Starting phenix.real_space_refine on Sun Apr 7 05:15:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/04_2024/6vq8_21319_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/04_2024/6vq8_21319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/04_2024/6vq8_21319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/04_2024/6vq8_21319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/04_2024/6vq8_21319_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/04_2024/6vq8_21319_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.070 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 311 5.16 5 C 38448 2.51 5 N 10527 2.21 5 O 11426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "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 TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "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 ARG 388": "NH1" <-> "NH2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "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 PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 323": "NH1" <-> "NH2" 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 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "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 PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "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 ARG 104": "NH1" <-> "NH2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "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 ARG 338": "NH1" <-> "NH2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C PHE 417": "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 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 529": "OD1" <-> "OD2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 534": "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 TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "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 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 52": "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 GLU 90": "OE1" <-> "OE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 197": "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 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 214": "OE1" <-> "OE2" 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 ASP 77": "OD1" <-> "OD2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 40": "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 PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 8": "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 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 PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "g TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 139": "OE1" <-> "OE2" Residue "i TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 14": "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 GLU 139": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 139": "OE1" <-> "OE2" Residue "k TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "n PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 139": "OE1" <-> "OE2" 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 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 60714 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" 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: "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: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "G" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1790 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 350} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1192 Unresolved non-hydrogen angles: 1522 Unresolved non-hydrogen dihedrals: 998 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 645 Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1726 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 3, 'TRANS': 210} Chain: "I" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1602 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 218} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "K" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "L" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 866 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "O" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 709 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "Q" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1878 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "S" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "a" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 3703 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 668} Link IDs: {'PTRANS': 31, 'TRANS': 717} Chain breaks: 2 Unresolved chain link angles: 31 Unresolved non-hydrogen bonds: 2555 Unresolved non-hydrogen angles: 3282 Unresolved non-hydrogen dihedrals: 2176 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 19, 'TYR:plan': 23, 'ASN:plan1': 41, 'TRP:plan': 12, 'ASP:plan': 22, 'PHE:plan': 63, 'GLU:plan': 47, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1418 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: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "e" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 384 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 137 Chain: "f" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 412 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" 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: 24.12, per 1000 atoms: 0.40 Number of scatterers: 60714 At special positions: 0 Unit cell: (173.84, 174.9, 272.42, 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 311 16.00 P 2 15.00 O 11426 8.00 N 10527 7.00 C 38448 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: 20.02 Conformation dependent library (CDL) restraints added in 9.1 seconds 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15618 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 291 helices and 40 sheets defined 59.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.63 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 281 through 293 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.641A pdb=" N SER A 326 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 330 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 331 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.358A pdb=" N GLY A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 384 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 387 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 458 through 468 removed outlier: 4.455A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 4.140A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) 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 585 removed outlier: 4.968A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 320 through 340 removed outlier: 4.616A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 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 378 through 386 Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 458 through 468 removed outlier: 4.282A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 496 removed outlier: 3.867A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) 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 573 Processing helix chain 'B' and resid 575 through 586 removed outlier: 5.130A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.652A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 281 through 293 Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 320 through 340 removed outlier: 4.594A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.725A pdb=" N ARG C 388 " --> 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 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 472 through 496 removed outlier: 4.598A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 558 removed outlier: 3.810A pdb=" N THR C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 586 removed outlier: 4.851A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 removed outlier: 3.971A pdb=" N LEU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) 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 removed outlier: 3.601A pdb=" N ARG D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 327 through 335 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: 4.049A 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 removed outlier: 4.343A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) 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 removed outlier: 4.348A pdb=" N TYR D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.005A 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 removed outlier: 5.012A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) 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 270 through 287 removed outlier: 3.580A pdb=" N THR E 274 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Proline residue: E 275 - end of helix removed outlier: 3.591A pdb=" N ALA E 278 " --> pdb=" O PRO E 275 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 279 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 280 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 286 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR E 287 " --> pdb=" O PHE E 284 " (cutoff:3.500A) 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 327 through 335 removed outlier: 3.852A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (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 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 400 through 403 removed outlier: 4.189A pdb=" N LYS E 403 " --> pdb=" O ARG E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 403' Processing helix chain 'E' and resid 415 through 439 removed outlier: 4.031A 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: 3.830A 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 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 268 through 288 removed outlier: 3.580A pdb=" N ILE F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) Proline residue: F 275 - end of helix Processing helix chain 'F' and resid 300 through 313 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 removed outlier: 3.845A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 402 through 405 No H-bonds generated for 'chain 'F' and resid 402 through 405' Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.691A 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: 4.109A 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 14 through 21 Processing helix chain 'G' and resid 28 through 31 Processing helix chain 'G' and resid 48 through 79 Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 118 through 156 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 191 through 203 removed outlier: 5.311A pdb=" N ASN G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR G 201 " --> pdb=" O ILE G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 removed outlier: 4.064A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE G 237 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG G 238 " --> pdb=" O ASP G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 310 Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 328 through 340 Processing helix chain 'H' and resid 13 through 76 Processing helix chain 'H' and resid 79 through 85 Processing helix chain 'H' and resid 128 through 174 Processing helix chain 'H' and resid 176 through 215 Processing helix chain 'I' and resid 5 through 106 Processing helix chain 'I' and resid 109 through 127 removed outlier: 4.629A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 158 Proline residue: I 142 - end of helix removed outlier: 3.833A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS I 150 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.692A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 216 removed outlier: 3.949A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix Processing helix chain 'J' and resid 5 through 106 removed outlier: 3.574A pdb=" N LYS J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 127 Processing helix chain 'J' and resid 138 through 159 Proline residue: J 142 - end of helix removed outlier: 3.750A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.722A pdb=" N LYS J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE J 157 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 Processing helix chain 'J' and resid 208 through 216 removed outlier: 3.613A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 106 Processing helix chain 'K' and resid 110 through 127 Processing helix chain 'K' and resid 138 through 159 Proline residue: K 142 - end of helix removed outlier: 3.713A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 150 " --> pdb=" O ALA K 147 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.695A pdb=" N LYS K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 206 Processing helix chain 'K' and resid 208 through 216 removed outlier: 3.507A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 45 through 56 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 4 through 90 removed outlier: 4.043A pdb=" N SER M 70 " --> pdb=" O GLN M 66 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 104 Processing helix chain 'N' and resid 4 through 103 removed outlier: 3.793A pdb=" N GLN N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 90 removed outlier: 3.845A pdb=" N GLN O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 104 Processing helix chain 'Q' and resid 15 through 36 Processing helix chain 'Q' and resid 43 through 48 Processing helix chain 'Q' and resid 50 through 55 removed outlier: 5.008A pdb=" N TRP Q 55 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 70 Processing helix chain 'Q' and resid 78 through 98 removed outlier: 3.907A pdb=" N LEU Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'Q' and resid 125 through 141 removed outlier: 3.524A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) 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 204 Processing helix chain 'Q' and resid 219 through 232 removed outlier: 3.561A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 55 removed outlier: 3.673A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 78 through 96 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 142 removed outlier: 3.949A pdb=" N ASN R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 Processing helix chain 'R' and resid 173 through 186 Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 219 through 234 Processing helix chain 'S' and resid 15 through 36 removed outlier: 3.506A pdb=" N HIS S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 53 removed outlier: 3.679A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL S 52 " --> pdb=" O ASP S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 71 Processing helix chain 'S' and resid 78 through 98 removed outlier: 4.015A pdb=" N ILE S 98 " --> pdb=" O LEU S 94 " (cutoff:3.500A) 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 142 removed outlier: 3.694A pdb=" N LEU S 140 " --> pdb=" O LEU S 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS S 141 " --> pdb=" O THR S 137 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 removed outlier: 3.541A pdb=" N GLN S 165 " --> pdb=" O MET S 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 186 Processing helix chain 'S' and resid 194 through 206 Processing helix chain 'a' and resid 19 through 32 Processing helix chain 'a' and resid 46 through 49 No H-bonds generated for 'chain 'a' and resid 46 through 49' Processing helix chain 'a' and resid 52 through 74 Processing helix chain 'a' and resid 85 through 87 No H-bonds generated for 'chain 'a' and resid 85 through 87' Processing helix chain 'a' and resid 92 through 131 Processing helix chain 'a' and resid 180 through 190 Processing helix chain 'a' and resid 227 through 239 Processing helix chain 'a' and resid 252 through 308 Processing helix chain 'a' and resid 327 through 343 Processing helix chain 'a' and resid 371 through 381 removed outlier: 3.987A pdb=" N TYR a 381 " --> pdb=" O ILE a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 392 through 406 removed outlier: 4.686A 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 431 Processing helix chain 'a' and resid 438 through 445 Processing helix chain 'a' and resid 447 through 464 Processing helix chain 'a' and resid 482 through 487 removed outlier: 3.631A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 499 removed outlier: 3.753A pdb=" N SER a 498 " --> pdb=" O THR a 494 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER a 499 " --> pdb=" O LEU a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 521 through 525 Processing helix chain 'a' and resid 529 through 562 removed outlier: 4.577A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 570 Processing helix chain 'a' and resid 573 through 597 removed