: 0.8402 (p) REVERT: H 7 ILE cc_start: 0.8673 (mm) cc_final: 0.8339 (mm) REVERT: H 27 GLN cc_start: 0.8281 (mt0) cc_final: 0.8060 (mt0) REVERT: H 51 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8463 (tp) REVERT: H 86 ASN cc_start: 0.8360 (m-40) cc_final: 0.8070 (m110) REVERT: H 163 LYS cc_start: 0.8768 (mttt) cc_final: 0.8452 (mmtm) REVERT: I 112 TYR cc_start: 0.8981 (t80) cc_final: 0.8751 (t80) REVERT: I 115 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8311 (mp) REVERT: I 133 ILE cc_start: 0.9239 (mt) cc_final: 0.8933 (mm) REVERT: I 168 ASP cc_start: 0.7264 (t0) cc_final: 0.6834 (t0) REVERT: J 88 ASP cc_start: 0.8355 (m-30) cc_final: 0.7889 (m-30) REVERT: J 89 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7600 (t0) REVERT: J 172 TYR cc_start: 0.8610 (m-80) cc_final: 0.7876 (m-10) REVERT: K 72 MET cc_start: 0.8357 (tpp) cc_final: 0.8059 (tpp) REVERT: K 75 LEU cc_start: 0.9290 (tp) cc_final: 0.8702 (tt) REVERT: K 132 MET cc_start: 0.8427 (mpp) cc_final: 0.8002 (mpp) REVERT: L 13 ASP cc_start: 0.8356 (p0) cc_final: 0.8036 (p0) REVERT: L 89 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8303 (mm) REVERT: M 90 GLN cc_start: 0.8530 (tp40) cc_final: 0.7938 (tp40) REVERT: M 100 LEU cc_start: 0.9291 (tp) cc_final: 0.8895 (mm) REVERT: N 34 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8096 (mmtt) REVERT: N 48 ARG cc_start: 0.9170 (ttt90) cc_final: 0.8899 (tpt-90) REVERT: O 86 ASN cc_start: 0.8626 (m-40) cc_final: 0.8276 (m110) REVERT: Q 54 ILE cc_start: 0.8406 (pt) cc_final: 0.8109 (pt) REVERT: Q 103 MET cc_start: 0.6914 (mmm) cc_final: 0.6582 (mmm) REVERT: Q 130 LEU cc_start: 0.9088 (mm) cc_final: 0.8726 (mm) REVERT: Q 157 SER cc_start: 0.8614 (m) cc_final: 0.8379 (p) REVERT: Q 178 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8021 (mm) REVERT: Q 213 PHE cc_start: 0.6461 (m-80) cc_final: 0.6140 (m-80) REVERT: R 194 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7971 (p0) REVERT: S 10 MET cc_start: 0.7539 (mpp) cc_final: 0.7150 (mpp) REVERT: S 17 GLN cc_start: 0.7999 (tt0) cc_final: 0.7664 (tp40) REVERT: S 28 TYR cc_start: 0.8481 (t80) cc_final: 0.8048 (t80) REVERT: S 46 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8153 (tpp80) REVERT: S 120 ASN cc_start: 0.7103 (t0) cc_final: 0.6818 (t0) REVERT: S 150 ASN cc_start: 0.9121 (m-40) cc_final: 0.8790 (m110) REVERT: S 151 PHE cc_start: 0.8109 (m-10) cc_final: 0.7272 (m-10) REVERT: S 200 PHE cc_start: 0.7241 (t80) cc_final: 0.6227 (t80) REVERT: T 62 LEU cc_start: 0.7963 (mm) cc_final: 0.7240 (tp) REVERT: T 117 MET cc_start: 0.4929 (tpt) cc_final: 0.3892 (tpt) REVERT: T 155 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8527 (tptt) REVERT: T 213 GLN cc_start: 0.7917 (tt0) cc_final: 0.7407 (tp40) REVERT: a 80 MET cc_start: 0.4909 (pmm) cc_final: 0.4688 (pmm) REVERT: a 355 MET cc_start: 0.1090 (pmm) cc_final: 0.0885 (pmm) REVERT: a 451 LEU cc_start: 0.8155 (mt) cc_final: 0.7691 (mt) REVERT: a 453 MET cc_start: 0.8745 (ppp) cc_final: 0.7804 (ppp) REVERT: a 484 MET cc_start: 0.2869 (mtp) cc_final: 0.1552 (ttp) REVERT: a 617 PHE cc_start: 0.6389 (t80) cc_final: 0.6181 (t80) REVERT: a 629 LEU cc_start: 0.4208 (mt) cc_final: 0.3242 (tp) REVERT: a 777 PHE cc_start: 0.8058 (t80) cc_final: 0.7783 (t80) REVERT: b 6 LEU cc_start: 0.9158 (tp) cc_final: 0.8835 (tt) REVERT: b 51 ASN cc_start: 0.8387 (m110) cc_final: 0.8145 (m-40) REVERT: b 82 LYS cc_start: 0.8143 (tppp) cc_final: 0.7876 (mttp) REVERT: b 96 PHE cc_start: 0.8655 (m-80) cc_final: 0.8376 (m-80) REVERT: b 180 GLU cc_start: 0.7807 (mp0) cc_final: 0.7480 (mp0) REVERT: c 277 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8133 (mmmm) REVERT: c 295 PHE cc_start: 0.8050 (t80) cc_final: 0.7590 (t80) REVERT: c 361 TYR cc_start: 0.8861 (m-10) cc_final: 0.8599 (m-10) REVERT: c 404 GLN cc_start: 0.8382 (pm20) cc_final: 0.8110 (pm20) REVERT: d 17 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: d 30 GLN cc_start: 0.8329 (tp-100) cc_final: 0.8084 (tp-100) REVERT: d 186 TYR cc_start: 0.8889 (t80) cc_final: 0.8447 (t80) REVERT: d 265 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7483 (tppp) REVERT: d 292 ASP cc_start: 0.8559 (m-30) cc_final: 0.8330 (m-30) REVERT: d 343 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7742 (mtmt) REVERT: e 40 MET cc_start: 0.5679 (ptm) cc_final: 0.5227 (ppp) REVERT: g 17 MET cc_start: 0.9088 (tpp) cc_final: 0.8759 (mmt) REVERT: g 23 MET cc_start: 0.9113 (tpt) cc_final: 0.8882 (tpp) REVERT: g 131 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7986 (tmm) REVERT: g 144 TYR cc_start: 0.7824 (m-10) cc_final: 0.7374 (m-10) REVERT: h 26 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8644 (t) REVERT: h 87 TYR cc_start: 0.8547 (t80) cc_final: 0.8205 (t80) REVERT: h 97 LEU cc_start: 0.8674 (mt) cc_final: 0.8457 (tp) REVERT: i 23 MET cc_start: 0.7599 (tpp) cc_final: 0.7205 (tpp) REVERT: i 139 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7089 (tm-30) REVERT: j 139 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7857 (tm-30) REVERT: l 10 TYR cc_start: 0.8508 (p90) cc_final: 0.8263 (p90) REVERT: l 52 ILE cc_start: 0.9258 (pt) cc_final: 0.8873 (mt) REVERT: l 78 ASN cc_start: 0.8117 (t0) cc_final: 0.7863 (t0) REVERT: l 90 PHE cc_start: 0.9336 (m-10) cc_final: 0.9014 (m-80) REVERT: l 124 GLN cc_start: 0.8722 (tm-30) cc_final: 0.7302 (tm-30) REVERT: m 28 MET cc_start: 0.8058 (mmt) cc_final: 0.7580 (mmm) REVERT: m 53 MET cc_start: 0.6770 (tmm) cc_final: 0.6512 (tmm) REVERT: m 54 LYS cc_start: 0.7920 (mttt) cc_final: 0.7211 (mmtt) REVERT: m 124 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7715 (tm-30) REVERT: n 87 TYR cc_start: 0.8435 (t80) cc_final: 0.8123 (t80) REVERT: n 91 LEU cc_start: 0.9241 (mt) cc_final: 0.8998 (mt) REVERT: o 7 ASN cc_start: 0.7639 (p0) cc_final: 0.7377 (p0) REVERT: p 294 ASN cc_start: 0.8749 (t0) cc_final: 0.8423 (t0) REVERT: p 303 TYR cc_start: 0.8582 (t80) cc_final: 0.8094 (t80) outliers start: 257 outliers final: 198 residues processed: 1937 average time/residue: 0.6539 time to fit residues: 2162.6229 Evaluate side-chains 1960 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1747 time to evaluate : 6.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 165 GLN Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 198 HIS Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 308 ASN Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 39 TRP Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 105 ILE Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain c residue 249 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 385 LEU Chi-restraints excluded: chain c residue 429 MET Chi-restraints excluded: chain c residue 450 ASP Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 39 CYS Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 68 SER Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 9 GLU Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 47 MET Chi-restraints excluded: chain o residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 520 optimal weight: 9.9990 chunk 837 optimal weight: 0.6980 chunk 511 optimal weight: 0.5980 chunk 397 optimal weight: 40.0000 chunk 582 optimal weight: 5.9990 chunk 878 optimal weight: 2.9990 chunk 808 optimal weight: 0.9980 chunk 699 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 540 optimal weight: 0.0070 chunk 429 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN H 206 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN N 91 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 HIS Q 17 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS S 50 GLN ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 71099 Z= 0.222 Angle : 0.711 20.698 96090 Z= 0.358 Chirality : 0.044 0.292 10909 Planarity : 0.005 0.138 12296 Dihedral : 4.984 92.779 9657 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.04 % Allowed : 22.86 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.09), residues: 8831 helix: 0.62 (0.07), residues: 5214 sheet: -1.04 (0.17), residues: 817 loop : -0.30 (0.12), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP e 52 HIS 0.015 0.001 HIS B 164 PHE 0.034 0.002 PHE Q 101 TYR 0.048 0.002 TYR c 272 ARG 0.015 0.001 ARG B 552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17662 Ramachandran restraints generated. 8831 Oldfield, 0 Emsley, 8831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2022 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1793 time to evaluate : 6.160 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 25 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.8037 (p) REVERT: A 34 MET cc_start: 0.9059 (mmm) cc_final: 0.8399 (ttm) REVERT: A 80 LEU cc_start: 0.8925 (tp) cc_final: 0.8384 (mt) REVERT: A 268 ASN cc_start: 0.7947 (m-40) cc_final: 0.7282 (t0) REVERT: A 387 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8403 (tp30) REVERT: A 436 ASP cc_start: 0.8070 (t0) cc_final: 0.7618 (t0) REVERT: B 117 TYR cc_start: 0.8933 (m-80) cc_final: 0.7958 (m-80) REVERT: B 205 MET cc_start: 0.8417 (mtm) cc_final: 0.8216 (mtm) REVERT: B 268 ASN cc_start: 0.8349 (t0) cc_final: 0.7483 (t0) REVERT: B 320 VAL cc_start: 0.9494 (t) cc_final: 0.9177 (p) REVERT: B 356 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: B 393 LYS cc_start: 0.8432 (mttt) cc_final: 0.8218 (ttmt) REVERT: B 445 PHE cc_start: 0.8439 (m-80) cc_final: 0.8108 (m-80) REVERT: B 478 LYS cc_start: 0.8960 (mttt) cc_final: 0.8656 (mmmm) REVERT: B 508 THR cc_start: 0.9165 (m) cc_final: 0.8783 (p) REVERT: B 518 ASP cc_start: 0.7368 (m-30) cc_final: 0.7144 (m-30) REVERT: B 523 ASN cc_start: 0.8109 (t0) cc_final: 0.7853 (t0) REVERT: B 525 TYR cc_start: 0.8089 (m-80) cc_final: 0.7834 (m-80) REVERT: B 550 MET cc_start: 0.8857 (mmm) cc_final: 0.8582 (mtt) REVERT: C 80 LEU cc_start: 0.9061 (tp) cc_final: 0.8591 (mt) REVERT: C 235 ASP cc_start: 0.7591 (m-30) cc_final: 0.7286 (m-30) REVERT: C 263 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8638 (tt) REVERT: C 264 SER cc_start: 0.9630 (m) cc_final: 0.9182 (p) REVERT: C 285 SER cc_start: 0.9504 (m) cc_final: 0.9123 (t) REVERT: C 293 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 307 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8356 (mttt) REVERT: C 346 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8642 (ttt) REVERT: C 372 SER cc_start: 0.8765 (m) cc_final: 0.8457 (t) REVERT: C 441 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7235 (mm-40) REVERT: C 494 GLN cc_start: 0.8503 (tp40) cc_final: 0.8042 (tt0) REVERT: C 532 CYS cc_start: 