outlier: 4.227A 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 618 Processing helix chain 'a' and resid 633 through 646 Processing helix chain 'a' and resid 648 through 666 removed outlier: 5.798A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 714 through 758 removed outlier: 3.572A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU a 740 " --> pdb=" O THR a 736 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG a 741 " --> pdb=" O ALA a 737 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU a 742 " --> pdb=" O SER a 738 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 762 through 764 No H-bonds generated for 'chain 'a' and resid 762 through 764' Processing helix chain 'a' and resid 769 through 790 Processing helix chain 'a' and resid 794 through 809 Processing helix chain 'a' and resid 812 through 814 No H-bonds generated for 'chain 'a' and resid 812 through 814' Processing helix chain 'b' and resid 3 through 28 Processing helix chain 'b' and resid 37 through 43 Processing helix chain 'b' and resid 46 through 81 removed outlier: 3.666A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 114 removed outlier: 3.596A pdb=" N LYS b 87 " --> pdb=" O PRO b 84 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN b 90 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU b 91 " --> pdb=" O THR b 88 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE b 96 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE b 106 " --> pdb=" O TYR b 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE b 111 " --> pdb=" O ALA b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 166 Processing helix chain 'b' and resid 170 through 197 removed outlier: 3.740A pdb=" N PHE b 173 " --> pdb=" O PRO b 170 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL b 174 " --> pdb=" O SER b 171 " (cutoff:3.500A) Processing helix chain 'c' and resid 417 through 441 Processing helix chain 'd' and resid 9 through 26 removed outlier: 6.519A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY d 26 " --> pdb=" O GLY d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 37 Processing helix chain 'd' and resid 42 through 51 removed outlier: 3.914A pdb=" N SER d 51 " --> pdb=" O LEU d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 87 Processing helix chain 'd' and resid 91 through 115 removed outlier: 4.898A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (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 147 through 156 Processing helix chain 'd' and resid 159 through 166 removed outlier: 4.100A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP d 166 " --> pdb=" O PHE d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 171 through 175 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: 3.549A pdb=" N PHE d 228 " --> pdb=" O THR d 224 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY d 229 " --> pdb=" O ILE d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 240 removed outlier: 3.637A pdb=" N LEU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 252 through 257 Processing helix chain 'd' and resid 261 through 270 removed outlier: 3.990A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 272 through 280 removed outlier: 4.437A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 307 removed outlier: 4.145A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) removed outlier: 4.364A 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 343 No H-bonds generated for 'chain 'd' and resid 341 through 343' Processing helix chain 'e' and resid 6 through 22 Processing helix chain 'e' and resid 24 through 26 No H-bonds generated for 'chain 'e' and resid 24 through 26' Processing helix chain 'e' and resid 34 through 57 Processing helix chain 'e' and resid 70 through 78 removed outlier: 3.575A pdb=" N ARG e 77 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 35 Processing helix chain 'f' and resid 55 through 89 Processing helix chain 'g' and resid 11 through 45 removed outlier: 4.138A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 51 No H-bonds generated for 'chain 'g' and resid 49 through 51' Processing helix chain 'g' and resid 54 through 79 Proline residue: g 58 - end of helix removed outlier: 3.519A pdb=" N VAL g 74 " --> pdb=" O VAL g 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE g 76 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN g 78 " --> pdb=" O LEU g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 123 Processing helix chain 'g' and resid 125 through 154 removed outlier: 4.344A pdb=" N VAL g 129 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL g 148 " --> pdb=" O GLY g 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU g 152 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 3.775A pdb=" N PHE h 14 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA h 22 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE h 25 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS h 36 " --> pdb=" O GLY h 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY h 38 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER h 45 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 51 No H-bonds generated for 'chain 'h' and resid 49 through 51' Processing helix chain 'h' and resid 57 through 79 Processing helix chain 'h' and resid 87 through 123 Processing helix chain 'h' and resid 125 through 153 removed outlier: 4.163A pdb=" N VAL h 129 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER h 153 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 47 removed outlier: 4.261A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 51 No H-bonds generated for 'chain 'i' and resid 49 through 51' Processing helix chain 'i' and resid 57 through 79 Processing helix chain 'i' and resid 87 through 123 removed outlier: 3.900A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 153 removed outlier: 4.003A pdb=" N VAL i 129 " --> pdb=" O ARG i 126 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 47 removed outlier: 3.659A pdb=" N PHE j 14 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL j 16 " --> pdb=" O PHE j 13 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA j 22 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE j 25 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY j 38 " --> pdb=" O ALA j 35 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER j 45 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL j 46 " --> pdb=" O ALA j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 51 No H-bonds generated for 'chain 'j' and resid 49 through 51' Processing helix chain 'j' and resid 54 through 79 Proline residue: j 58 - end of helix removed outlier: 3.557A pdb=" N MET j 61 " --> pdb=" O PRO j 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL j 74 " --> pdb=" O VAL j 71 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE j 76 " --> pdb=" O ALA j 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN j 78 " --> pdb=" O LEU j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 123 Processing helix chain 'j' and resid 125 through 153 removed outlier: 3.988A pdb=" N VAL j 129 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER j 153 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 47 removed outlier: 4.313A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 51 No H-bonds generated for 'chain 'k' and resid 49 through 51' Processing helix chain 'k' and resid 54 through 79 Proline residue: k 58 - end of helix removed outlier: 3.518A pdb=" N ILE k 76 " --> pdb=" O ALA k 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN k 78 " --> pdb=" O LEU k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 123 Processing helix chain 'k' and resid 125 through 153 removed outlier: 4.215A pdb=" N VAL k 129 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER k 153 " --> pdb=" O LEU k 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 47 removed outlier: 3.638A pdb=" N PHE l 14 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER l 20 " --> pdb=" O MET l 17 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA l 22 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE l 25 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA l 30 " --> pdb=" O ALA l 27 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS l 36 " --> pdb=" O GLY l 33 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 51 No H-bonds generated for 'chain 'l' and resid 49 through 51' Processing helix chain 'l' and resid 54 through 79 Proline residue: l 58 - end of helix removed outlier: 3.526A pdb=" N ILE l 76 " --> pdb=" O ALA l 73 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 123 removed outlier: 3.737A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 154 removed outlier: 3.893A pdb=" N VAL l 129 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 46 removed outlier: 3.641A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 51 No H-bonds generated for 'chain 'm' and resid 49 through 51' Processing helix chain 'm' and resid 53 through 55 No H-bonds generated for 'chain 'm' and resid 53 through 55' Processing helix chain 'm' and resid 57 through 79 Processing helix chain 'm' and resid 87 through 123 removed outlier: 3.990A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 154 removed outlier: 3.763A pdb=" N VAL m 129 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER m 153 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 47 removed outlier: 3.693A pdb=" N PHE n 14 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER n 20 " --> pdb=" O MET n 17 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA n 22 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE n 25 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS n 36 " --> pdb=" O GLY n 33 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY n 38 " --> pdb=" O ALA n 35 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER n 45 " --> pdb=" O ALA n 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL n 46 " --> pdb=" O ALA n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 51 No H-bonds generated for 'chain 'n' and resid 49 through 51' Processing helix chain 'n' and resid 57 through 79 removed outlier: 3.567A pdb=" N SER n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 123 removed outlier: 3.590A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 154 removed outlier: 4.105A pdb=" N VAL n 129 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER n 153 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 47 removed outlier: 4.370A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 51 No H-bonds generated for 'chain 'o' and resid 49 through 51' Processing helix chain 'o' and resid 54 through 79 removed outlier: 3.837A pdb=" N ILE o 57 " --> pdb=" O LYS o 54 " (cutoff:3.500A) Proline residue: o 58 - end of helix removed outlier: 3.509A pdb=" N VAL o 72 " --> pdb=" O GLY o 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL o 74 " --> pdb=" O VAL o 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE o 76 " --> pdb=" O ALA o 73 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN o 78 " --> pdb=" O LEU o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 123 Processing helix chain 'o' and resid 125 through 154 removed outlier: 4.238A pdb=" N VAL o 129 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER o 153 " --> pdb=" O LEU o 150 " (cutoff:3.500A) Processing helix chain 'p' and resid 303 through 329 Processing helix chain 'p' and resid 339 through 342 No H-bonds generated for 'chain 'p' and resid 339 through 342' Processing sheet with id= A, first strand: chain 'A' and resid 78 through 80 removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (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 185 Processing sheet with id= D, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.319A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 245 through 248 removed outlier: 8.571A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 272 through 277 Processing sheet with id= G, first strand: chain 'A' and resid 390 through 393 Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 185 removed outlier: 6.909A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.175A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.066A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 245 through 247 removed outlier: 8.414A pdb=" N THR B 246 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 406 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= O, first strand: chain 'C' and resid 18 through 20 removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'C' and resid 183 through 185 removed outlier: 4.721A pdb=" N GLU C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.263A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 309 through 312 removed outlier: 6.306A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL C 344 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER C 403 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N MET C 346 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 405 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA C 348 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= U, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.783A 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 131 through 133 removed outlier: 7.955A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 351 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.724A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= Z, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.642A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 191 through 193 Processing sheet with id= AB, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.651A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AD, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.181A pdb=" N PHE F 132 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU F 259 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS F 292 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 230 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU F 294 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA F 232 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE F 296 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET F 234 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR F 298 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 236 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'F' and resid 191 through 194 Processing sheet with id= AF, first strand: chain 'G' and resid 370 through 374 Processing sheet with id= AG, first strand: chain 'G' and resid 247 through 249 removed outlier: 6.399A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 93 through 99 Processing sheet with id= AI, first strand: chain 'I' and resid 164 through 167 removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 164 through 167 Processing sheet with id= AL, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.550A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE L 63 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE L 11 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU L 65 " --> pdb=" O ILE L 11 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'a' and resid 351 through 353 removed outlier: 3.512A pdb=" N ILE a 351 " --> pdb=" O PHE a 16 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN a 36 " --> pdb=" O TRP a 324 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'a' and resid 198 through 202 removed outlier: 4.519A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) 3920 hydrogen bonds defined for protein. 9894 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: 22.17 Time building geometry restraints manager: 21.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10391 1.30 - 1.43: 14561 1.43 - 1.56: 36122 1.56 - 1.69: 3 1.69 - 1.81: 561 Bond restraints: 61638 Sorted by residual: bond pdb=" C ASP B 290 " pdb=" N PHE B 291 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.76e+01 bond pdb=" N PRO F 391 " pdb=" CA PRO F 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.16e+01 bond pdb=" C TYR E 504 " pdb=" N PRO E 505 " ideal model delta sigma weight residual 1.337 1.407 -0.070 1.06e-02 8.90e+03 4.38e+01 bond pdb=" N PRO E 352 " pdb=" CA PRO E 352 " ideal model delta sigma weight residual 1.466 1.537 -0.071 1.24e-02 6.50e+03 3.29e+01 bond pdb=" C ASN A 397 " pdb=" N PRO A 398 " ideal model delta sigma weight residual 1.336 1.397 -0.061 1.08e-02 8.57e+03 3.19e+01 ... (remaining 61633 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.50: 1655 106.50 - 113.43: 33819 113.43 - 120.35: 25449 120.35 - 127.28: 22372 127.28 - 134.20: 378 Bond angle restraints: 83673 Sorted by residual: angle pdb=" C ILE F 189 " pdb=" N PRO F 190 " pdb=" CA PRO F 190 " ideal model delta sigma weight residual 119.85 129.35 -9.50 1.01e+00 9.80e-01 8.85e+01 angle pdb=" C ARG A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta sigma weight residual 119.76 129.35 -9.59 1.03e+00 9.43e-01 8.66e+01 angle pdb=" C SER B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 120.38 129.06 -8.68 1.03e+00 9.43e-01 7.10e+01 angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.76 127.77 -8.01 1.00e+00 1.00e+00 6.42e+01 angle pdb=" C LEU F 395 " pdb=" N PRO F 396 " pdb=" CA PRO F 396 " ideal model delta sigma weight residual 120.04 128.50 -8.46 1.08e+00 8.57e-01 6.14e+01 ... (remaining 83668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 36324 23.67 - 47.34: 640 47.34 - 71.01: 144 71.01 - 94.68: 57 94.68 - 118.35: 2 Dihedral angle restraints: 37167 sinusoidal: 12878 harmonic: 24289 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.35 118.35 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" CA GLY O 64 " pdb=" C GLY O 64 " pdb=" N SER O 65 " pdb=" CA SER O 65 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.47 -98.47 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 37164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 7026 0.063 - 0.125: 2278 0.125 - 0.188: 413 0.188 - 0.250: 145 0.250 - 0.313: 9 Chirality restraints: 9871 Sorted by residual: chirality pdb=" CA TYR o 68 " pdb=" N TYR o 68 " pdb=" C TYR o 68 " pdb=" CB TYR o 68 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA TYR l 68 " pdb=" N TYR l 68 " pdb=" C TYR l 68 " pdb=" CB TYR l 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA MET a 10 " pdb=" N MET a 10 " pdb=" C MET a 10 " pdb=" CB MET a 10 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 9868 not shown) Planarity restraints: 10900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEU o 86 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU o 86 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR o 87 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR a 113 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR a 113 " -0.075 2.00e-02 2.50e+03 pdb=" O THR a 113 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN a 114 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN k 7 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASN k 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 ... (remaining 10897 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9672 2.76 - 3.29: 65171 3.29 - 3.83: 102023 3.83 - 4.36: 123320 4.36 - 4.90: 202631 Nonbonded interactions: 502817 Sorted by model distance: nonbonded pdb=" N ASP a 208 " pdb=" O ASP a 213 " model vdw 2.220 2.520 nonbonded pdb=" OH TYR Q 126 " pdb=" OG1 THR Q 169 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP D 266 " pdb=" NZ LYS S 9 " model vdw 2.305 2.520 nonbonded pdb=" CB ALA B 499 " pdb=" CA GLY H 103 " model vdw 2.331 3.860 nonbonded pdb=" O THR G 18 " pdb=" N LEU G 22 " model vdw 2.332 2.520 ... (remaining 502812 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and resid 3 through 226) selection = chain 'J' selection = (chain 'K' and resid 3 through 226) } ncs_group { reference = (chain 'M' and resid 4 through 116) selection = (chain 'N' and resid 4 through 116) selection = chain 'O' } ncs_group { reference = (chain 'Q' and resid 12 through 218) selection = (chain 'R' and resid 12 through 218) selection = (chain 'S' and resid 12 through 218) } 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: 0.010 Normalize map: mean=0, sd=1: 1.990 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: 0.060 Extract box with map and model: 10.620 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 131.670 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.009 0.118 61638 Z= 0.612 Angle : 0.975 10.874 83673 Z= 0.721 Chirality : 0.064 0.313 9871 Planarity : 0.005 0.046 10900 Dihedral : 10.710 118.352 21549 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.52 % Favored : 97.29 % Rotamer: Outliers : 0.78 % Allowed : 0.80 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.61 (0.09), residues: 8369 helix: 0.90 (0.07), residues: 4959 sheet: -0.12 (0.18), residues: 703 loop : -0.18 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 55 HIS 0.002 0.000 HIS F 199 PHE 0.013 0.000 PHE H 44 TYR 0.016 0.000 TYR D 389 ARG 0.004 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1952 time to evaluate : 5.401 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: A 53 GLU cc_start: 0.7603 (tt0) cc_final: 0.7339 (tt0) REVERT: A 231 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8988 (mm-40) REVERT: A 254 CYS cc_start: 0.8355 (m) cc_final: 0.7616 (m) REVERT: A 318 MET cc_start: 0.9183 (mtt) cc_final: 0.8801 (mtp) REVERT: A 331 ILE cc_start: 0.9592 (tt) cc_final: 0.9340 (tt) REVERT: A 436 ASP cc_start: 0.8480 (t0) cc_final: 0.7961 (t70) REVERT: A 491 GLU cc_start: 0.8959 (tt0) cc_final: 0.8740 (tm-30) REVERT: A 516 LYS cc_start: 0.9347 (mttt) cc_final: 0.9081 (tttm) REVERT: A 523 ASN cc_start: 0.8800 (t0) cc_final: 0.8594 (t0) REVERT: A 550 MET cc_start: 0.8642 (mtm) cc_final: 0.8125 (mtm) REVERT: B 306 MET cc_start: 0.8558 (ptm) cc_final: 0.7795 (tmm) REVERT: B 309 THR cc_start: 0.9166 (m) cc_final: 0.8786 (m) REVERT: B 324 GLU cc_start: 0.9123 (tt0) cc_final: 0.8842 (tm-30) REVERT: B 356 GLU cc_start: 0.9234 (tp30) cc_final: 0.8971 (tp30) REVERT: B 433 TRP cc_start: 0.8589 (m-10) cc_final: 0.8329 (m-10) REVERT: B 458 MET cc_start: 0.8695 (mmt) cc_final: 0.8449 (mmt) REVERT: B 550 MET cc_start: 0.9266 (mtm) cc_final: 0.7778 (mtp) REVERT: B 584 MET cc_start: 0.8667 (mtm) cc_final: 0.8335 (mtp) REVERT: C 166 ILE cc_start: 0.9335 (mm) cc_final: 0.8804 (tp) REVERT: C 205 MET cc_start: 0.8593 (mtm) cc_final: 0.8156 (mtt) REVERT: C 286 GLU cc_start: 0.9013 (tt0) cc_final: 0.8572 (tp30) REVERT: C 323 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8235 (mtm-85) REVERT: C 340 MET cc_start: 0.8684 (mtt) cc_final: 0.8483 (mtm) REVERT: C 347 MET cc_start: 0.8410 (ttm) cc_final: 0.8062 (tmm) REVERT: C 349 ASP cc_start: 0.7941 (t0) cc_final: 0.7355 (t70) REVERT: C 361 ILE cc_start: 0.9297 (mt) cc_final: 0.9070 (tp) REVERT: C 399 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6674 (mm-30) REVERT: C 416 ASP cc_start: 0.7424 (t0) cc_final: 0.6773 (t0) REVERT: C 458 MET cc_start: 0.8799 (mtp) cc_final: 0.7629 (mtt) REVERT: C 465 TYR cc_start: 0.9035 (m-80) cc_final: 0.8739 (m-80) REVERT: C 536 LYS cc_start: 0.9235 (tttt) cc_final: 0.8699 (tttp) REVERT: D 128 LEU cc_start: 0.9299 (mt) cc_final: 0.9000 (pt) REVERT: D 257 VAL cc_start: 0.9434 (t) cc_final: 0.9021 (p) REVERT: D 382 GLN cc_start: 0.9059 (mp10) cc_final: 0.8842 (mp10) REVERT: D 484 LEU cc_start: 0.9735 (mt) cc_final: 0.9483 (mt) REVERT: D 495 ILE cc_start: 0.9606 (mt) cc_final: 0.9232 (tt) REVERT: E 72 VAL cc_start: 0.9265 (t) cc_final: 0.8990 (m) REVERT: E 202 ILE cc_start: 0.9672 (mt) cc_final: 0.9463 (mm) REVERT: E 262 ASN cc_start: 0.9129 (t0) cc_final: 0.8856 (t0) REVERT: E 270 GLU cc_start: 0.8871 (tt0) cc_final: 0.8490 (tm-30) REVERT: E 309 GLU cc_start: 0.8410 (tt0) cc_final: 0.8206 (tm-30) REVERT: E 328 TYR cc_start: 0.8843 (t80) cc_final: 0.8201 (t80) REVERT: E 341 VAL cc_start: 0.8775 (m) cc_final: 0.8434 (p) REVERT: F 88 GLU cc_start: 0.8350 (tt0) cc_final: 0.8096 (tm-30) REVERT: F 183 ILE cc_start: 0.9716 (mt) cc_final: 0.9440 (pt) REVERT: F 205 GLN cc_start: 0.9315 (tt0) cc_final: 0.8899 (tp40) REVERT: F 298 THR cc_start: 0.8760 (m) cc_final: 0.8356 (m) REVERT: F 299 ASP cc_start: 0.8437 (m-30) cc_final: 0.7758 (m-30) REVERT: F 309 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8852 (tm-30) REVERT: F 317 VAL cc_start: 0.9171 (t) cc_final: 0.8941 (p) REVERT: F 351 ILE cc_start: 0.9574 (mt) cc_final: 0.9237 (mm) REVERT: F 353 ILE cc_start: 0.9609 (mt) cc_final: 0.9384 (mm) REVERT: F 435 MET cc_start: 0.9097 (tpp) cc_final: 0.8684 (tpt) REVERT: F 492 LEU cc_start: 0.9368 (mt) cc_final: 0.8992 (mp) REVERT: H 58 MET cc_start: 0.8740 (tmm) cc_final: 0.8520 (mmt) REVERT: H 67 PHE cc_start: 0.9154 (t80) cc_final: 0.8580 (t80) REVERT: H 94 ILE cc_start: 0.9400 (mm) cc_final: 0.8897 (pt) REVERT: H 99 ASP cc_start: 0.8513 (t0) cc_final: 0.7926 (p0) REVERT: H 155 PHE cc_start: 0.8481 (t80) cc_final: 0.8186 (t80) REVERT: H 190 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8632 (tm-30) REVERT: I 70 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9079 (mt) REVERT: I 97 GLU cc_start: 0.9354 (tp30) cc_final: 0.8852 (tp30) REVERT: I 177 ILE cc_start: 0.9334 (mm) cc_final: 0.8950 (mm) REVERT: I 203 ILE cc_start: 0.9505 (mt) cc_final: 0.9215 (tp) REVERT: J 81 LEU cc_start: 0.9651 (mt) cc_final: 0.9384 (mt) REVERT: J 119 LEU cc_start: 0.9550 (mt) cc_final: 0.9154 (mt) REVERT: J 194 ASN cc_start: 0.8734 (t0) cc_final: 0.7406 (t0) REVERT: J 221 ASN cc_start: 0.8986 (m-40) cc_final: 0.8594 (t0) REVERT: K 70 ILE cc_start: 0.9694 (mt) cc_final: 0.9482 (mm) REVERT: K 73 SER cc_start: 0.8678 (m) cc_final: 0.8006 (p) REVERT: K 92 THR cc_start: 0.9580 (m) cc_final: 0.9230 (p) REVERT: K 121 LEU cc_start: 0.9645 (mt) cc_final: 0.9403 (mm) REVERT: K 125 TYR cc_start: 0.9068 (m-80) cc_final: 0.8786 (m-10) REVERT: K 133 ILE cc_start: 0.9467 (mt) cc_final: 0.9107 (tp) REVERT: K 164 ASP cc_start: 0.8342 (t0) cc_final: 0.8011 (t0) REVERT: K 177 ILE cc_start: 0.9508 (mt) cc_final: 0.9302 (mp) REVERT: K 194 ASN cc_start: 0.8915 (t0) cc_final: 0.8574 (t0) REVERT: K 203 ILE cc_start: 0.9705 (mt) cc_final: 0.9476 (tp) REVERT: L 8 ILE cc_start: 0.9517 (mt) cc_final: 0.9271 (mp) REVERT: L 22 LEU cc_start: 0.9647 (mt) cc_final: 0.9264 (mt) REVERT: L 27 GLU cc_start: 0.8957 (pt0) cc_final: 0.8215 (pt0) REVERT: L 33 HIS cc_start: 0.8629 (m170) cc_final: 0.8181 (m90) REVERT: L 35 ASN cc_start: 0.8991 (p0) cc_final: 0.8422 (p0) REVERT: L 37 LEU cc_start: 0.8540 (tp) cc_final: 0.8117 (tp) REVERT: L 46 ASN cc_start: 0.9589 (m-40) cc_final: 0.9267 (p0) REVERT: L 47 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8615 (mm-30) REVERT: L 51 THR cc_start: 0.9116 (m) cc_final: 0.8818 (p) REVERT: Q 66 LEU cc_start: 0.9550 (tp) cc_final: 0.9297 (tt) REVERT: Q 132 GLN cc_start: 0.9345 (mt0) cc_final: 0.9141 (mt0) REVERT: Q 151 PHE cc_start: 0.8769 (m-10) cc_final: 0.8191 (m-10) REVERT: Q 197 TYR cc_start: 0.7817 (m-80) cc_final: 0.7292 (m-80) REVERT: Q 228 THR cc_start: 0.8982 (m) cc_final: 0.8607 (p) REVERT: Q 229 MET cc_start: 0.9118 (tpp) cc_final: 0.8721 (tpt) REVERT: R 46 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8407 (ttp-110) REVERT: R 90 GLU cc_start: 0.9328 (mm-30) cc_final: 0.9121 (mm-30) REVERT: R 109 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8244 (mm-30) REVERT: R 125 ASP cc_start: 0.9026 (m-30) cc_final: 0.8705 (p0) REVERT: R 130 LEU cc_start: 0.9580 (mt) cc_final: 0.9220 (tp) REVERT: R 137 THR cc_start: 0.9547 (p) cc_final: 0.9322 (t) REVERT: R 139 TYR cc_start: 0.8962 (t80) cc_final: 0.8738 (t80) REVERT: R 151 PHE cc_start: 0.9168 (m-10) cc_final: 0.8646 (m-10) REVERT: R 170 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8114 (pp20) REVERT: b 4 LEU cc_start: 0.8628 (mt) cc_final: 0.8363 (mm) REVERT: b 8 TYR cc_start: 0.8723 (m-80) cc_final: 0.8397 (m-80) REVERT: b 74 SER cc_start: 0.8115 (m) cc_final: 0.7260 (p) REVERT: b 157 ILE cc_start: 0.8993 (mt) cc_final: 0.8743 (mm) REVERT: c 431 PHE cc_start: 0.9068 (m-80) cc_final: 0.8800 (m-80) REVERT: c 449 PHE cc_start: 0.5677 (m-80) cc_final: 0.5164 (m-10) REVERT: d 10 ASN cc_start: 0.9008 (m-40) cc_final: 0.8646 (t0) REVERT: d 85 MET cc_start: 0.9245 (mtm) cc_final: 0.9015 (mtt) REVERT: d 139 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8560 (tp30) REVERT: d 185 LEU cc_start: 0.9662 (mt) cc_final: 0.9432 (mm) REVERT: d 190 LEU cc_start: 0.9565 (tp) cc_final: 0.9301 (pp) REVERT: d 244 CYS cc_start: 0.7855 (m) cc_final: 0.7413 (m) REVERT: d 279 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8892 (pt0) REVERT: d 298 GLU cc_start: 0.9342 (tt0) cc_final: 0.9135 (pt0) REVERT: d 325 GLU cc_start: 0.9147 (tt0) cc_final: 0.8687 (tp30) REVERT: d 334 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8770 (pt0) REVERT: d 340 HIS cc_start: 0.7985 (m-70) cc_final: 0.7716 (m90) REVERT: g 23 MET cc_start: 0.8951 (tpt) cc_final: 0.8673 (mmm) REVERT: g 32 TYR cc_start: 0.9111 (t80) cc_final: 0.8786 (t80) REVERT: g 76 ILE cc_start: 0.8485 (mt) cc_final: 0.8110 (tt) REVERT: g 112 ILE cc_start: 0.9364 (mt) cc_final: 0.9027 (mt) REVERT: g 119 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7425 (ptt180) REVERT: g 152 LEU cc_start: 0.9149 (mt) cc_final: 0.8857 (mt) REVERT: h 28 MET cc_start: 0.9269 (mtp) cc_final: 0.9004 (tpt) REVERT: h 32 TYR cc_start: 0.8182 (t80) cc_final: 0.7924 (t80) REVERT: h 112 ILE cc_start: 0.9001 (mm) cc_final: 0.8529 (mt) REVERT: h 139 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: i 13 PHE cc_start: 0.8665 (t80) cc_final: 0.8334 (t80) REVERT: i 25 PHE cc_start: 0.9233 (m-80) cc_final: 0.8804 (m-80) REVERT: i 32 TYR cc_start: 0.7166 (t80) cc_final: 0.6834 (t80) REVERT: i 48 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7906 (mtm110) REVERT: i 65 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8635 (mm) REVERT: i 88 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7879 (ttp-170) REVERT: k 25 PHE cc_start: 0.8965 (m-80) cc_final: 0.8290 (m-80) REVERT: l 14 PHE cc_start: 0.8986 (m-80) cc_final: 0.8768 (m-80) REVERT: l 134 ILE cc_start: 0.9102 (mt) cc_final: 0.8729 (tt) REVERT: m 39 THR cc_start: 0.7438 (m) cc_final: 0.7088 (p) REVERT: m 141 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7059 (tp) REVERT: n 13 PHE cc_start: 0.9011 (t80) cc_final: 0.8792 (t80) REVERT: n 139 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6099 (mm-30) REVERT: n 141 LEU cc_start: 0.6582 (mt) cc_final: 0.5446 (tp) REVERT: o 25 PHE cc_start: 0.9067 (m-80) cc_final: 0.8860 (m-80) REVERT: o 28 MET cc_start: 0.8669 (mtp) cc_final: 0.8435 (mtp) REVERT: o 119 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7716 (mtt-85) REVERT: p 312 TRP cc_start: 0.8372 (m100) cc_final: 0.7956 (m100) outliers start: 44 outliers final: 13 residues processed: 1974 average time/residue: 0.5718 time to fit residues: 1881.7165 Evaluate side-chains 1173 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1155 time to evaluate : 5.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 139 GLU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 143 LEU Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 139 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 65 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 10.0000 chunk 633 optimal weight: 0.9980 chunk 351 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 427 optimal weight: 7.9990 chunk 338 optimal weight: 40.0000 chunk 655 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 398 optimal weight: 6.9990 chunk 487 optimal weight: 1.9990 chunk 759 optimal weight: 20.