0.8709 (t) cc_final: 0.8218 (t) REVERT: C 553 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7201 (mtm110) REVERT: D 169 MET cc_start: 0.9422 (tmm) cc_final: 0.8919 (tmm) REVERT: D 254 MET cc_start: 0.8958 (tpt) cc_final: 0.8701 (tpp) REVERT: D 283 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7207 (tm-30) REVERT: D 374 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: D 389 TYR cc_start: 0.8156 (t80) cc_final: 0.7836 (t80) REVERT: D 435 MET cc_start: 0.8779 (ptm) cc_final: 0.8526 (ptm) REVERT: D 451 TYR cc_start: 0.8533 (m-80) cc_final: 0.8203 (m-80) REVERT: D 491 MET cc_start: 0.8545 (mmp) cc_final: 0.8309 (tpp) REVERT: E 254 MET cc_start: 0.8137 (mmt) cc_final: 0.7931 (mmt) REVERT: E 345 ASN cc_start: 0.8245 (m-40) cc_final: 0.7938 (m110) REVERT: E 355 THR cc_start: 0.8656 (m) cc_final: 0.8012 (p) REVERT: E 435 MET cc_start: 0.7715 (tmm) cc_final: 0.7140 (tmm) REVERT: F 145 VAL cc_start: 0.9343 (t) cc_final: 0.9033 (m) REVERT: F 201 GLU cc_start: 0.8416 (mp0) cc_final: 0.8158 (mp0) REVERT: F 238 MET cc_start: 0.8281 (tpp) cc_final: 0.8045 (tpp) REVERT: F 298 THR cc_start: 0.8788 (m) cc_final: 0.8366 (p) REVERT: F 380 ASP cc_start: 0.8064 (t0) cc_final: 0.7836 (t0) REVERT: F 395 LEU cc_start: 0.9274 (tt) cc_final: 0.8071 (tp) REVERT: F 401 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8707 (mm) REVERT: F 435 MET cc_start: 0.8736 (mmp) cc_final: 0.8477 (tpp) REVERT: F 493 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8799 (mtpp) REVERT: G 100 THR cc_start: 0.8611 (m) cc_final: 0.8379 (p) REVERT: H 27 GLN cc_start: 0.8285 (mt0) cc_final: 0.8045 (mt0) REVERT: H 51 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8485 (tp) REVERT: H 86 ASN cc_start: 0.8329 (m-40) cc_final: 0.7995 (m110) REVERT: H 106 LEU cc_start: 0.8260 (mm) cc_final: 0.8057 (mm) REVERT: H 163 LYS cc_start: 0.8763 (mttt) cc_final: 0.8466 (mmtm) REVERT: I 112 TYR cc_start: 0.8945 (t80) cc_final: 0.8613 (t80) REVERT: I 115 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8285 (mp) REVERT: I 116 LEU cc_start: 0.8497 (tp) cc_final: 0.8049 (mp) REVERT: I 133 ILE cc_start: 0.9212 (mt) cc_final: 0.8935 (mm) REVERT: I 208 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8688 (mmm) REVERT: J 88 ASP cc_start: 0.8357 (m-30) cc_final: 0.7860 (m-30) REVERT: J 89 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7633 (t0) REVERT: J 172 TYR cc_start: 0.8591 (m-80) cc_final: 0.7846 (m-10) REVERT: K 72 MET cc_start: 0.8338 (tpp) cc_final: 0.8038 (tpp) REVERT: K 75 LEU cc_start: 0.9278 (tp) cc_final: 0.8698 (tt) REVERT: L 13 ASP cc_start: 0.8348 (p0) cc_final: 0.8019 (p0) REVERT: L 89 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8361 (mm) REVERT: M 80 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8768 (mmtm) REVERT: M 90 GLN cc_start: 0.8538 (tp40) cc_final: 0.7921 (tp-100) REVERT: M 100 LEU cc_start: 0.9278 (tp) cc_final: 0.8905 (mm) REVERT: N 48 ARG cc_start: 0.9205 (ttt90) cc_final: 0.8913 (tpt-90) REVERT: O 86 ASN cc_start: 0.8524 (m-40) cc_final: 0.8147 (m110) REVERT: Q 54 ILE cc_start: 0.8166 (pt) cc_final: 0.7783 (mt) REVERT: Q 61 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7132 (ttp80) REVERT: Q 103 MET cc_start: 0.7009 (mmm) cc_final: 0.6491 (mmm) REVERT: Q 130 LEU cc_start: 0.9055 (mm) cc_final: 0.8686 (mm) REVERT: Q 157 SER cc_start: 0.8483 (m) cc_final: 0.8251 (p) REVERT: Q 178 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8032 (mm) REVERT: Q 213 PHE cc_start: 0.6495 (m-80) cc_final: 0.6246 (m-80) REVERT: R 122 TRP cc_start: 0.8894 (m100) cc_final: 0.8683 (m100) REVERT: R 194 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8067 (p0) REVERT: S 10 MET cc_start: 0.7531 (mpp) cc_final: 0.7158 (mpp) REVERT: S 17 GLN cc_start: 0.8031 (tt0) cc_final: 0.7707 (tp40) REVERT: S 28 TYR cc_start: 0.8471 (t80) cc_final: 0.8074 (t80) REVERT: S 46 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8101 (tpp80) REVERT: S 150 ASN cc_start: 0.9113 (m-40) cc_final: 0.8770 (m110) REVERT: S 151 PHE cc_start: 0.8308 (m-10) cc_final: 0.7645 (m-10) REVERT: S 200 PHE cc_start: 0.7298 (t80) cc_final: 0.6768 (t80) REVERT: T 62 LEU cc_start: 0.7938 (mm) cc_final: 0.7096 (tp) REVERT: T 69 GLN cc_start: 0.8488 (pt0) cc_final: 0.8150 (pt0) REVERT: T 117 MET cc_start: 0.4895 (tpt) cc_final: 0.3863 (tpt) REVERT: T 147 PHE cc_start: 0.7370 (m-10) cc_final: 0.7131 (m-10) REVERT: T 213 GLN cc_start: 0.7925 (tt0) cc_final: 0.7544 (tp40) REVERT: a 355 MET cc_start: 0.1259 (pmm) cc_final: 0.1029 (pmm) REVERT: a 451 LEU cc_start: 0.8159 (mt) cc_final: 0.7740 (mt) REVERT: a 453 MET cc_start: 0.8737 (ppp) cc_final: 0.7845 (ppp) REVERT: a 484 MET cc_start: 0.2815 (mtp) cc_final: 0.1540 (ttp) REVERT: a 580 MET cc_start: 0.7399 (ttt) cc_final: 0.7189 (ttt) REVERT: a 629 LEU cc_start: 0.4187 (mt) cc_final: 0.3209 (tp) REVERT: a 777 PHE cc_start: 0.8061 (t80) cc_final: 0.7794 (t80) REVERT: b 6 LEU cc_start: 0.9110 (tp) cc_final: 0.8795 (tt) REVERT: b 96 PHE cc_start: 0.8694 (m-80) cc_final: 0.8442 (m-80) REVERT: b 180 GLU cc_start: 0.7814 (mp0) cc_final: 0.7450 (mp0) REVERT: c 277 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8127 (mmmm) REVERT: c 295 PHE cc_start: 0.8003 (t80) cc_final: 0.7490 (t80) REVERT: c 404 GLN cc_start: 0.8431 (pm20) cc_final: 0.8100 (pm20) REVERT: d 17 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: d 186 TYR cc_start: 0.8877 (t80) cc_final: 0.8462 (t80) REVERT: d 208 MET cc_start: 0.9057 (tpp) cc_final: 0.8734 (mmt) REVERT: d 292 ASP cc_start: 0.8582 (m-30) cc_final: 0.8322 (m-30) REVERT: d 343 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7724 (mtmt) REVERT: e 40 MET cc_start: 0.5678 (ptm) cc_final: 0.5228 (ppp) REVERT: g 9 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7247 (mm-30) REVERT: g 17 MET cc_start: 0.9071 (tpp) cc_final: 0.8739 (mmt) REVERT: g 23 MET cc_start: 0.9054 (tpt) cc_final: 0.8804 (tpp) REVERT: g 131 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8125 (tmm) REVERT: g 144 TYR cc_start: 0.7750 (m-10) cc_final: 0.7278 (m-10) REVERT: h 26 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8661 (t) REVERT: h 87 TYR cc_start: 0.8559 (t80) cc_final: 0.8222 (t80) REVERT: i 23 MET cc_start: 0.7587 (tpp) cc_final: 0.7188 (tpp) REVERT: i 139 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7113 (tm-30) REVERT: j 139 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7904 (tm-30) REVERT: l 52 ILE cc_start: 0.9276 (pt) cc_final: 0.8918 (mt) REVERT: l 78 ASN cc_start: 0.8086 (t0) cc_final: 0.7834 (t0) REVERT: l 90 PHE cc_start: 0.9327 (m-10) cc_final: 0.8994 (m-80) REVERT: m 28 MET cc_start: 0.8062 (mmt) cc_final: 0.7572 (mmm) REVERT: m 53 MET cc_start: 0.6781 (tmm) cc_final: 0.6487 (tmm) REVERT: m 54 LYS cc_start: 0.7933 (mttt) cc_final: 0.7238 (mmtp) REVERT: m 124 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7573 (tm-30) REVERT: n 87 TYR cc_start: 0.8488 (t80) cc_final: 0.8202 (t80) REVERT: n 91 LEU cc_start: 0.9239 (mt) cc_final: 0.9003 (mt) REVERT: o 7 ASN cc_start: 0.7596 (p0) cc_final: 0.7318 (p0) REVERT: p 294 ASN cc_start: 0.8811 (t0) cc_final: 0.8506 (t0) REVERT: p 303 TYR cc_start: 0.8636 (t80) cc_final: 0.8344 (t80) outliers start: 229 outliers final: 185 residues processed: 1907 average time/residue: 0.6575 time to fit residues: 2139.5148 Evaluate side-chains 1932 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1731 time to evaluate : 6.