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 146 HIS B 314 ASN B 573 HIS C 468 HIS ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN H 88 ASN H 137 ASN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN Q 207 GLN R 50 GLN R 207 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS ** h 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 GLN i 123 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 61638 Z= 0.294 Angle : 0.698 13.162 83673 Z= 0.365 Chirality : 0.045 0.336 9871 Planarity : 0.006 0.076 10900 Dihedral : 5.193 110.611 9057 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.10 % Favored : 97.89 % Rotamer: Outliers : 3.12 % Allowed : 11.95 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8369 helix: 1.78 (0.07), residues: 4887 sheet: -0.10 (0.19), residues: 728 loop : 0.06 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 567 HIS 0.010 0.001 HIS Q 184 PHE 0.036 0.002 PHE m 25 TYR 0.041 0.002 TYR b 103 ARG 0.010 0.001 ARG j 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1184 time to evaluate : 5.539 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: A 53 GLU cc_start: 0.7883 (tt0) cc_final: 0.7294 (tt0) REVERT: A 95 MET cc_start: 0.8277 (mmt) cc_final: 0.7887 (tpp) REVERT: A 254 CYS cc_start: 0.8760 (m) cc_final: 0.8556 (m) REVERT: A 306 MET cc_start: 0.8463 (tpp) cc_final: 0.8238 (tpp) REVERT: A 347 MET cc_start: 0.8488 (ptp) cc_final: 0.8241 (ptp) REVERT: A 436 ASP cc_start: 0.8452 (t0) cc_final: 0.8109 (t0) REVERT: A 472 PHE cc_start: 0.8438 (t80) cc_final: 0.8172 (t80) REVERT: A 491 GLU cc_start: 0.9054 (tt0) cc_final: 0.8798 (tm-30) REVERT: A 507 ILE cc_start: 0.9383 (pt) cc_final: 0.8840 (pt) REVERT: A 516 LYS cc_start: 0.9315 (mttt) cc_final: 0.8900 (tmtt) REVERT: A 590 VAL cc_start: 0.9322 (m) cc_final: 0.8839 (p) REVERT: B 90 LEU cc_start: 0.9431 (mp) cc_final: 0.9205 (tp) REVERT: B 95 MET cc_start: 0.8747 (tpp) cc_final: 0.8505 (tpp) REVERT: B 167 MET cc_start: 0.8261 (mtt) cc_final: 0.7721 (mtt) REVERT: B 284 MET cc_start: 0.9448 (mmm) cc_final: 0.9234 (mmm) REVERT: B 306 MET cc_start: 0.8564 (ptm) cc_final: 0.7870 (tmm) REVERT: B 324 GLU cc_start: 0.9307 (tt0) cc_final: 0.9099 (tm-30) REVERT: B 347 MET cc_start: 0.8701 (tpp) cc_final: 0.8427 (tpp) REVERT: B 356 GLU cc_start: 0.9201 (tp30) cc_final: 0.8851 (tp30) REVERT: B 458 MET cc_start: 0.8648 (mmt) cc_final: 0.8352 (mmt) REVERT: B 550 MET cc_start: 0.9354 (mtm) cc_final: 0.9000 (mtp) REVERT: B 574 MET cc_start: 0.8796 (ptp) cc_final: 0.8512 (mpp) REVERT: B 608 MET cc_start: 0.8901 (ttp) cc_final: 0.7946 (ttp) REVERT: C 61 MET cc_start: 0.9033 (mmm) cc_final: 0.8713 (mmp) REVERT: C 166 ILE cc_start: 0.9291 (mm) cc_final: 0.8808 (tp) REVERT: C 205 MET cc_start: 0.8703 (mtm) cc_final: 0.8397 (mtt) REVERT: C 286 GLU cc_start: 0.9159 (tt0) cc_final: 0.8714 (tp30) REVERT: C 347 MET cc_start: 0.8431 (ttm) cc_final: 0.8163 (tmm) REVERT: C 349 ASP cc_start: 0.7961 (t0) cc_final: 0.7311 (t0) REVERT: C 416 ASP cc_start: 0.7495 (t0) cc_final: 0.7081 (t0) REVERT: C 458 MET cc_start: 0.8821 (mtp) cc_final: 0.8536 (mtt) REVERT: C 461 LEU cc_start: 0.9596 (mt) cc_final: 0.9348 (mm) REVERT: C 536 LYS cc_start: 0.9024 (tttt) cc_final: 0.8749 (tttp) REVERT: C 540 MET cc_start: 0.8866 (mmm) cc_final: 0.8521 (mmm) REVERT: C 550 MET cc_start: 0.9532 (mmp) cc_final: 0.9282 (mtt) REVERT: C 608 MET cc_start: 0.8680 (tmm) cc_final: 0.8058 (tmm) REVERT: D 254 MET cc_start: 0.8525 (tpp) cc_final: 0.7975 (mmm) REVERT: D 270 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7982 (tt0) REVERT: D 356 MET cc_start: 0.8828 (mtp) cc_final: 0.8612 (mtp) REVERT: D 382 GLN cc_start: 0.9148 (mp10) cc_final: 0.8840 (mp10) REVERT: D 484 LEU cc_start: 0.9695 (mt) cc_final: 0.9442 (mt) REVERT: D 495 ILE cc_start: 0.9551 (mt) cc_final: 0.9265 (tt) REVERT: E 169 MET cc_start: 0.8388 (ttt) cc_final: 0.8099 (ttt) REVERT: E 234 MET cc_start: 0.8649 (mtm) cc_final: 0.8108 (pmm) REVERT: E 254 MET cc_start: 0.8172 (mmm) cc_final: 0.7887 (mmm) REVERT: E 262 ASN cc_start: 0.9118 (t0) cc_final: 0.8681 (t0) REVERT: E 270 GLU cc_start: 0.8947 (tt0) cc_final: 0.8510 (tm-30) REVERT: E 283 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8430 (mt-10) REVERT: E 309 GLU cc_start: 0.8531 (tt0) cc_final: 0.8304 (tm-30) REVERT: E 316 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7457 (mt-10) REVERT: E 330 ASP cc_start: 0.9274 (m-30) cc_final: 0.8806 (t0) REVERT: E 341 VAL cc_start: 0.9083 (m) cc_final: 0.8881 (p) REVERT: E 402 MET cc_start: 0.8959 (tmm) cc_final: 0.8624 (tpp) REVERT: F 153 ILE cc_start: 0.9074 (pt) cc_final: 0.8620 (tt) REVERT: F 169 MET cc_start: 0.8676 (tmm) cc_final: 0.8433 (tmm) REVERT: F 183 ILE cc_start: 0.9689 (mt) cc_final: 0.9176 (pt) REVERT: F 187 GLN cc_start: 0.9064 (pp30) cc_final: 0.8694 (pp30) REVERT: F 205 GLN cc_start: 0.9394 (tt0) cc_final: 0.9026 (tt0) REVERT: F 234 MET cc_start: 0.8857 (mpp) cc_final: 0.8259 (mtm) REVERT: F 299 ASP cc_start: 0.8561 (m-30) cc_final: 0.7836 (m-30) REVERT: F 309 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8959 (tm-30) REVERT: F 317 VAL cc_start: 0.9290 (t) cc_final: 0.9037 (p) REVERT: F 351 ILE cc_start: 0.9579 (mt) cc_final: 0.9291 (mm) REVERT: F 353 ILE cc_start: 0.9642 (mt) cc_final: 0.9432 (mp) REVERT: F 410 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7935 (mmm) REVERT: F 411 THR cc_start: 0.9253 (p) cc_final: 0.9042 (p) REVERT: F 435 MET cc_start: 0.9244 (tpp) cc_final: 0.8920 (tpt) REVERT: F 492 LEU cc_start: 0.9465 (mt) cc_final: 0.9100 (mp) REVERT: H 16 GLN cc_start: 0.9129 (tt0) cc_final: 0.8705 (tm-30) REVERT: H 67 PHE cc_start: 0.9138 (t80) cc_final: 0.8592 (t80) REVERT: H 91 GLN cc_start: 0.9323 (pt0) cc_final: 0.8950 (pm20) REVERT: H 155 PHE cc_start: 0.8526 (t80) cc_final: 0.8183 (t80) REVERT: H 190 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8898 (mm-30) REVERT: H 193 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8692 (tm-30) REVERT: H 206 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8941 (tm-30) REVERT: I 97 GLU cc_start: 0.9351 (tp30) cc_final: 0.9132 (tm-30) REVERT: I 129 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8506 (tp30) REVERT: I 177 ILE cc_start: 0.9134 (mm) cc_final: 0.8901 (mm) REVERT: J 182 GLU cc_start: 0.8440 (tt0) cc_final: 0.7738 (tt0) REVERT: J 207 MET cc_start: 0.9223 (mmp) cc_final: 0.8993 (mmm) REVERT: J 208 MET cc_start: 0.8995 (mmm) cc_final: 0.8776 (mmm) REVERT: K 75 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9403 (mt) REVERT: K 125 TYR cc_start: 0.9085 (m-80) cc_final: 0.8817 (m-10) REVERT: K 132 MET cc_start: 0.8597 (mtt) cc_final: 0.8143 (mmt) REVERT: K 164 ASP cc_start: 0.8461 (t0) cc_final: 0.8133 (t0) REVERT: K 184 TYR cc_start: 0.8669 (m-10) cc_final: 0.7930 (m-80) REVERT: K 194 ASN cc_start: 0.9006 (t0) cc_final: 0.8686 (t0) REVERT: K 207 MET cc_start: 0.8695 (tpp) cc_final: 0.8343 (tpp) REVERT: L 18 THR cc_start: 0.9484 (p) cc_final: 0.9208 (p) REVERT: L 22 LEU cc_start: 0.9677 (mt) cc_final: 0.9136 (mm) REVERT: L 27 GLU cc_start: 0.9073 (pt0) cc_final: 0.8654 (pt0) REVERT: L 33 HIS cc_start: 0.8545 (m170) cc_final: 0.8274 (m170) REVERT: L 37 LEU cc_start: 0.8457 (tp) cc_final: 0.8152 (tp) REVERT: L 46 ASN cc_start: 0.9566 (m-40) cc_final: 0.9338 (t0) REVERT: L 47 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8833 (mm-30) REVERT: L 51 THR cc_start: 0.9148 (m) cc_final: 0.8917 (p) REVERT: L 79 ASP cc_start: 0.9245 (m-30) cc_final: 0.9039 (m-30) REVERT: M 73 VAL cc_start: 0.9599 (t) cc_final: 0.9113 (t) REVERT: M 74 GLU cc_start: 0.9537 (OUTLIER) cc_final: 0.9306 (mp0) REVERT: M 102 MET cc_start: 0.9269 (mtt) cc_final: 0.8735 (mtp) REVERT: N 102 MET cc_start: 0.8992 (mpp) cc_final: 0.8781 (mpp) REVERT: O 84 MET cc_start: 0.8988 (mmm) cc_final: 0.8722 (mmt) REVERT: Q 33 MET cc_start: 0.8433 (tpt) cc_final: 0.8110 (tmm) REVERT: Q 66 LEU cc_start: 0.9604 (tp) cc_final: 0.9301 (tt) REVERT: Q 188 MET cc_start: 0.8484 (mmm) cc_final: 0.8279 (mmm) REVERT: R 46 ARG cc_start: 0.9311 (mtp85) cc_final: 0.9056 (ttm110) REVERT: R 109 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8813 (pp20) REVERT: R 125 ASP cc_start: 0.9149 (m-30) cc_final: 0.8738 (p0) REVERT: R 130 LEU cc_start: 0.9530 (mt) cc_final: 0.9200 (tp) REVERT: R 139 TYR cc_start: 0.9006 (t80) cc_final: 0.8774 (t80) REVERT: S 109 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8995 (mp0) REVERT: S 126 TYR cc_start: 0.8915 (m-80) cc_final: 0.8707 (m-10) REVERT: S 197 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: b 4 LEU cc_start: 0.8591 (mt) cc_final: 0.8344 (mm) REVERT: b 8 TYR cc_start: 0.8768 (m-80) cc_final: 0.8329 (m-80) REVERT: b 52 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8608 (tt) REVERT: b 138 PHE cc_start: 0.8962 (t80) cc_final: 0.8762 (t80) REVERT: b 157 ILE cc_start: 0.8960 (mt) cc_final: 0.8736 (mm) REVERT: c 431 PHE cc_start: 0.9059 (m-80) cc_final: 0.8680 (m-80) REVERT: c 440 ILE cc_start: 0.9657 (mt) cc_final: 0.9455 (pt) REVERT: c 449 PHE cc_start: 0.5717 (m-80) cc_final: 0.4166 (m-10) REVERT: d 10 ASN cc_start: 0.8943 (m-40) cc_final: 0.8571 (t0) REVERT: d 105 MET cc_start: 0.9023 (mmm) cc_final: 0.8757 (mmt) REVERT: d 138 MET cc_start: 0.8365 (mmp) cc_final: 0.8102 (mmm) REVERT: d 152 ASN cc_start: 0.9299 (m-40) cc_final: 0.9091 (m-40) REVERT: d 180 ILE cc_start: 0.9689 (mm) cc_final: 0.9489 (mp) REVERT: d 190 LEU cc_start: 0.9564 (tp) cc_final: 0.9272 (pp) REVERT: d 197 CYS cc_start: 0.9397 (m) cc_final: 0.8896 (p) REVERT: d 325 GLU cc_start: 0.9223 (tt0) cc_final: 0.8818 (tm-30) REVERT: d 334 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8680 (pt0) REVERT: g 23 MET cc_start: 0.8875 (tpt) cc_final: 0.8610 (tpp) REVERT: g 32 TYR cc_start: 0.8981 (t80) cc_final: 0.8351 (t80) REVERT: g 53 MET cc_start: 0.8598 (ptt) cc_final: 0.8152 (pmm) REVERT: g 108 PHE cc_start: 0.9029 (m-10) cc_final: 0.8486 (m-10) REVERT: h 53 MET cc_start: 0.8206 (pmm) cc_final: 0.7608 (pmm) REVERT: h 112 ILE cc_start: 0.9192 (mm) cc_final: 0.8857 (mt) REVERT: h 123 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8673 (mt0) REVERT: h 139 GLU cc_start: 0.7969 (tp30) cc_final: 0.7733 (mm-30) REVERT: h 144 TYR cc_start: 0.8557 (m-10) cc_final: 0.8351 (m-80) REVERT: i 25 PHE cc_start: 0.9256 (m-80) cc_final: 0.8813 (m-80) REVERT: i 88 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7583 (ttp-170) REVERT: j 25 PHE cc_start: 0.8541 (m-80) cc_final: 0.8326 (m-10) REVERT: k 152 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7923 (mm) REVERT: l 23 MET cc_start: 0.7554 (tpt) cc_final: 0.6619 (tpp) REVERT: l 44 MET cc_start: 0.6252 (mmt) cc_final: 0.6048 (mmm) REVERT: l 131 MET cc_start: 0.4318 (ptt) cc_final: 0.3489 (ppp) REVERT: m 17 MET cc_start: 0.8913 (mmm) cc_final: 0.8713 (ptm) REVERT: m 39 THR cc_start: 0.8129 (m) cc_final: 0.7715 (p) REVERT: m 55 SER cc_start: 0.8755 (m) cc_final: 0.8397 (p) REVERT: m 141 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.6452 (tp) REVERT: m 144 TYR cc_start: 0.8239 (m-10) cc_final: 0.7990 (m-80) REVERT: n 141 LEU cc_start: 0.6953 (mt) cc_final: 0.6296 (tp) REVERT: o 17 MET cc_start: 0.8680 (mtp) cc_final: 0.8410 (mtp) REVERT: o 25 PHE cc_start: 0.9067 (m-80) cc_final: 0.8840 (m-80) REVERT: o 104 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7721 (mt) REVERT: o 131 MET cc_start: 0.8558 (ppp) cc_final: 0.8101 (ppp) REVERT: p 312 TRP cc_start: 0.8469 (m100) cc_final: 0.8110 (m100) REVERT: p 338 ILE cc_start: 0.8009 (pt) cc_final: 0.7796 (pt) outliers start: 176 outliers final: 97 residues processed: 1279 average time/residue: 0.5550 time to fit residues: 1211.6891 Evaluate side-chains 1112 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1006 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 414 PHE Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 132 ILE Chi-restraints excluded: chain h residue 148 VAL Chi-restraints excluded: chain i residue 14 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 131 MET Chi-restraints excluded: chain i residue 136 ILE Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 155 LYS Chi-restraints excluded: chain j residue 41 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 14 PHE Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 152 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 104 LEU Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 20.0000 chunk 235 optimal weight: 0.3980 chunk 631 optimal weight: 2.9990 chunk 516 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 760 optimal weight: 5.9990 chunk 821 optimal weight: 3.9990 chunk 677 optimal weight: 9.9990 chunk 754 optimal weight: 10.0000 chunk 259 optimal weight: 0.2980 chunk 610 optimal weight: 30.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 146 HIS ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 HIS B 65 GLN C 114 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN S 198 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS g 123 GLN ** h 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 300 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 61638 Z= 0.242 Angle : 0.639 11.429 83673 Z= 0.330 Chirality : 0.043 0.414 9871 Planarity : 0.005 0.058 10900 Dihedral : 4.777 114.230 9035 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.58 % Favored : 97.41 % Rotamer: Outliers : 2.87 % Allowed : 12.97 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 8369 helix: 1.76 (0.07), residues: 4926 sheet: -0.00 (0.19), residues: 721 loop : -0.10 (0.12), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 567 HIS 0.006 0.001 HIS b 128 PHE 0.040 0.002 PHE m 25 TYR 0.040 0.002 TYR b 103 ARG 0.009 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1061 time to evaluate : 5.628 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: A 95 MET cc_start: 0.8323 (mmt) cc_final: 0.8051 (tpp) REVERT: A 164 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8475 (t-170) REVERT: A 254 CYS cc_start: 0.8779 (m) cc_final: 0.8124 (m) REVERT: A 472 PHE cc_start: 0.8392 (t80) cc_final: 0.8139 (t80) REVERT: A 491 GLU cc_start: 0.8988 (tt0) cc_final: 0.8760 (tm-30) REVERT: A 516 LYS cc_start: 0.9362 (mttt) cc_final: 0.9111 (tttm) REVERT: A 574 MET cc_start: 0.8872 (mtt) cc_final: 0.8412 (mmt) REVERT: B 39 MET cc_start: 0.8291 (ttm) cc_final: 0.8061 (tpp) REVERT: B 90 LEU cc_start: 0.9439 (mp) cc_final: 0.9160 (mt) REVERT: B 95 MET cc_start: 0.8841 (tpp) cc_final: 0.8632 (tpp) REVERT: B 167 MET cc_start: 0.8417 (mtt) cc_final: 0.8000 (mtt) REVERT: B 306 MET cc_start: 0.8523 (ptm) cc_final: 0.7817 (tmm) REVERT: B 324 GLU cc_start: 0.9319 (tt0) cc_final: 0.8987 (tm-30) REVERT: B 356 GLU cc_start: 0.9122 (tp30) cc_final: 0.8787 (tp30) REVERT: B 426 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9070 (mm) REVERT: B 432 PHE cc_start: 0.8955 (t80) cc_final: 0.8410 (t80) REVERT: B 458 MET cc_start: 0.8642 (mmt) cc_final: 0.8279 (mmt) REVERT: B 544 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8850 (mmm) REVERT: B 550 MET cc_start: 0.9373 (mtm) cc_final: 0.9096 (mtp) REVERT: B 608 MET cc_start: 0.8860 (ttp) cc_final: 0.7894 (ttp) REVERT: C 39 MET cc_start: 0.8643 (tmm) cc_final: 0.8131 (tmm) REVERT: C 56 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8474 (mmm-85) REVERT: C 61 MET cc_start: 0.9021 (mmm) cc_final: 0.8786 (mpp) REVERT: C 166 ILE cc_start: 0.9421 (mm) cc_final: 0.8913 (tp) REVERT: C 286 GLU cc_start: 0.9171 (tt0) cc_final: 0.8687 (tp30) REVERT: C 340 MET cc_start: 0.8568 (mtm) cc_final: 0.8149 (ttm) REVERT: C 416 ASP cc_start: 0.7640 (t0) cc_final: 0.7260 (t0) REVERT: C 458 MET cc_start: 0.8840 (mtp) cc_final: 0.8448 (mtt) REVERT: C 536 LYS cc_start: 0.9046 (tttt) cc_final: 0.8683 (tttp) REVERT: C 540 MET cc_start: 0.8899 (mmm) cc_final: 0.8319 (mmm) REVERT: C 550 MET cc_start: 0.9545 (mmp) cc_final: 0.9188 (mtp) REVERT: C 608 MET cc_start: 0.8710 (tmm) cc_final: 0.7887 (tmm) REVERT: D 169 MET cc_start: 0.8347 (tmm) cc_final: 0.8024 (tmm) REVERT: D 254 MET cc_start: 0.8654 (tpp) cc_final: 0.8156 (mmm) REVERT: D 270 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8062 (tt0) REVERT: D 382 GLN cc_start: 0.9209 (mp10) cc_final: 0.8904 (mp10) REVERT: D 402 MET cc_start: 0.8793 (ttp) cc_final: 0.8585 (mtp) REVERT: D 459 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: D 484 LEU cc_start: 0.9718 (mt) cc_final: 0.9485 (mt) REVERT: D 495 ILE cc_start: 0.9550 (mt) cc_final: 0.9253 (tt) REVERT: E 87 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9037 (mp) REVERT: E 148 GLU cc_start: 0.8261 (tt0) cc_final: 0.7932 (tt0) REVERT: E 169 MET cc_start: 0.8456 (ttt) cc_final: 0.7955 (tmm) REVERT: E 234 MET cc_start: 0.8800 (mtm) cc_final: 0.7849 (pmm) REVERT: E 254 MET cc_start: 0.8234 (mmm) cc_final: 0.7970 (mmm) REVERT: E 262 ASN cc_start: 0.9088 (t0) cc_final: 0.8127 (t0) REVERT: E 270 GLU cc_start: 0.8985 (tt0) cc_final: 0.8608 (pt0) REVERT: E 283 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8368 (mt-10) REVERT: E 309 GLU cc_start: 0.8556 (tt0) cc_final: 0.8352 (tm-30) REVERT: E 316 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7418 (mt-10) REVERT: E 330 ASP cc_start: 0.9321 (m-30) cc_final: 0.8805 (t0) REVERT: E 356 MET cc_start: 0.8766 (mtm) cc_final: 0.8227 (mtm) REVERT: E 382 GLN cc_start: 0.8976 (mp10) cc_final: 0.8765 (mp10) REVERT: F 153 ILE cc_start: 0.9045 (pt) cc_final: 0.8706 (tt) REVERT: F 169 MET cc_start: 0.8674 (tmm) cc_final: 0.8433 (tmm) REVERT: F 183 ILE cc_start: 0.9708 (mt) cc_final: 0.9229 (pt) REVERT: F 187 GLN cc_start: 0.9123 (pp30) cc_final: 0.8703 (pp30) REVERT: F 205 GLN cc_start: 0.9347 (tt0) cc_final: 0.9032 (tt0) REVERT: F 234 MET cc_start: 0.8836 (mpp) cc_final: 0.8343 (mtm) REVERT: F 299 ASP cc_start: 0.8503 (m-30) cc_final: 0.7845 (m-30) REVERT: F 309 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8941 (tm-30) REVERT: F 317 VAL cc_start: 0.9320 (t) cc_final: 0.8963 (p) REVERT: F 351 ILE cc_start: 0.9562 (mt) cc_final: 0.9324 (mm) REVERT: F 353 ILE cc_start: 0.9654 (mt) cc_final: 0.9432 (mp) REVERT: F 356 MET cc_start: 0.8635 (mtm) cc_final: 0.8386 (mtt) REVERT: F 410 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7926 (mmm) REVERT: F 435 MET cc_start: 0.9252 (tpp) cc_final: 0.8827 (tpt) REVERT: F 491 MET cc_start: 0.8529 (mtp) cc_final: 0.8223 (ptp) REVERT: F 492 LEU cc_start: 0.9464 (mt) cc_final: 0.9060 (mp) REVERT: H 67 PHE cc_start: 0.9113 (t80) cc_final: 0.8614 (t80) REVERT: H 190 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8823 (mm-30) REVERT: H 193 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8726 (tm-30) REVERT: I 97 GLU cc_start: 0.9324 (tp30) cc_final: 0.9111 (tm-30) REVERT: I 129 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8430 (tp30) REVERT: I 177 ILE cc_start: 0.9118 (mm) cc_final: 0.8874 (mm) REVERT: I 182 GLU cc_start: 0.7901 (pt0) cc_final: 0.7689 (pt0) REVERT: J 72 MET cc_start: 0.8926 (ppp) cc_final: 0.8699 (ppp) REVERT: J 76 MET cc_start: 0.8921 (mmm) cc_final: 0.8694 (mmm) REVERT: J 182 GLU cc_start: 0.8496 (tt0) cc_final: 0.7812 (tt0) REVERT: J 207 MET cc_start: 0.9238 (mmp) cc_final: 0.8853 (mmp) REVERT: J 208 MET cc_start: 0.9014 (mmm) cc_final: 0.8732 (mmt) REVERT: K 75 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9472 (mt) REVERT: K 125 TYR cc_start: 0.9127 (m-80) cc_final: 0.8897 (m-10) REVERT: K 132 MET cc_start: 0.8256 (mtt) cc_final: 0.8017 (mmt) REVERT: K 154 MET cc_start: 0.9439 (mtt) cc_final: 0.9043 (ptp) REVERT: K 184 TYR cc_start: 0.8713 (m-10) cc_final: 0.8163 (m-10) REVERT: K 194 ASN cc_start: 0.8928 (t0) cc_final: 0.8671 (t0) REVERT: K 207 MET cc_start: 0.8728 (tpp) cc_final: 0.8360 (tpp) REVERT: L 22 LEU cc_start: 0.9668 (mt) cc_final: 0.9419 (tp) REVERT: L 27 GLU cc_start: 0.9124 (pt0) cc_final: 0.8744 (pt0) REVERT: L 33 HIS cc_start: 0.8646 (m170) cc_final: 0.8382 (m170) REVERT: L 37 LEU cc_start: 0.8457 (tp) cc_final: 0.8138 (tp) REVERT: L 46 ASN cc_start: 0.9513 (m-40) cc_final: 0.9296 (t0) REVERT: L 47 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8787 (mm-30) REVERT: L 51 THR cc_start: 0.9112 (m) cc_final: 0.8831 (p) REVERT: M 102 MET cc_start: 0.9180 (mtt) cc_final: 0.8956 (mtp) REVERT: N 102 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8438 (mtm) REVERT: O 84 MET cc_start: 0.9013 (mmm) cc_final: 0.8757 (mmt) REVERT: Q 66 LEU cc_start: 0.9628 (tp) cc_final: 0.9282 (tt) REVERT: Q 151 PHE cc_start: 0.8719 (m-10) cc_final: 0.8493 (m-10) REVERT: R 109 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8827 (pp20) REVERT: R 125 ASP cc_start: 0.9182 (m-30) cc_final: 0.8742 (p0) REVERT: R 130 LEU cc_start: 0.9482 (mt) cc_final: 0.9192 (tp) REVERT: R 139 TYR cc_start: 0.8992 (t80) cc_final: 0.8787 (t80) REVERT: R 229 MET cc_start: 0.9090 (mmm) cc_final: 0.8655 (mmm) REVERT: S 197 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6552 (m-80) REVERT: b 4 LEU cc_start: 0.8418 (mt) cc_final: 0.8212 (mm) REVERT: b 52 LEU cc_start: 0.8970 (tp) cc_final: 0.8707 (tt) REVERT: b 114 MET cc_start: 0.5883 (mpp) cc_final: 0.5574 (mpp) REVERT: b 138 PHE cc_start: 0.8836 (t80) cc_final: 0.8612 (t80) REVERT: b 157 ILE cc_start: 0.9038 (mt) cc_final: 0.8806 (mm) REVERT: c 424 LEU cc_start: 0.9204 (mt) cc_final: 0.8991 (pp) REVERT: c 435 TYR cc_start: 0.9133 (t80) cc_final: 0.8819 (t80) REVERT: c 449 PHE cc_start: 0.5887 (m-80) cc_final: 0.5616 (m-10) REVERT: d 10 ASN cc_start: 0.8988 (m-40) cc_final: 0.8576 (t0) REVERT: d 105 MET cc_start: 0.8974 (mmm) cc_final: 0.8632 (mmt) REVERT: d 138 MET cc_start: 0.8409 (mmp) cc_final: 0.8201 (mmm) REVERT: d 152 ASN cc_start: 0.9318 (m-40) cc_final: 0.9094 (t0) REVERT: d 190 LEU cc_start: 0.9552 (tp) cc_final: 0.9258 (pp) REVERT: d 197 CYS cc_start: 0.9416 (m) cc_final: 0.9102 (p) REVERT: d 221 PHE cc_start: 0.8873 (m-80) cc_final: 0.8478 (m-80) REVERT: d 307 LEU cc_start: 0.9228 (mp) cc_final: 0.8943 (tp) REVERT: d 325 GLU cc_start: 0.9278 (tt0) cc_final: 0.8799 (tm-30) REVERT: d 334 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8721 (pt0) REVERT: d 340 HIS cc_start: 0.8192 (m-70) cc_final: 0.7750 (m90) REVERT: g 32 TYR cc_start: 0.8910 (t80) cc_final: 0.8643 (t80) REVERT: g 53 MET cc_start: 0.8652 (ptt) cc_final: 0.8080 (pmm) REVERT: h 53 MET cc_start: 0.8274 (pmm) cc_final: 0.7669 (pmm) REVERT: h 61 MET cc_start: 0.6795 (mtp) cc_final: 0.6411 (ptp) REVERT: i 13 PHE cc_start: 0.8447 (t80) cc_final: 0.8179 (t80) REVERT: i 25 PHE cc_start: 0.9223 (m-80) cc_final: 0.8797 (m-80) REVERT: i 88 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7393 (ttp-170) REVERT: j 25 PHE cc_start: 0.8516 (m-80) cc_final: 0.8201 (m-10) REVERT: j 47 MET cc_start: 0.8771 (ppp) cc_final: 0.8158 (ppp) REVERT: j 131 MET cc_start: 0.8622 (ppp) cc_final: 0.8170 (ppp) REVERT: k 25 PHE cc_start: 0.8749 (m-80) cc_final: 0.8327 (m-80) REVERT: k 115 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: k 131 MET cc_start: 0.7070 (ppp) cc_final: 0.6863 (ppp) REVERT: l 131 MET cc_start: 0.4232 (ptt) cc_final: 0.3633 (ppp) REVERT: m 39 THR cc_start: 0.7922 (m) cc_final: 0.7549 (p) REVERT: m 55 SER cc_start: 0.8787 (m) cc_final: 0.8405 (p) REVERT: m 141 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.6544 (tp) REVERT: n 143 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8917 (mt) REVERT: o 17 MET cc_start: 0.8720 (mtp) cc_final: 0.8439 (mtp) REVERT: o 115 ASP cc_start: 0.8000 (t70) cc_final: 0.7775 (t0) REVERT: o 131 MET cc_start: 0.8609 (ppp) cc_final: 0.8282 (ppp) REVERT: p 330 ASN cc_start: 0.9156 (m-40) cc_final: 0.8870 (m110) REVERT: p 338 ILE cc_start: 0.8049 (pt) cc_final: 0.7712 (pt) REVERT: p 342 MET cc_start: 0.7449 (mmt) cc_final: 0.7198 (mmm) outliers start: 162 outliers final: 96 residues processed: 1152 average time/residue: 0.5452 time to fit residues: 1077.1356 Evaluate side-chains 1048 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 939 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 194 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 414 PHE Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 136 ILE Chi-restraints excluded: chain j residue 41 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 44 MET Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 751 optimal weight: 40.0000 chunk 571 optimal weight: 40.0000 chunk 394 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 362 optimal weight: 6.9990 chunk 510 optimal weight: 10.0000 chunk 763 optimal weight: 8.9990 chunk 808 optimal weight: 20.0000 chunk 398 optimal weight: 10.0000 chunk 723 optimal weight: 0.0980 chunk 217 optimal weight: 10.0000 overall best weight: 5.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 543 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN Q 160 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 61638 Z= 0.377 Angle : 0.705 16.063 83673 Z= 0.364 Chirality : 0.044 0.326 9871 Planarity : 0.005 0.051 10900 Dihedral : 4.918 119.654 9033 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.17 % Favored : 96.82 % Rotamer: Outliers : 3.77 % Allowed : 14.35 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8369 helix: 1.51 (0.07), residues: 4978 sheet: 0.03 (0.19), residues: 715 loop : -0.24 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 567 HIS 0.026 0.002 HIS S 198 PHE 0.044 0.002 PHE o 25 TYR 0.035 0.002 TYR b 103 ARG 0.011 0.001 ARG R 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 927 time to evaluate : 5.553 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: A 95 MET cc_start: 0.8327 (mmt) cc_final: 0.8106 (mmm) REVERT: A 164 HIS cc_start: 0.8954 (OUTLIER) cc_final: 0.8546 (t70) REVERT: A 167 MET cc_start: 0.9226 (mtm) cc_final: 0.8980 (mtt) REVERT: A 254 CYS cc_start: 0.8684 (m) cc_final: 0.8147 (m) REVERT: A 318 MET cc_start: 0.9193 (mtt) cc_final: 0.8685 (mtp) REVERT: A 472 PHE cc_start: 0.8528 (t80) cc_final: 0.8265 (t80) REVERT: A 491 GLU cc_start: 0.9019 (tt0) cc_final: 0.8808 (tm-30) REVERT: A 516 LYS cc_start: 0.9459 (mttt) cc_final: 0.9130 (tttm) REVERT: A 517 ASP cc_start: 0.8963 (m-30) cc_final: 0.8682 (m-30) REVERT: A 540 MET cc_start: 0.8963 (ptm) cc_final: 0.7847 (ppp) REVERT: A 544 MET cc_start: 0.9053 (mtp) cc_final: 0.8352 (mtp) REVERT: B 167 MET cc_start: 0.8521 (mtt) cc_final: 0.8186 (mtt) REVERT: B 228 LEU cc_start: 0.9266 (pt) cc_final: 0.9057 (pp) REVERT: B 306 MET cc_start: 0.8595 (ptm) cc_final: 0.7905 (tmm) REVERT: B 318 MET cc_start: 0.9382 (tpp) cc_final: 0.8155 (mpp) REVERT: B 356 GLU cc_start: 0.9253 (tp30) cc_final: 0.8885 (tp30) REVERT: B 426 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9141 (mm) REVERT: B 428 ILE cc_start: 0.9468 (mt) cc_final: 0.9212 (mm) REVERT: B 432 PHE cc_start: 0.9042 (t80) cc_final: 0.8688 (t80) REVERT: B 458 MET cc_start: 0.8751 (mmt) cc_final: 0.8365 (mmt) REVERT: B 492 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9370 (mm) REVERT: B 544 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8894 (mmm) REVERT: B 550 MET cc_start: 0.9387 (mtm) cc_final: 0.9162 (mtp) REVERT: B 606 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8907 (mt-10) REVERT: B 608 MET cc_start: 0.8928 (ttp) cc_final: 0.8011 (ttp) REVERT: C 39 MET cc_start: 0.8821 (tmm) cc_final: 0.8244 (tmm) REVERT: C 42 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8978 (mm) REVERT: C 56 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8724 (tpp80) REVERT: C 61 MET cc_start: 0.9006 (mmm) cc_final: 0.8675 (mmp) REVERT: C 340 MET cc_start: 0.8762 (ttm) cc_final: 0.8497 (ttm) REVERT: C 416 ASP cc_start: 0.7964 (t0) cc_final: 0.7675 (t0) REVERT: C 458 MET cc_start: 0.8874 (mtp) cc_final: 0.8019 (mtt) REVERT: C 540 MET cc_start: 0.8931 (mmm) cc_final: 0.8219 (mmm) REVERT: C 550 MET cc_start: 0.9551 (mmp) cc_final: 0.9144 (mtp) REVERT: C 584 MET cc_start: 0.8833 (ptm) cc_final: 0.8219 (ptm) REVERT: C 608 MET cc_start: 0.8753 (tmm) cc_final: 0.7781 (tmm) REVERT: D 254 MET cc_start: 0.8682 (tpp) cc_final: 0.8244 (mmm) REVERT: D 270 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: D 382 GLN cc_start: 0.9349 (mp10) cc_final: 0.9084 (mp10) REVERT: D 459 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: D 484 LEU cc_start: 0.9762 (mt) cc_final: 0.9556 (mt) REVERT: D 495 ILE cc_start: 0.9531 (mt) cc_final: 0.9253 (tt) REVERT: E 87 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8776 (mp) REVERT: E 148 GLU cc_start: 0.8463 (tt0) cc_final: 0.8174 (tt0) REVERT: E 238 MET cc_start: 0.8588 (tpt) cc_final: 0.8304 (tpt) REVERT: E 254 MET cc_start: 0.8432 (mmm) cc_final: 0.8137 (mmm) REVERT: E 262 ASN cc_start: 0.9144 (t0) cc_final: 0.8765 (t0) REVERT: E 270 GLU cc_start: 0.8953 (tt0) cc_final: 0.8516 (tm-30) REVERT: E 283 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8402 (mt-10) REVERT: E 314 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8830 (ttp80) REVERT: E 316 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7193 (mt-10) REVERT: E 330 ASP cc_start: 0.9377 (m-30) cc_final: 0.8873 (t70) REVERT: E 382 GLN cc_start: 0.8972 (mp10) cc_final: 0.8755 (mp10) REVERT: F 121 THR cc_start: 0.9693 (OUTLIER) cc_final: 0.9430 (t) REVERT: F 123 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8868 (p) REVERT: F 153 ILE cc_start: 0.9091 (pt) cc_final: 0.8822 (tt) REVERT: F 169 MET cc_start: 0.8698 (tmm) cc_final: 0.8470 (tmm) REVERT: F 183 ILE cc_start: 0.9689 (mt) cc_final: 0.9258 (pt) REVERT: F 187 GLN cc_start: 0.9306 (pp30) cc_final: 0.8923 (pp30) REVERT: F 234 MET cc_start: 0.8940 (mpp) cc_final: 0.8368 (mtm) REVERT: F 256 ASN cc_start: 0.8999 (m-40) cc_final: 0.8703 (p0) REVERT: F 309 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8913 (tm-30) REVERT: F 351 ILE cc_start: 0.9548 (mt) cc_final: 0.9280 (mm) REVERT: F 353 ILE cc_start: 0.9656 (mt) cc_final: 0.9433 (mm) REVERT: F 410 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7962 (mmm) REVERT: F 435 MET cc_start: 0.9252 (tpp) cc_final: 0.8855 (tpp) REVERT: F 492 LEU cc_start: 0.9507 (mt) cc_final: 0.9122 (mp) REVERT: H 190 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8872 (mm-30) REVERT: H 193 GLU cc_start: 0.9308 (tm-30) cc_final: 0.8865 (tm-30) REVERT: I 207 MET cc_start: 0.9141 (mmp) cc_final: 0.8872 (mmt) REVERT: J 72 MET cc_start: 0.9044 (ppp) cc_final: 0.8634 (ppp) REVERT: J 76 MET cc_start: 0.8880 (mmm) cc_final: 0.8672 (mmm) REVERT: J 182 GLU cc_start: 0.8501 (tt0) cc_final: 0.7828 (tt0) REVERT: J 207 MET cc_start: 0.9343 (mmp) cc_final: 0.8966 (mmm) REVERT: J 208 MET cc_start: 0.9096 (mmm) cc_final: 0.8766 (mmt) REVERT: K 75 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9527 (mt) REVERT: K 129 GLU cc_start: 0.8390 (tt0) cc_final: 0.8028 (tt0) REVERT: K 132 MET cc_start: 0.8254 (mtt) cc_final: 0.7892 (mtt) REVERT: K 184 TYR cc_start: 0.8767 (m-10) cc_final: 0.8243 (m-80) REVERT: K 194 ASN cc_start: 0.9118 (t0) cc_final: 0.8755 (t0) REVERT: K 207 MET cc_start: 0.8766 (tpp) cc_final: 0.8506 (tpp) REVERT: L 22 LEU cc_start: 0.9669 (mt) cc_final: 0.9430 (tp) REVERT: L 27 GLU cc_start: 0.9240 (pt0) cc_final: 0.8865 (pt0) REVERT: L 33 HIS cc_start: 0.8654 (m170) cc_final: 0.8390 (m90) REVERT: L 37 LEU cc_start: 0.8502 (tp) cc_final: 0.8212 (tp) REVERT: L 47 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8743 (mm-30) REVERT: L 51 THR cc_start: 0.9181 (m) cc_final: 0.8943 (p) REVERT: M 102 MET cc_start: 0.9220 (mtt) cc_final: 0.8995 (mtt) REVERT: N 96 LEU cc_start: 0.9664 (pp) cc_final: 0.9401 (pp) REVERT: N 102 MET cc_start: 0.8953 (mpp) cc_final: 0.8474 (mtm) REVERT: Q 33 MET cc_start: 0.8941 (tmm) cc_final: 0.8343 (tmm) REVERT: Q 66 LEU cc_start: 0.9670 (tp) cc_final: 0.9312 (tt) REVERT: Q 234 MET cc_start: 0.8918 (tmm) cc_final: 0.8685 (tmm) REVERT: R 109 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8864 (pp20) REVERT: R 130 LEU cc_start: 0.9450 (mt) cc_final: 0.9090 (tp) REVERT: R 229 MET cc_start: 0.9064 (mmm) cc_final: 0.8716 (mmm) REVERT: S 188 MET cc_start: 0.8544 (tpp) cc_final: 0.8332 (ttt) REVERT: S 197 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: b 19 MET cc_start: 0.7697 (tmm) cc_final: 0.7483 (ppp) REVERT: b 52 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (tt) REVERT: b 138 PHE cc_start: 0.8794 (t80) cc_final: 0.8564 (t80) REVERT: b 157 ILE cc_start: 0.9046 (mt) cc_final: 0.8805 (mm) REVERT: c 435 TYR cc_start: 0.9052 (t80) cc_final: 0.8844 (t80) REVERT: c 446 MET cc_start: 0.7166 (tpp) cc_final: 0.6919 (tpp) REVERT: d 10 ASN cc_start: 0.9109 (m-40) cc_final: 0.8829 (t0) REVERT: d 105 MET cc_start: 0.8965 (mmm) cc_final: 0.8700 (mmt) REVERT: d 138 MET cc_start: 0.8479 (mmp) cc_final: 0.8182 (mmm) REVERT: d 139 GLU cc_start: 0.7952 (tp30) cc_final: 0.7133 (tm-30) REVERT: d 152 ASN cc_start: 0.9351 (m-40) cc_final: 0.8944 (p0) REVERT: d 325 GLU cc_start: 0.9322 (tt0) cc_final: 0.8809 (tm-30) REVERT: d 329 ILE cc_start: 0.9697 (mt) cc_final: 0.9170 (mp) REVERT: d 334 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8640 (pt0) REVERT: g 23 MET cc_start: 0.7567 (tpp) cc_final: 0.7209 (tpt) REVERT: g 32 TYR cc_start: 0.9022 (t80) cc_final: 0.8741 (t80) REVERT: g 53 MET cc_start: 0.8575 (ptt) cc_final: 0.8021 (pmm) REVERT: g 119 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8061 (mmp80) REVERT: h 53 MET cc_start: 0.8392 (pmm) cc_final: 0.8183 (pmm) REVERT: i 13 PHE cc_start: 0.8557 (t80) cc_final: 0.8224 (t80) REVERT: i 25 PHE cc_start: 0.9233 (m-80) cc_final: 0.8818 (m-80) REVERT: i 88 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7342 (ttp-170) REVERT: j 47 MET cc_start: 0.8504 (ppp) cc_final: 0.8103 (ppp) REVERT: j 131 MET cc_start: 0.8722 (ppp) cc_final: 0.8460 (ppp) REVERT: k 25 PHE cc_start: 0.8732 (m-80) cc_final: 0.8338 (m-80) REVERT: k 32 TYR cc_start: 0.7584 (t80) cc_final: 0.6820 (t80) REVERT: k 47 MET cc_start: 0.7580 (pmm) cc_final: 0.7297 (pmm) REVERT: k 115 ASP cc_start: 0.7928 (m-30) cc_final: 0.7298 (m-30) REVERT: l 44 MET cc_start: 0.6177 (mmp) cc_final: 0.5786 (mmm) REVERT: l 47 MET cc_start: 0.5666 (OUTLIER) cc_final: 0.5082 (ptm) REVERT: l 131 MET cc_start: 0.5141 (ptt) cc_final: 0.4672 (ptt) REVERT: l 134 ILE cc_start: 0.9078 (mp) cc_final: 0.8869 (tp) REVERT: m 47 MET cc_start: 0.6170 (mmm) cc_final: 0.5916 (mmm) REVERT: m 55 SER cc_start: 0.8696 (m) cc_final: 0.8333 (p) REVERT: m 131 MET cc_start: 0.6858 (ppp) cc_final: 0.6588 (ppp) REVERT: m 141 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6365 (tp) REVERT: n 23 MET cc_start: 0.4642 (tpt) cc_final: 0.3756 (ttt) REVERT: n 44 MET cc_start: 0.5665 (tpt) cc_final: 0.4462 (tpt) REVERT: n 47 MET cc_start: 0.8435 (tmm) cc_final: 0.7808 (pmm) REVERT: n 68 TYR cc_start: 0.7137 (m-10) cc_final: 0.6816 (m-10) REVERT: n 141 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6274 (tp) REVERT: n 143 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8962 (mt) REVERT: o 17 MET cc_start: 0.8766 (mtp) cc_final: 0.8563 (mtp) REVERT: o 47 MET cc_start: 0.8713 (ppp) cc_final: 0.8374 (ppp) REVERT: o 131 MET cc_start: 0.8583 (ppp) cc_final: 0.8199 (ppp) REVERT: p 312 TRP cc_start: 0.8345 (m100) cc_final: 0.7681 (m100) REVERT: p 338 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7583 (pt) outliers start: 213 outliers final: 135 residues processed: 1054 average time/residue: 0.5355 time to fit residues: 975.8452 Evaluate side-chains 1022 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 865 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 314 ARG Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 154 ILE Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 119 ARG Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 123 GLN Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 143 LEU Chi-restraints excluded: chain j residue 41 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain k residue 53 MET Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 47 MET Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 148 VAL Chi-restraints excluded: chain n residue 32 TYR Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain n residue 141 LEU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain p residue 338 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 673 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 601 optimal weight: 40.0000 chunk 333 optimal