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 452 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 67 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 88 SER Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 173 LEU Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 308 ASN Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 805 ARG Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 39 TRP Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 158 VAL Chi-restraints excluded: chain c residue 249 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain c residue 429 MET Chi-restraints excluded: chain c residue 450 ASP Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 39 CYS Chi-restraints excluded: chain d residue 44 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 68 SER Chi-restraints excluded: chain d residue 110 ILE Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 290 LEU Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 131 MET Chi-restraints excluded: chain h residue 6 ASN Chi-restraints excluded: chain h residue 9 GLU Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain h residue 41 ILE Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 151 ILE Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 132 ILE Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 102 SER Chi-restraints excluded: chain l residue 129 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 61 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 47 MET Chi-restraints excluded: chain o residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 555 optimal weight: 30.0000 chunk 745 optimal weight: 0.8980 chunk 214 optimal weight: 0.0970 chunk 645 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 700 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 719 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 129 optimal weight: 0.1980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN I 67 GLN ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 HIS Q 17 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 GLN m 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.188760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133479 restraints weight = 103359.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129481 restraints weight = 76250.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131638 restraints weight = 75519.917| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 71099 Z= 0.215 Angle : 0.715 18.018 96090 Z= 0.360 Chirality : 0.044 0.296 10909 Planarity : 0.005 0.083 12296 Dihedral : 4.947 94.488 9657 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.72 % Allowed : 23.46 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 8831 helix: 0.61 (0.07), residues: 5221 sheet: -1.01 (0.18), residues: 799 loop : -0.34 (0.12), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP e 52 HIS 0.012 0.001 HIS B 164 PHE 0.066 0.002 PHE K 38 TYR 0.043 0.002 TYR a 728 ARG 0.015 0.001 ARG A 530 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29251.46 seconds wall clock time: 507 minutes 6.15 seconds (30426.15 seconds total)