weight: 50.0000 chunk 689 optimal weight: 50.0000 chunk 558 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 412 optimal weight: 2.9990 chunk 725 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN H 113 HIS ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 HIS R 207 GLN S 19 HIS S 50 GLN S 198 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 61638 Z= 0.404 Angle : 0.716 14.890 83673 Z= 0.368 Chirality : 0.044 0.380 9871 Planarity : 0.005 0.097 10900 Dihedral : 4.796 121.027 9029 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.60 % Favored : 96.39 % Rotamer: Outliers : 4.07 % Allowed : 15.27 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 8369 helix: 1.40 (0.07), residues: 4985 sheet: -0.05 (0.20), residues: 690 loop : -0.42 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 567 HIS 0.007 0.002 HIS d 340 PHE 0.046 0.002 PHE m 25 TYR 0.038 0.002 TYR b 8 ARG 0.008 0.001 ARG m 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 890 time to evaluate : 5.493 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: A 95 MET cc_start: 0.8403 (mmt) cc_final: 0.8130 (mmm) REVERT: A 164 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8223 (t70) REVERT: A 167 MET cc_start: 0.9187 (mtm) cc_final: 0.8791 (mtt) REVERT: A 254 CYS cc_start: 0.8618 (m) cc_final: 0.8083 (m) REVERT: A 318 MET cc_start: 0.9184 (mtt) cc_final: 0.8633 (mtp) REVERT: A 491 GLU cc_start: 0.9045 (tt0) cc_final: 0.8828 (tm-30) REVERT: A 516 LYS cc_start: 0.9519 (mttt) cc_final: 0.9183 (tttm) REVERT: A 517 ASP cc_start: 0.8954 (m-30) cc_final: 0.8655 (m-30) REVERT: A 518 ASP cc_start: 0.7535 (m-30) cc_final: 0.7192 (m-30) REVERT: A 540 MET cc_start: 0.8990 (ptm) cc_final: 0.8649 (ptm) REVERT: A 574 MET cc_start: 0.8842 (mtt) cc_final: 0.8421 (mmt) REVERT: B 167 MET cc_start: 0.8630 (mtt) cc_final: 0.8363 (mtt) REVERT: B 306 MET cc_start: 0.8607 (ptm) cc_final: 0.8046 (tmm) REVERT: B 318 MET cc_start: 0.9409 (tpp) cc_final: 0.8239 (mpp) REVERT: B 368 MET cc_start: 0.9126 (mmm) cc_final: 0.8689 (ttm) REVERT: B 426 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9262 (mm) REVERT: B 432 PHE cc_start: 0.9106 (t80) cc_final: 0.8678 (t80) REVERT: B 458 MET cc_start: 0.8804 (mmt) cc_final: 0.8435 (mmt) REVERT: B 544 MET cc_start: 0.9112 (mtp) cc_final: 0.8799 (mmm) REVERT: B 550 MET cc_start: 0.9373 (mtm) cc_final: 0.9032 (mtp) REVERT: B 606 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8898 (mt-10) REVERT: B 608 MET cc_start: 0.8950 (ttp) cc_final: 0.8196 (ttp) REVERT: C 42 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8990 (mm) REVERT: C 56 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (tpp80) REVERT: C 61 MET cc_start: 0.9058 (mmm) cc_final: 0.8709 (mmp) REVERT: C 437 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9310 (mmmm) REVERT: C 458 MET cc_start: 0.8895 (mtp) cc_final: 0.8403 (mtt) REVERT: C 540 MET cc_start: 0.8897 (mmm) cc_final: 0.8206 (mmm) REVERT: C 550 MET cc_start: 0.9540 (mmp) cc_final: 0.9085 (mtp) REVERT: C 584 MET cc_start: 0.8839 (ptm) cc_final: 0.8480 (ptm) REVERT: C 608 MET cc_start: 0.8826 (tmm) cc_final: 0.7817 (tmm) REVERT: D 254 MET cc_start: 0.8762 (tpp) cc_final: 0.8332 (mmm) REVERT: D 270 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: D 382 GLN cc_start: 0.9395 (mp10) cc_final: 0.9030 (mp10) REVERT: D 402 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8725 (mtp) REVERT: D 495 ILE cc_start: 0.9520 (mt) cc_final: 0.9251 (tt) REVERT: E 87 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8802 (mp) REVERT: E 169 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8397 (ttt) REVERT: E 234 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8775 (pmm) REVERT: E 254 MET cc_start: 0.8534 (mmm) cc_final: 0.8224 (mmm) REVERT: E 270 GLU cc_start: 0.9018 (tt0) cc_final: 0.8691 (tt0) REVERT: E 283 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8513 (mt-10) REVERT: E 309 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8467 (tm-30) REVERT: E 316 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7550 (mt-10) REVERT: E 330 ASP cc_start: 0.9388 (OUTLIER) cc_final: 0.8873 (t70) REVERT: F 153 ILE cc_start: 0.9123 (pt) cc_final: 0.8854 (tt) REVERT: F 169 MET cc_start: 0.8787 (tmm) cc_final: 0.8524 (tmm) REVERT: F 180 MET cc_start: 0.8674 (mmm) cc_final: 0.8179 (mmm) REVERT: F 183 ILE cc_start: 0.9628 (mt) cc_final: 0.9263 (pt) REVERT: F 187 GLN cc_start: 0.9353 (pp30) cc_final: 0.8841 (pp30) REVERT: F 234 MET cc_start: 0.8936 (mpp) cc_final: 0.8515 (mtm) REVERT: F 299 ASP cc_start: 0.8653 (m-30) cc_final: 0.8178 (m-30) REVERT: F 309 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8941 (tm-30) REVERT: F 351 ILE cc_start: 0.9552 (mt) cc_final: 0.9287 (mm) REVERT: F 353 ILE cc_start: 0.9675 (mt) cc_final: 0.9432 (mm) REVERT: F 402 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9026 (tpp) REVERT: F 410 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8001 (mtp) REVERT: F 435 MET cc_start: 0.9273 (tpp) cc_final: 0.8899 (tpt) REVERT: F 491 MET cc_start: 0.8557 (mtp) cc_final: 0.8220 (ptp) REVERT: H 190 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8742 (tm-30) REVERT: H 193 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8937 (tm-30) REVERT: I 129 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8323 (tp30) REVERT: I 182 GLU cc_start: 0.7806 (pt0) cc_final: 0.7570 (pt0) REVERT: J 72 MET cc_start: 0.9136 (ppp) cc_final: 0.8656 (ppp) REVERT: J 76 MET cc_start: 0.8922 (mmm) cc_final: 0.8680 (mmm) REVERT: J 182 GLU cc_start: 0.8567 (tt0) cc_final: 0.7810 (tt0) REVERT: J 207 MET cc_start: 0.9402 (mmp) cc_final: 0.9071 (mmm) REVERT: J 208 MET cc_start: 0.9136 (mmm) cc_final: 0.8774 (mmt) REVERT: K 75 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9532 (mt) REVERT: K 129 GLU cc_start: 0.8275 (tt0) cc_final: 0.7855 (tt0) REVERT: K 132 MET cc_start: 0.8370 (mtt) cc_final: 0.7881 (mtt) REVERT: K 184 TYR cc_start: 0.8822 (m-10) cc_final: 0.8285 (m-10) REVERT: K 194 ASN cc_start: 0.9161 (t0) cc_final: 0.8838 (t0) REVERT: K 207 MET cc_start: 0.8775 (tpp) cc_final: 0.8505 (tpp) REVERT: L 22 LEU cc_start: 0.9684 (mt) cc_final: 0.9446 (tp) REVERT: L 27 GLU cc_start: 0.9233 (pt0) cc_final: 0.8915 (pt0) REVERT: L 33 HIS cc_start: 0.8574 (m170) cc_final: 0.8296 (m-70) REVERT: L 37 LEU cc_start: 0.8671 (tp) cc_final: 0.8401 (tp) REVERT: L 47 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8843 (mm-30) REVERT: N 84 MET cc_start: 0.9142 (mtm) cc_final: 0.8659 (ptm) REVERT: N 96 LEU cc_start: 0.9660 (pp) cc_final: 0.9452 (pp) REVERT: N 102 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8596 (mtm) REVERT: Q 33 MET cc_start: 0.8889 (tmm) cc_final: 0.8311 (tmm) REVERT: Q 66 LEU cc_start: 0.9678 (tp) cc_final: 0.9289 (tt) REVERT: Q 83 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8350 (tmm-80) REVERT: Q 234 MET cc_start: 0.8964 (tmm) cc_final: 0.8725 (tmm) REVERT: R 109 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8927 (pp20) REVERT: R 130 LEU cc_start: 0.9428 (mt) cc_final: 0.9044 (tp) REVERT: R 229 MET cc_start: 0.9081 (mmm) cc_final: 0.8758 (mmm) REVERT: S 33 MET cc_start: 0.8106 (tpt) cc_final: 0.7853 (tpt) REVERT: S 188 MET cc_start: 0.8645 (tpp) cc_final: 0.8405 (ttt) REVERT: S 197 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: b 48 MET cc_start: 0.8346 (ppp) cc_final: 0.8137 (ppp) REVERT: b 100 VAL cc_start: 0.9098 (t) cc_final: 0.8781 (p) REVERT: b 157 ILE cc_start: 0.9088 (mt) cc_final: 0.8850 (mm) REVERT: c 441 LEU cc_start: 0.9376 (mm) cc_final: 0.9122 (mt) REVERT: d 10 ASN cc_start: 0.9187 (m-40) cc_final: 0.8953 (t0) REVERT: d 88 HIS cc_start: 0.8743 (m90) cc_final: 0.7855 (m90) REVERT: d 105 MET cc_start: 0.8955 (mmm) cc_final: 0.8631 (tpp) REVERT: d 138 MET cc_start: 0.8298 (mmp) cc_final: 0.8088 (mmm) REVERT: d 152 ASN cc_start: 0.9388 (m-40) cc_final: 0.9184 (t0) REVERT: d 176 MET cc_start: 0.8523 (tpp) cc_final: 0.8092 (tmm) REVERT: d 325 GLU cc_start: 0.9333 (tt0) cc_final: 0.9023 (tm-30) REVERT: d 329 ILE cc_start: 0.9705 (mt) cc_final: 0.9327 (mm) REVERT: d 334 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8590 (pt0) REVERT: g 119 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7756 (mmp80) REVERT: h 28 MET cc_start: 0.9415 (mtp) cc_final: 0.9093 (tpt) REVERT: h 53 MET cc_start: 0.8382 (pmm) cc_final: 0.8148 (pmm) REVERT: h 61 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6847 (ptp) REVERT: i 13 PHE cc_start: 0.8586 (t80) cc_final: 0.8322 (t80) REVERT: i 25 PHE cc_start: 0.9238 (m-80) cc_final: 0.8809 (m-80) REVERT: i 47 MET cc_start: 0.8354 (ptt) cc_final: 0.7870 (ppp) REVERT: i 61 MET cc_start: 0.5630 (ptp) cc_final: 0.5141 (ptp) REVERT: i 88 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7174 (ttp-170) REVERT: j 53 MET cc_start: 0.7033 (mtm) cc_final: 0.6735 (mtm) REVERT: k 25 PHE cc_start: 0.8781 (m-80) cc_final: 0.8418 (m-80) REVERT: k 47 MET cc_start: 0.7447 (pmm) cc_final: 0.7158 (pmm) REVERT: k 131 MET cc_start: 0.7515 (ppp) cc_final: 0.7269 (ppp) REVERT: l 23 MET cc_start: 0.8491 (tpt) cc_final: 0.8270 (tpt) REVERT: l 47 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5156 (ptm) REVERT: l 131 MET cc_start: 0.5284 (ptt) cc_final: 0.4715 (ptt) REVERT: l 134 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8916 (tp) REVERT: m 55 SER cc_start: 0.8721 (m) cc_final: 0.8474 (p) REVERT: m 141 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6443 (tp) REVERT: n 23 MET cc_start: 0.4379 (tpt) cc_final: 0.3607 (ttt) REVERT: n 68 TYR cc_start: 0.7273 (m-10) cc_final: 0.6998 (m-10) REVERT: n 97 LEU cc_start: 0.9169 (mm) cc_final: 0.8963 (mm) REVERT: n 143 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8941 (mt) REVERT: o 47 MET cc_start: 0.8529 (ppp) cc_final: 0.8226 (ppp) REVERT: o 110 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7702 (mm) REVERT: o 131 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8213 (ppp) REVERT: o 144 TYR cc_start: 0.7053 (m-10) cc_final: 0.6769 (m-10) REVERT: p 311 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8824 (pp) REVERT: p 312 TRP cc_start: 0.8284 (m100) cc_final: 0.7547 (m100) outliers start: 230 outliers final: 158 residues processed: 1027 average time/residue: 0.5259 time to fit residues: 940.1982 Evaluate side-chains 1014 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 831 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 437 LYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 125 ASP Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 445 THR Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 154 ILE Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 119 ARG Chi-restraints excluded: chain g residue 129 VAL Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 61 MET Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 48 ARG Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 143 LEU Chi-restraints excluded: chain j residue 41 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain k residue 53 MET Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 47 MET Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 134 ILE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 148 VAL Chi-restraints excluded: chain n residue 32 TYR Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 311 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 271 optimal weight: 6.9990 chunk 727 optimal weight: 7.9990 chunk 159 optimal weight: 0.3980 chunk 474 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 chunk 808 optimal weight: 40.0000 chunk 671 optimal weight: 20.0000 chunk 374 optimal weight: 50.0000 chunk 67 optimal weight: 0.6980 chunk 267 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 61638 Z= 0.266 Angle : 0.656 11.762 83673 Z= 0.333 Chirality : 0.043 0.478 9871 Planarity : 0.004 0.063 10900 Dihedral : 4.665 119.910 9029 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.48 % Favored : 96.51 % Rotamer: Outliers : 3.27 % Allowed : 16.80 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 8369 helix: 1.54 (0.07), residues: 4975 sheet: -0.12 (0.20), residues: 682 loop : -0.41 (0.12), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP p 329 HIS 0.021 0.001 HIS S 198 PHE 0.045 0.002 PHE g 25 TYR 0.038 0.002 TYR b 8 ARG 0.009 0.000 ARG E 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 903 time to evaluate : 5.520 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: A 164 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8182 (t70) REVERT: A 167 MET cc_start: 0.9075 (mtm) cc_final: 0.8621 (mtt) REVERT: A 254 CYS cc_start: 0.8666 (m) cc_final: 0.8111 (m) REVERT: A 318 MET cc_start: 0.9189 (mtt) cc_final: 0.8660 (mtp) REVERT: A 491 GLU cc_start: 0.9023 (tt0) cc_final: 0.8812 (tm-30) REVERT: A 516 LYS cc_start: 0.9482 (mttt) cc_final: 0.9120 (tttm) REVERT: A 517 ASP cc_start: 0.8974 (m-30) cc_final: 0.8671 (m-30) REVERT: A 518 ASP cc_start: 0.7437 (m-30) cc_final: 0.7045 (m-30) REVERT: A 544 MET cc_start: 0.9076 (mtp) cc_final: 0.8591 (mtp) REVERT: A 574 MET cc_start: 0.8781 (mtt) cc_final: 0.8361 (mmt) REVERT: B 95 MET cc_start: 0.9188 (tpp) cc_final: 0.8853 (tpp) REVERT: B 167 MET cc_start: 0.8596 (mtt) cc_final: 0.8300 (mtt) REVERT: B 306 MET cc_start: 0.8606 (ptm) cc_final: 0.8056 (tmm) REVERT: B 318 MET cc_start: 0.9398 (tpp) cc_final: 0.8240 (mpp) REVERT: B 340 MET cc_start: 0.8923 (ttm) cc_final: 0.8690 (tpp) REVERT: B 356 GLU cc_start: 0.9179 (tp30) cc_final: 0.8840 (tp30) REVERT: B 368 MET cc_start: 0.9100 (mmm) cc_final: 0.8712 (ttm) REVERT: B 432 PHE cc_start: 0.9049 (t80) cc_final: 0.8602 (t80) REVERT: B 458 MET cc_start: 0.8841 (mmt) cc_final: 0.8451 (mmt) REVERT: B 606 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8890 (mt-10) REVERT: C 42 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8937 (mm) REVERT: C 56 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8746 (tpp80) REVERT: C 61 MET cc_start: 0.9121 (mmm) cc_final: 0.8724 (mmp) REVERT: C 458 MET cc_start: 0.8954 (mtp) cc_final: 0.8495 (mtt) REVERT: C 540 MET cc_start: 0.8857 (mmm) cc_final: 0.8441 (mmm) REVERT: C 550 MET cc_start: 0.9540 (mmp) cc_final: 0.9156 (mtp) REVERT: C 584 MET cc_start: 0.8768 (ptm) cc_final: 0.7414 (ptm) REVERT: C 608 MET cc_start: 0.8806 (tmm) cc_final: 0.7818 (tmm) REVERT: D 254 MET cc_start: 0.8798 (tpp) cc_final: 0.8337 (mmm) REVERT: D 270 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8171 (tt0) REVERT: D 309 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8741 (mm-30) REVERT: D 382 GLN cc_start: 0.9369 (mp10) cc_final: 0.9010 (mp10) REVERT: D 402 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8797 (mtp) REVERT: D 410 MET cc_start: 0.8325 (mtm) cc_final: 0.7923 (mtt) REVERT: D 433 GLN cc_start: 0.9452 (tt0) cc_final: 0.8976 (tm-30) REVERT: E 148 GLU cc_start: 0.8487 (tt0) cc_final: 0.7964 (tm-30) REVERT: E 169 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7822 (tmm) REVERT: E 234 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8529 (pmm) REVERT: E 254 MET cc_start: 0.8502 (mmm) cc_final: 0.8157 (mmm) REVERT: E 270 GLU cc_start: 0.9015 (tt0) cc_final: 0.8691 (tm-30) REVERT: E 283 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8477 (mt-10) REVERT: E 305 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8637 (mp0) REVERT: E 309 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8408 (tm-30) REVERT: E 316 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7571 (mt-10) REVERT: E 330 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.8751 (t70) REVERT: E 356 MET cc_start: 0.9110 (mtm) cc_final: 0.8521 (pmm) REVERT: F 153 ILE cc_start: 0.9044 (pt) cc_final: 0.8814 (tt) REVERT: F 169 MET cc_start: 0.8862 (tmm) cc_final: 0.8597 (tmm) REVERT: F 180 MET cc_start: 0.8597 (mmm) cc_final: 0.8132 (mmm) REVERT: F 183 ILE cc_start: 0.9645 (mt) cc_final: 0.9286 (pt) REVERT: F 187 GLN cc_start: 0.9291 (pp30) cc_final: 0.8828 (pp30) REVERT: F 256 ASN cc_start: 0.9023 (m-40) cc_final: 0.8765 (p0) REVERT: F 299 ASP cc_start: 0.8635 (m-30) cc_final: 0.8039 (m-30) REVERT: F 309 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8850 (tm-30) REVERT: F 351 ILE cc_start: 0.9544 (mt) cc_final: 0.9308 (mm) REVERT: F 353 ILE cc_start: 0.9677 (mt) cc_final: 0.9441 (mm) REVERT: F 402 MET cc_start: 0.9414 (tpp) cc_final: 0.9119 (tpp) REVERT: F 410 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7941 (mtp) REVERT: F 435 MET cc_start: 0.9248 (tpp) cc_final: 0.8855 (tpt) REVERT: F 491 MET cc_start: 0.8581 (mtp) cc_final: 0.8294 (ptp) REVERT: H 190 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8741 (tm-30) REVERT: H 193 GLU cc_start: 0.9358 (tm-30) cc_final: 0.8903 (tm-30) REVERT: I 76 MET cc_start: 0.9414 (mpp) cc_final: 0.9162 (mpp) REVERT: I 129 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8349 (tp30) REVERT: I 182 GLU cc_start: 0.7835 (pt0) cc_final: 0.7599 (pt0) REVERT: I 207 MET cc_start: 0.9348 (mmt) cc_final: 0.9015 (mmm) REVERT: J 72 MET cc_start: 0.9126 (ppp) cc_final: 0.8799 (ppp) REVERT: J 182 GLU cc_start: 0.8587 (tt0) cc_final: 0.7778 (tt0) REVERT: J 194 ASN cc_start: 0.8623 (t0) cc_final: 0.7941 (t0) REVERT: J 207 MET cc_start: 0.9377 (mmp) cc_final: 0.9035 (mmm) REVERT: J 208 MET cc_start: 0.9165 (mmm) cc_final: 0.8844 (mmt) REVERT: K 75 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9542 (mt) REVERT: K 129 GLU cc_start: 0.8251 (tt0) cc_final: 0.7831 (tt0) REVERT: K 184 TYR cc_start: 0.8785 (m-10) cc_final: 0.8273 (m-10) REVERT: K 194 ASN cc_start: 0.9133 (t0) cc_final: 0.8833 (t0) REVERT: K 207 MET cc_start: 0.8730 (tpp) cc_final: 0.8460 (tpp) REVERT: L 22 LEU cc_start: 0.9660 (mt) cc_final: 0.9425 (tp) REVERT: L 27 GLU cc_start: 0.9214 (pt0) cc_final: 0.8887 (pt0) REVERT: L 33 HIS cc_start: 0.8709 (m170) cc_final: 0.8444 (m90) REVERT: L 37 LEU cc_start: 0.8687 (tp) cc_final: 0.8458 (tp) REVERT: L 47 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8883 (mm-30) REVERT: M 102 MET cc_start: 0.9504 (mtt) cc_final: 0.9099 (mpp) REVERT: N 74 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9218 (mp0) REVERT: N 84 MET cc_start: 0.9056 (mtm) cc_final: 0.8705 (ptp) REVERT: N 96 LEU cc_start: 0.9646 (pp) cc_final: 0.9434 (pp) REVERT: N 102 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8546 (mtm) REVERT: Q 33 MET cc_start: 0.8861 (tmm) cc_final: 0.8325 (tmm) REVERT: Q 66 LEU cc_start: 0.9687 (tp) cc_final: 0.9282 (tt) REVERT: Q 109 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9091 (mm-30) REVERT: R 130 LEU cc_start: 0.9430 (mt) cc_final: 0.9085 (tp) REVERT: R 139 TYR cc_start: 0.9031 (t80) cc_final: 0.8804 (t80) REVERT: R 229 MET cc_start: 0.9078 (mmm) cc_final: 0.8765 (mmm) REVERT: S 33 MET cc_start: 0.8082 (tpt) cc_final: 0.7852 (tpt) REVERT: S 152 LEU cc_start: 0.9023 (mt) cc_final: 0.8807 (mt) REVERT: S 188 MET cc_start: 0.8642 (tpp) cc_final: 0.8420 (ttt) REVERT: S 197 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: b 19 MET cc_start: 0.7697 (tmm) cc_final: 0.7452 (ppp) REVERT: b 122 ASP cc_start: 0.7784 (t70) cc_final: 0.7581 (t70) REVERT: b 157 ILE cc_start: 0.9140 (mt) cc_final: 0.8900 (mm) REVERT: c 441 LEU cc_start: 0.9326 (mm) cc_final: 0.9076 (mt) REVERT: d 10 ASN cc_start: 0.9176 (m-40) cc_final: 0.8945 (t0) REVERT: d 105 MET cc_start: 0.8935 (mmm) cc_final: 0.8684 (mmt) REVERT: d 138 MET cc_start: 0.8254 (mmp) cc_final: 0.7900 (mmm) REVERT: d 325 GLU cc_start: 0.9318 (tt0) cc_final: 0.8927 (tm-30) REVERT: d 329 ILE cc_start: 0.9690 (mt) cc_final: 0.9300 (mm) REVERT: d 334 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8570 (pt0) REVERT: g 108 PHE cc_start: 0.9199 (m-10) cc_final: 0.8726 (m-10) REVERT: h 23 MET cc_start: 0.7388 (tpt) cc_final: 0.7186 (tpt) REVERT: h 28 MET cc_start: 0.9387 (mtp) cc_final: 0.9129 (tpt) REVERT: h 53 MET cc_start: 0.8454 (pmm) cc_final: 0.8216 (pmm) REVERT: i 13 PHE cc_start: 0.8664 (t80) cc_final: 0.8301 (t80) REVERT: i 44 MET cc_start: 0.6845 (mmm) cc_final: 0.5359 (tpp) REVERT: i 61 MET cc_start: 0.5643 (ptp) cc_final: 0.5109 (ptp) REVERT: i 88 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7174 (ttp-170) REVERT: j 55 SER cc_start: 0.8416 (t) cc_final: 0.8129 (p) REVERT: j 141 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8309 (tp) REVERT: k 25 PHE cc_start: 0.8774 (m-80) cc_final: 0.8357 (m-80) REVERT: k 47 MET cc_start: 0.7546 (pmm) cc_final: 0.7284 (pmm) REVERT: l 13 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: l 23 MET cc_start: 0.8353 (tpt) cc_final: 0.8131 (tpt) REVERT: l 131 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.5021 (ptt) REVERT: m 141 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6671 (tp) REVERT: n 44 MET cc_start: 0.5986 (tpt) cc_final: 0.4722 (tpt) REVERT: n 47 MET cc_start: 0.8191 (tmm) cc_final: 0.7791 (pmm) REVERT: n 68 TYR cc_start: 0.7221 (m-10) cc_final: 0.6950 (m-10) REVERT: n 143 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8907 (mt) REVERT: o 47 MET cc_start: 0.8659 (ppp) cc_final: 0.8405 (ppp) REVERT: o 131 MET cc_start: 0.8697 (ppp) cc_final: 0.8229 (ppp) REVERT: p 312 TRP cc_start: 0.8236 (m100) cc_final: 0.7396 (m100) REVERT: p 338 ILE cc_start: 0.7942 (pt) cc_final: 0.7359 (pp) outliers start: 185 outliers final: 122 residues processed: 1008 average time/residue: 0.5266 time to fit residues: 923.2891 Evaluate side-chains 989 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 851 time to evaluate : 5.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain c residue 432 ILE Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 48 ARG Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 143 LEU Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 53 MET Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 32 TYR Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 137 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 779 optimal weight: 40.0000 chunk 91 optimal weight: 8.9990 chunk 460 optimal weight: 30.0000 chunk 590 optimal weight: 50.0000 chunk 457 optimal weight: 6.9990 chunk 680 optimal weight: 0.4980 chunk 451 optimal weight: 10.0000 chunk 805 optimal weight: 30.0000 chunk 504 optimal weight: 10.0000 chunk 491 optimal weight: 0.9990 chunk 372 optimal weight: 30.0000 overall best weight: 5.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 HIS S 177 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 GLN ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 61638 Z= 0.359 Angle : 0.708 13.354 83673 Z= 0.360 Chirality : 0.044 0.453 9871 Planarity : 0.005 0.054 10900 Dihedral : 4.716 119.685 9029 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer: Outliers : 3.47 % Allowed : 17.15 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.93 (0.09), residues: 8369 helix: 1.40 (0.07), residues: 4991 sheet: -0.14 (0.20), residues: 670 loop : -0.59 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 567 HIS 0.022 0.001 HIS S 198 PHE 0.045 0.002 PHE m 25 TYR 0.037 0.002 TYR b 70 ARG 0.010 0.001 ARG g 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 856 time to evaluate : 5.590 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: A 95 MET cc_start: 0.8388 (tpp) cc_final: 0.8090 (tpp) REVERT: A 164 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8157 (t70) REVERT: A 167 MET cc_start: 0.9046 (mtm) cc_final: 0.8407 (mtt) REVERT: A 254 CYS cc_start: 0.8533 (m) cc_final: 0.7985 (m) REVERT: A 318 MET cc_start: 0.9186 (mtt) cc_final: 0.8667 (mtp) REVERT: A 491 GLU cc_start: 0.8988 (tt0) cc_final: 0.8678 (tm-30) REVERT: A 516 LYS cc_start: 0.9493 (mttt) cc_final: 0.9143 (tmtt) REVERT: A 574 MET cc_start: 0.8812 (mtt) cc_final: 0.8521 (mmt) REVERT: B 167 MET cc_start: 0.8648 (mtt) cc_final: 0.8348 (mtt) REVERT: B 306 MET cc_start: 0.8610 (ptm) cc_final: 0.8125 (tmm) REVERT: B 318 MET cc_start: 0.9404 (tpp) cc_final: 0.8276 (mpp) REVERT: B 368 MET cc_start: 0.9087 (mmm) cc_final: 0.8699 (ttm) REVERT: B 432 PHE cc_start: 0.9089 (t80) cc_final: 0.8648 (t80) REVERT: B 458 MET cc_start: 0.8874 (mmt) cc_final: 0.8483 (mmt) REVERT: B 606 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8894 (mt-10) REVERT: C 39 MET cc_start: 0.8738 (tmm) cc_final: 0.7807 (tmm) REVERT: C 42 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 56 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8735 (tpp80) REVERT: C 61 MET cc_start: 0.9130 (mmm) cc_final: 0.8731 (mmp) REVERT: C 458 MET cc_start: 0.8995 (mtp) cc_final: 0.8508 (mtt) REVERT: C 540 MET cc_start: 0.8864 (mmm) cc_final: 0.8113 (mmm) REVERT: C 550 MET cc_start: 0.9552 (mmp) cc_final: 0.9151 (mtp) REVERT: C 584 MET cc_start: 0.8856 (ptm) cc_final: 0.8451 (ptm) REVERT: C 608 MET cc_start: 0.8769 (tmm) cc_final: 0.7702 (tmm) REVERT: D 254 MET cc_start: 0.8855 (tpp) cc_final: 0.8395 (mmm) REVERT: D 270 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: D 382 GLN cc_start: 0.9378 (mp10) cc_final: 0.9054 (mp10) REVERT: D 402 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8860 (mtp) REVERT: D 433 GLN cc_start: 0.9447 (tt0) cc_final: 0.9013 (tm-30) REVERT: E 169 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8468 (ttt) REVERT: E 180 MET cc_start: 0.9038 (mtp) cc_final: 0.8781 (ptp) REVERT: E 234 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8867 (pmm) REVERT: E 270 GLU cc_start: 0.9024 (tt0) cc_final: 0.8808 (tm-30) REVERT: E 309 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8443 (tm-30) REVERT: E 316 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7616 (mt-10) REVERT: E 330 ASP cc_start: 0.9356 (OUTLIER) cc_final: 0.8835 (t70) REVERT: E 356 MET cc_start: 0.9104 (mtm) cc_final: 0.8632 (pmm) REVERT: E 432 VAL cc_start: 0.9633 (t) cc_final: 0.9416 (p) REVERT: E 447 ASP cc_start: 0.9509 (OUTLIER) cc_final: 0.9114 (p0) REVERT: F 153 ILE cc_start: 0.9056 (pt) cc_final: 0.8849 (tt) REVERT: F 169 MET cc_start: 0.8887 (tmm) cc_final: 0.8624 (tmm) REVERT: F 180 MET cc_start: 0.8714 (mmm) cc_final: 0.8313 (mmm) REVERT: F 183 ILE cc_start: 0.9618 (mt) cc_final: 0.9231 (pt) REVERT: F 187 GLN cc_start: 0.9352 (pp30) cc_final: 0.8897 (pp30) REVERT: F 299 ASP cc_start: 0.8632 (m-30) cc_final: 0.7925 (m-30) REVERT: F 309 GLU cc_start: 0.9233 (tm-30) cc_final: 0.9024 (tm-30) REVERT: F 351 ILE cc_start: 0.9539 (mt) cc_final: 0.9307 (mm) REVERT: F 353 ILE cc_start: 0.9671 (mt) cc_final: 0.9444 (mm) REVERT: F 356 MET cc_start: 0.8753 (mtm) cc_final: 0.8186 (mtm) REVERT: F 410 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: F 435 MET cc_start: 0.9259 (tpp) cc_final: 0.8872 (tpt) REVERT: F 491 MET cc_start: 0.8519 (mtp) cc_final: 0.8271 (ptp) REVERT: H 190 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9031 (mm-30) REVERT: H 193 GLU cc_start: 0.9391 (tm-30) cc_final: 0.8959 (tm-30) REVERT: I 76 MET cc_start: 0.9456 (mpp) cc_final: 0.9188 (mpp) REVERT: I 129 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8320 (tp30) REVERT: I 182 GLU cc_start: 0.7831 (pt0) cc_final: 0.7552 (pt0) REVERT: I 196 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9637 (mm) REVERT: I 207 MET cc_start: 0.9355 (mmt) cc_final: 0.9061 (mmm) REVERT: J 72 MET cc_start: 0.9237 (ppp) cc_final: 0.8826 (ppp) REVERT: J 182 GLU cc_start: 0.8552 (tt0) cc_final: 0.7731 (tt0) REVERT: J 194 ASN cc_start: 0.8665 (t0) cc_final: 0.7983 (t0) REVERT: J 207 MET cc_start: 0.9415 (mmp) cc_final: 0.8939 (mmm) REVERT: J 208 MET cc_start: 0.9165 (mmm) cc_final: 0.8771 (mmt) REVERT: K 75 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9543 (mt) REVERT: K 129 GLU cc_start: 0.8247 (tt0) cc_final: 0.7589 (tt0) REVERT: K 184 TYR cc_start: 0.8840 (m-10) cc_final: 0.8371 (m-10) REVERT: K 194 ASN cc_start: 0.9138 (t0) cc_final: 0.8827 (t0) REVERT: K 207 MET cc_start: 0.8762 (tpp) cc_final: 0.8482 (tpp) REVERT: L 22 LEU cc_start: 0.9685 (mt) cc_final: 0.9463 (tp) REVERT: L 27 GLU cc_start: 0.9230 (pt0) cc_final: 0.8881 (pt0) REVERT: L 33 HIS cc_start: 0.8707 (m170) cc_final: 0.8429 (m-70) REVERT: L 47 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8932 (mm-30) REVERT: M 99 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9432 (tt) REVERT: M 102 MET cc_start: 0.9514 (mtt) cc_final: 0.9102 (mpp) REVERT: N 84 MET cc_start: 0.9113 (mtm) cc_final: 0.8689 (ptp) REVERT: N 96 LEU cc_start: 0.9645 (pp) cc_final: 0.9427 (pp) REVERT: N 102 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8583 (mtm) REVERT: Q 33 MET cc_start: 0.8831 (tmm) cc_final: 0.8311 (tmm) REVERT: Q 66 LEU cc_start: 0.9689 (tp) cc_final: 0.9267 (tt) REVERT: Q 109 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9107 (mm-30) REVERT: R 139 TYR cc_start: 0.9079 (t80) cc_final: 0.8746 (t80) REVERT: R 229 MET cc_start: 0.9116 (mmm) cc_final: 0.8815 (mmm) REVERT: S 188 MET cc_start: 0.8663 (tpp) cc_final: 0.8443 (ttt) REVERT: S 197 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: b 19 MET cc_start: 0.7764 (tmm) cc_final: 0.7541 (ppp) REVERT: b 70 TYR cc_start: 0.7561 (p90) cc_final: 0.7332 (p90) REVERT: b 122 ASP cc_start: 0.7840 (t70) cc_final: 0.7630 (t70) REVERT: b 157 ILE cc_start: 0.9150 (mt) cc_final: 0.8926 (mm) REVERT: c 421 MET cc_start: 0.8959 (mtp) cc_final: 0.8486 (mmm) REVERT: c 441 LEU cc_start: 0.9312 (mm) cc_final: 0.9046 (mt) REVERT: c 449 PHE cc_start: 0.6670 (m-10) cc_final: 0.5999 (m-10) REVERT: d 10 ASN cc_start: 0.9230 (m-40) cc_final: 0.9018 (t0) REVERT: d 105 MET cc_start: 0.8941 (mmm) cc_final: 0.8635 (tpp) REVERT: d 138 MET cc_start: 0.8278 (mmp) cc_final: 0.8009 (mmm) REVERT: d 176 MET cc_start: 0.8491 (tpp) cc_final: 0.8043 (tmm) REVERT: d 325 GLU cc_start: 0.9384 (tt0) cc_final: 0.8982 (tm-30) REVERT: d 329 ILE cc_start: 0.9695 (mt) cc_final: 0.9319 (mm) REVERT: d 334 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8622 (pt0) REVERT: g 131 MET cc_start: 0.8263 (tmm) cc_final: 0.8009 (ppp) REVERT: h 28 MET cc_start: 0.9359 (mtp) cc_final: 0.9134 (tpt) REVERT: h 144 TYR cc_start: 0.8153 (m-10) cc_final: 0.7856 (m-10) REVERT: h 146 LEU cc_start: 0.8238 (mt) cc_final: 0.7971 (mt) REVERT: i 61 MET cc_start: 0.5564 (ptp) cc_final: 0.5014 (ptp) REVERT: i 88 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7047 (ttp-170) REVERT: i 123 GLN cc_start: 0.8516 (pm20) cc_final: 0.8071 (mm-40) REVERT: j 55 SER cc_start: 0.8539 (t) cc_final: 0.8253 (p) REVERT: j 141 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8289 (tp) REVERT: k 25 PHE cc_start: 0.8685 (m-80) cc_final: 0.8296 (m-80) REVERT: k 47 MET cc_start: 0.7681 (pmm) cc_final: 0.7375 (pmm) REVERT: k 78 ASN cc_start: 0.8329 (m-40) cc_final: 0.7725 (t0) REVERT: k 131 MET cc_start: 0.7722 (ppp) cc_final: 0.6386 (tpp) REVERT: l 13 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: l 23 MET cc_start: 0.8341 (tpt) cc_final: 0.8055 (tpt) REVERT: l 131 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5480 (ptt) REVERT: l 134 ILE cc_start: 0.8989 (mp) cc_final: 0.8711 (tp) REVERT: m 141 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6298 (tp) REVERT: n 44 MET cc_start: 0.5970 (tpt) cc_final: 0.5666 (tpt) REVERT: n 68 TYR cc_start: 0.7249 (m-10) cc_final: 0.6961 (m-10) REVERT: n 143 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8972 (mm) REVERT: o 110 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7611 (mm) REVERT: o 131 MET cc_start: 0.8739 (ppp) cc_final: 0.8247 (ppp) REVERT: p 338 ILE cc_start: 0.7940 (pt) cc_final: 0.7738 (pp) outliers start: 196 outliers final: 149 residues processed: 970 average time/residue: 0.5259 time to fit residues: 888.6547 Evaluate side-chains 992 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 822 time to evaluate : 5.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 437 LYS Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 125 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 315 PHE Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 143 LEU Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 53 MET Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 144 TYR Chi-restraints excluded: chain n residue 25 PHE Chi-restraints excluded: chain n residue 32 TYR Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 137 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 498 optimal weight: 0.0980 chunk 321 optimal weight: 9.9990 chunk 481 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 512 optimal weight: 9.9990 chunk 548 optimal weight: 50.0000 chunk 398 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 633 optimal weight: 0.3980 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 61638 Z= 0.315 Angle : 0.703 16.926 83673 Z= 0.354 Chirality : 0.044 0.337 9871 Planarity : 0.004 0.048 10900 Dihedral : 4.722 120.088 9029 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 3.27 % Allowed : 18.04 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.89 (0.09), residues: 8369 helix: 1.40 (0.07), residues: 4998 sheet: -0.24 (0.20), residues: 658 loop : -0.63 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 567 HIS 0.010 0.001 HIS S 198 PHE 0.049 0.002 PHE m 25 TYR 0.037 0.002 TYR b 70 ARG 0.007 0.000 ARG Q 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 857 time to evaluate : 5.472 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: A 95 MET cc_start: 0.8365 (tpp) cc_final: 0.8072 (tpp) REVERT: A 164 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8177 (t70) REVERT: A 193 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7373 (mt-10) REVERT: A 254 CYS cc_start: 0.8559 (m) cc_final: 0.7988 (m) REVERT: A 318 MET cc_start: 0.9169 (mtt) cc_final: 0.8645 (mtp) REVERT: A 491 GLU cc_start: 0.8953 (tt0) cc_final: 0.8610 (tm-30) REVERT: A 516 LYS cc_start: 0.9367 (mttt) cc_final: 0.9059 (tmtt) REVERT: A 540 MET cc_start: 0.8983 (ppp) cc_final: 0.8469 (ppp) REVERT: A 544 MET cc_start: 0.9004 (mtp) cc_final: 0.8499 (mtp) REVERT: A 574 MET cc_start: 0.8807 (mtt) cc_final: 0.8508 (mmt) REVERT: B 167 MET cc_start: 0.8675 (mtt) cc_final: 0.8365 (mtt) REVERT: B 306 MET cc_start: 0.8579 (ptm) cc_final: 0.8117 (tmm) REVERT: B 318 MET cc_start: 0.9407 (tpp) cc_final: 0.8286 (mpp) REVERT: B 340 MET cc_start: 0.8922 (ttm) cc_final: 0.8717 (tpp) REVERT: B 368 MET cc_start: 0.9049 (mmm) cc_final: 0.8806 (ttm) REVERT: B 458 MET cc_start: 0.8847 (mmt) cc_final: 0.8452 (mmt) REVERT: B 606 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8885 (mt-10) REVERT: C 42 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8963 (mm) REVERT: C 56 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8747 (tpp80) REVERT: C 61 MET cc_start: 0.9168 (mmm) cc_final: 0.8647 (mmp) REVERT: C 458 MET cc_start: 0.9000 (mtp) cc_final: 0.8536 (mtt) REVERT: C 540 MET cc_start: 0.8833 (mmm) cc_final: 0.8064 (mmm) REVERT: C 550 MET cc_start: 0.9549 (mmp) cc_final: 0.9226 (mtt) REVERT: C 584 MET cc_start: 0.8852 (ptm) cc_final: 0.8472 (ptm) REVERT: C 608 MET cc_start: 0.8756 (tmm) cc_final: 0.8012 (tmm) REVERT: D 169 MET cc_start: 0.8744 (tmm) cc_final: 0.8468 (tmm) REVERT: D 254 MET cc_start: 0.8860 (tpp) cc_final: 0.8395 (mmm) REVERT: D 270 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8349 (tt0) REVERT: D 382 GLN cc_start: 0.9366 (mp10) cc_final: 0.9083 (mp10) REVERT: D 402 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8712 (mtp) REVERT: D 410 MET cc_start: 0.8446 (mtm) cc_final: 0.8126 (mtp) REVERT: D 433 GLN cc_start: 0.9422 (tt0) cc_final: 0.9038 (tm-30) REVERT: E 169 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: E 234 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8868 (pmm) REVERT: E 254 MET cc_start: 0.8613 (mmm) cc_final: 0.8389 (mmm) REVERT: E 270 GLU cc_start: 0.9041 (tt0) cc_final: 0.8755 (tt0) REVERT: E 305 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8842 (mt-10) REVERT: E 309 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8506 (tm-30) REVERT: E 316 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 330 ASP cc_start: 0.9326 (OUTLIER) cc_final: 0.8789 (t70) REVERT: E 356 MET cc_start: 0.9058 (mtm) cc_final: 0.8681 (pmm) REVERT: E 432 VAL cc_start: 0.9669 (t) cc_final: 0.9464 (p) REVERT: E 447 ASP cc_start: 0.9516 (OUTLIER) cc_final: 0.9213 (p0) REVERT: F 121 THR cc_start: 0.9698 (OUTLIER) cc_final: 0.9432 (t) REVERT: F 169 MET cc_start: 0.8905 (tmm) cc_final: 0.8627 (tmm) REVERT: F 171 GLN cc_start: 0.8872 (pt0) cc_final: 0.8271 (pt0) REVERT: F 180 MET cc_start: 0.8745 (mmm) cc_final: 0.8469 (mmm) REVERT: F 183 ILE cc_start: 0.9595 (mt) cc_final: 0.9243 (pt) REVERT: F 187 GLN cc_start: 0.9318 (pp30) cc_final: 0.8894 (pp30) REVERT: F 298 THR cc_start: 0.9204 (m) cc_final: 0.8887 (p) REVERT: F 299 ASP cc_start: 0.8604 (m-30) cc_final: 0.8182 (m-30) REVERT: F 309 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8871 (tm-30) REVERT: F 353 ILE cc_start: 0.9659 (mt) cc_final: 0.9407 (mm) REVERT: F 356 MET cc_start: 0.8748 (mtm) cc_final: 0.8234 (mtm) REVERT: F 410 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8033 (mtp) REVERT: F 435 MET cc_start: 0.9254 (tpp) cc_final: 0.8851 (tpt) REVERT: F 491 MET cc_start: 0.8513 (mtp) cc_final: 0.8273 (ptp) REVERT: H 190 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9027 (mm-30) REVERT: H 193 GLU cc_start: 0.9393 (tm-30) cc_final: 0.8957 (tm-30) REVERT: I 76 MET cc_start: 0.9467 (mpp) cc_final: 0.9192 (mpp) REVERT: I 129 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8345 (tp30) REVERT: I 182 GLU cc_start: 0.7831 (pt0) cc_final: 0.7545 (pt0) REVERT: I 207 MET cc_start: 0.9371 (mmt) cc_final: 0.9057 (mmm) REVERT: J 72 MET cc_start: 0.9204 (ppp) cc_final: 0.8804 (ppp) REVERT: J 182 GLU cc_start: 0.8566 (tt0) cc_final: 0.7779 (tt0) REVERT: J 194 ASN cc_start: 0.8653 (t0) cc_final: 0.7987 (t0) REVERT: J 207 MET cc_start: 0.9414 (mmp) cc_final: 0.8930 (mmm) REVERT: J 208 MET cc_start: 0.9188 (mmm) cc_final: 0.8799 (mmt) REVERT: K 75 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9546 (mt) REVERT: K 129 GLU cc_start: 0.8228 (tt0) cc_final: 0.7527 (tt0) REVERT: K 132 MET cc_start: 0.8664 (mmt) cc_final: 0.8074 (mmm) REVERT: K 194 ASN cc_start: 0.9134 (t0) cc_final: 0.8818 (t0) REVERT: K 207 MET cc_start: 0.8713 (tpp) cc_final: 0.8419 (tpp) REVERT: L 22 LEU cc_start: 0.9689 (mt) cc_final: 0.9445 (tp) REVERT: L 27 GLU cc_start: 0.9201 (pt0) cc_final: 0.8857 (pt0) REVERT: L 33 HIS cc_start: 0.8776 (m170) cc_final: 0.8486 (m-70) REVERT: L 47 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8976 (mm-30) REVERT: M 99 LEU cc_start: 0.9701 (tt) cc_final: 0.9408 (tt) REVERT: M 102 MET cc_start: 0.9487 (mtt) cc_final: 0.9088 (mpp) REVERT: N 84 MET cc_start: 0.9091 (mtm) cc_final: 0.8753 (ptp) REVERT: N 96 LEU cc_start: 0.9628 (pp) cc_final: 0.9415 (pp) REVERT: N 102 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8555 (mtm) REVERT: Q 33 MET cc_start: 0.8813 (tmm) cc_final: 0.8317 (tmm) REVERT: Q 66 LEU cc_start: 0.9693 (tp) cc_final: 0.9260 (tt) REVERT: Q 109 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9067 (mm-30) REVERT: R 79 ASP cc_start: 0.9619 (OUTLIER) cc_final: 0.9298 (m-30) REVERT: R 139 TYR cc_start: 0.9034 (t80) cc_final: 0.8724 (t80) REVERT: R 229 MET cc_start: 0.9116 (mmm) cc_final: 0.8821 (mmm) REVERT: S 188 MET cc_start: 0.8720 (tpp) cc_final: 0.8504 (ttt) REVERT: S 197 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: b 19 MET cc_start: 0.7777 (tmm) cc_final: 0.7547 (ppp) REVERT: b 70 TYR cc_start: 0.7662 (p90) cc_final: 0.7453 (p90) REVERT: b 100 VAL cc_start: 0.9086 (t) cc_final: 0.8725 (p) REVERT: b 157 ILE cc_start: 0.9167 (mt) cc_final: 0.8959 (mm) REVERT: c 421 MET cc_start: 0.8981 (mtp) cc_final: 0.8528 (mmm) REVERT: c 441 LEU cc_start: 0.9259 (mm) cc_final: 0.8949 (mt) REVERT: c 444 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7374 (tttm) REVERT: d 105 MET cc_start: 0.8934 (mmm) cc_final: 0.8634 (tpp) REVERT: d 138 MET cc_start: 0.8337 (mmp) cc_final: 0.8122 (mmm) REVERT: d 176 MET cc_start: 0.8455 (tpp) cc_final: 0.8057 (tmm) REVERT: d 307 LEU cc_start: 0.9083 (mp) cc_final: 0.8660 (tt) REVERT: d 325 GLU cc_start: 0.9365 (tt0) cc_final: 0.8867 (tm-30) REVERT: d 329 ILE cc_start: 0.9694 (mt) cc_final: 0.9291 (mm) REVERT: d 334 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8625 (pt0) REVERT: h 28 MET cc_start: 0.9330 (mtp) cc_final: 0.9078 (tpt) REVERT: h 146 LEU cc_start: 0.8410 (mt) cc_final: 0.8188 (mt) REVERT: i 61 MET cc_start: 0.5629 (ptp) cc_final: 0.4826 (ptp) REVERT: i 88 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7255 (ttp-170) REVERT: j 141 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8229 (tp) REVERT: k 25 PHE cc_start: 0.8664 (m-80) cc_final: 0.8285 (m-80) REVERT: k 47 MET cc_start: 0.7592 (pmm) cc_final: 0.7234 (pmm) REVERT: k 78 ASN cc_start: 0.8311 (m-40) cc_final: 0.7726 (t0) REVERT: l 13 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: l 23 MET cc_start: 0.8325 (tpt) cc_final: 0.8005 (tpt) REVERT: l 131 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5810 (ptt) REVERT: l 134 ILE cc_start: 0.9027 (mp) cc_final: 0.8778 (tp) REVERT: m 141 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6368 (tp) REVERT: n 23 MET cc_start: 0.4066 (tpt) cc_final: 0.3565 (ttt) REVERT: n 44 MET cc_start: 0.6188 (tpt) cc_final: 0.5072 (tpt) REVERT: n 47 MET cc_start: 0.8231 (ppp) cc_final: 0.7727 (pmm) REVERT: n 68 TYR cc_start: 0.7253 (m-10) cc_final: 0.6700 (m-10) REVERT: o 131 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8178 (ppp) REVERT: o 144 TYR cc_start: 0.6916 (m-10) cc_final: 0.6511 (m-80) REVERT: p 308 ASN cc_start: 0.9226 (p0) cc_final: 0.8996 (p0) outliers start: 185 outliers final: 144 residues processed: 970 average time/residue: 0.5697 time to fit residues: 963.9945 Evaluate side-chains 980 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 817 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 437 LYS Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 432 ILE Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 131 MET Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 53 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 44 MET Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 32 TYR Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain p residue 342 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 732 optimal weight: 7.9990 chunk 771 optimal weight: 8.9990 chunk 704 optimal weight: 30.0000 chunk 750 optimal weight: 8.9990 chunk 451 optimal weight: 40.0000 chunk 327 optimal weight: 20.0000 chunk 589 optimal weight: 9.9990 chunk 230 optimal weight: 0.6980 chunk 678 optimal weight: 20.0000 chunk 710 optimal weight: 10.0000 chunk 748 optimal weight: 0.7980 overall best weight: 5.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 61638 Z= 0.361 Angle : 0.745 14.882 83673 Z= 0.376 Chirality : 0.045 0.375 9871 Planarity : 0.005 0.049 10900 Dihedral : 4.805 120.704 9027 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.35 % Favored : 95.64 % Rotamer: Outliers : 3.45 % Allowed : 18.48 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.74 (0.09), residues: 8369 helix: 1.28 (0.07), residues: 5012 sheet: -0.30 (0.20), residues: 667 loop : -0.71 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP b 49 HIS 0.006 0.001 HIS E 384 PHE 0.051 0.002 PHE m 25 TYR 0.037 0.002 TYR b 8 ARG 0.005 0.001 ARG g 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 824 time to evaluate : 5.586 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: A 95 MET cc_start: 0.8378 (tpp) cc_final: 0.8093 (tpp) REVERT: A 164 HIS cc_start: 0.9103 (OUTLIER) cc_final: 0.8265 (t70) REVERT: A 193 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 254 CYS cc_start: 0.8426 (m) cc_final: 0.7842 (m) REVERT: A 318 MET cc_start: 0.9162 (mtt) cc_final: 0.8647 (mtp) REVERT: A 491 GLU cc_start: 0.8933 (tt0) cc_final: 0.8619 (tm-30) REVERT: A 516 LYS cc_start: 0.9342 (mttt) cc_final: 0.9086 (tmtt) REVERT: A 540 MET cc_start: 0.8979 (ppp) cc_final: 0.8427 (ppp) REVERT: A 544 MET cc_start: 0.9021 (mtp) cc_final: 0.8505 (mtp) REVERT: A 574 MET cc_start: 0.8819 (mtt) cc_final: 0.8536 (mmt) REVERT: B 90 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9319 (tp) REVERT: B 167 MET cc_start: 0.8707 (mtt) cc_final: 0.8469 (mtt) REVERT: B 306 MET cc_start: 0.8586 (ptm) cc_final: 0.8129 (tmm) REVERT: B 318 MET cc_start: 0.9418 (tpp) cc_final: 0.8327 (mpp) REVERT: B 340 MET cc_start: 0.8984 (ttm) cc_final: 0.8714 (tpp) REVERT: B 347 MET cc_start: 0.8836 (tpp) cc_final: 0.8603 (tpt) REVERT: B 368 MET cc_start: 0.9031 (mmm) cc_final: 0.8806 (ttm) REVERT: B 458 MET cc_start: 0.8887 (mmt) cc_final: 0.8485 (mmt) REVERT: B 492 ILE cc_start: 0.9574 (mm) cc_final: 0.9336 (mm) REVERT: B 606 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8857 (mt-10) REVERT: C 39 MET cc_start: 0.8770 (tmm) cc_final: 0.7865 (tmm) REVERT: C 42 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8988 (mm) REVERT: C 56 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8745 (tpp80) REVERT: C 61 MET cc_start: 0.9170 (mmm) cc_final: 0.8649 (mmp) REVERT: C 234 LEU cc_start: 0.8978 (mp) cc_final: 0.8660 (tt) REVERT: C 340 MET cc_start: 0.9084 (tpp) cc_final: 0.8864 (tpp) REVERT: C 458 MET cc_start: 0.9017 (mtp) cc_final: 0.8549 (mtt) REVERT: C 540 MET cc_start: 0.8843 (mmm) cc_final: 0.8075 (mmm) REVERT: C 541 LEU cc_start: 0.9687 (tp) cc_final: 0.9485 (tp) REVERT: C 550 MET cc_start: 0.9547 (mmp) cc_final: 0.9213 (mtt) REVERT: C 584 MET cc_start: 0.8868 (ptm) cc_final: 0.8485 (ptm) REVERT: C 608 MET cc_start: 0.8764 (tmm) cc_final: 0.8035 (tmm) REVERT: D 169 MET cc_start: 0.8775 (tmm) cc_final: 0.8501 (tmm) REVERT: D 254 MET cc_start: 0.8898 (tpp) cc_final: 0.8439 (mmm) REVERT: D 270 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8340 (tt0) REVERT: D 382 GLN cc_start: 0.9381 (mp10) cc_final: 0.9097 (mp10) REVERT: D 402 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8721 (mtp) REVERT: D 433 GLN cc_start: 0.9406 (tt0) cc_final: 0.9056 (tm-30) REVERT: E 234 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8896 (pmm) REVERT: E 305 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8848 (mt-10) REVERT: E 309 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8517 (tm-30) REVERT: E 316 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7675 (mt-10) REVERT: E 330 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.8792 (t70) REVERT: E 356 MET cc_start: 0.9060 (mtm) cc_final: 0.8668 (pmm) REVERT: E 447 ASP cc_start: 0.9512 (OUTLIER) cc_final: 0.9219 (p0) REVERT: F 169 MET cc_start: 0.8906 (tmm) cc_final: 0.8633 (tmm) REVERT: F 171 GLN cc_start: 0.8903 (pt0) cc_final: 0.8286 (pt0) REVERT: F 180 MET cc_start: 0.8922 (mmm) cc_final: 0.8690 (mmm) REVERT: F 183 ILE cc_start: 0.9639 (mt) cc_final: 0.9281 (pt) REVERT: F 187 GLN cc_start: 0.9341 (pp30) cc_final: 0.8914 (pp30) REVERT: F 298 THR cc_start: 0.9205 (m) cc_final: 0.8917 (p) REVERT: F 299 ASP cc_start: 0.8543 (m-30) cc_final: 0.8147 (m-30) REVERT: F 300 MET cc_start: 0.9397 (mmm) cc_final: 0.8893 (mtm) REVERT: F 309 GLU cc_start: 0.9233 (tm-30) cc_final: 0.9025 (tm-30) REVERT: F 353 ILE cc_start: 0.9654 (mt) cc_final: 0.9419 (mm) REVERT: F 356 MET cc_start: 0.8791 (mtm) cc_final: 0.8309 (mtm) REVERT: F 410 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8088 (mtp) REVERT: F 435 MET cc_start: 0.9259 (tpp) cc_final: 0.8869 (tpt) REVERT: H 190 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9044 (mm-30) REVERT: H 193 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9009 (tm-30) REVERT: I 76 MET cc_start: 0.9477 (mpp) cc_final: 0.9235 (mpp) REVERT: I 121 LEU cc_start: 0.9556 (tt) cc_final: 0.9235 (tp) REVERT: I 129 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8281 (tp30) REVERT: I 182 GLU cc_start: 0.7803 (pt0) cc_final: 0.7517 (pt0) REVERT: I 196 LEU cc_start: 0.9841 (OUTLIER) cc_final: 0.9630 (mm) REVERT: I 207 MET cc_start: 0.9405 (mmt) cc_final: 0.9085 (mmm) REVERT: J 72 MET cc_start: 0.9203 (ppp) cc_final: 0.8823 (ppp) REVERT: J 182 GLU cc_start: 0.8555 (tt0) cc_final: 0.7714 (tt0) REVERT: J 194 ASN cc_start: 0.8635 (t0) cc_final: 0.8052 (t0) REVERT: J 207 MET cc_start: 0.9434 (mmp) cc_final: 0.8941 (mmm) REVERT: J 208 MET cc_start: 0.9184 (mmm) cc_final: 0.8792 (mmt) REVERT: K 129 GLU cc_start: 0.8210 (tt0) cc_final: 0.7716 (tt0) REVERT: K 194 ASN cc_start: 0.9169 (t0) cc_final: 0.8904 (t0) REVERT: K 207 MET cc_start: 0.8745 (tpp) cc_final: 0.8455 (tpp) REVERT: L 22 LEU cc_start: 0.9698 (mt) cc_final: 0.9466 (tp) REVERT: L 27 GLU cc_start: 0.9214 (pt0) cc_final: 0.8856 (pt0) REVERT: L 47 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8995 (mm-30) REVERT: M 99 LEU cc_start: 0.9713 (tt) cc_final: 0.9442 (tt) REVERT: M 102 MET cc_start: 0.9500 (mtt) cc_final: 0.9117 (mpp) REVERT: N 84 MET cc_start: 0.9104 (mtm) cc_final: 0.8754 (ptp) REVERT: N 102 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8569 (mtm) REVERT: Q 33 MET cc_start: 0.8764 (tmm) cc_final: 0.8254 (tmm) REVERT: Q 66 LEU cc_start: 0.9691 (tp) cc_final: 0.9249 (tt) REVERT: Q 109 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9107 (mm-30) REVERT: R 79 ASP cc_start: 0.9616 (OUTLIER) cc_final: 0.9298 (m-30) REVERT: R 139 TYR cc_start: 0.9063 (t80) cc_final: 0.8753 (t80) REVERT: R 229 MET cc_start: 0.9129 (mmm) cc_final: 0.8852 (mmm) REVERT: S 188 MET cc_start: 0.8750 (tpp) cc_final: 0.8528 (ttt) REVERT: S 197 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: b 70 TYR cc_start: 0.7571 (p90) cc_final: 0.7224 (p90) REVERT: b 100 VAL cc_start: 0.9085 (t) cc_final: 0.8716 (p) REVERT: b 157 ILE cc_start: 0.9188 (mt) cc_final: 0.8966 (mm) REVERT: c 421 MET cc_start: 0.9017 (mtp) cc_final: 0.8564 (mmm) REVERT: c 435 TYR cc_start: 0.9370 (t80) cc_final: 0.9133 (t80) REVERT: c 441 LEU cc_start: 0.9305 (mm) cc_final: 0.8991 (mt) REVERT: c 444 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7414 (tttm) REVERT: d 105 MET cc_start: 0.8948 (mmm) cc_final: 0.8641 (tpp) REVERT: d 138 MET cc_start: 0.8454 (mmp) cc_final: 0.8223 (mmm) REVERT: d 176 MET cc_start: 0.8404 (tpp) cc_final: 0.8049 (tmm) REVERT: d 307 LEU cc_start: 0.9082 (mp) cc_final: 0.8710 (tt) REVERT: d 334 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8635 (pt0) REVERT: h 28 MET cc_start: 0.9341 (mtp) cc_final: 0.9093 (tpt) REVERT: h 146 LEU cc_start: 0.8383 (mt) cc_final: 0.8131 (mt) REVERT: i 23 MET cc_start: 0.6449 (tpt) cc_final: 0.6080 (tpt) REVERT: i 61 MET cc_start: 0.5612 (ptp) cc_final: 0.5107 (ptp) REVERT: i 88 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7241 (ttp-170) REVERT: i 123 GLN cc_start: 0.8484 (pm20) cc_final: 0.7802 (mm-40) REVERT: j 55 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8276 (p) REVERT: j 141 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8244 (tp) REVERT: k 25 PHE cc_start: 0.8691 (m-80) cc_final: 0.8371 (m-80) REVERT: k 47 MET cc_start: 0.7590 (pmm) cc_final: 0.7202 (pmm) REVERT: k 78 ASN cc_start: 0.8280 (m-40) cc_final: 0.7771 (t0) REVERT: k 131 MET cc_start: 0.7938 (ppp) cc_final: 0.7235 (tpt) REVERT: l 13 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: l 23 MET cc_start: 0.8482 (tpt) cc_final: 0.8081 (tpt) REVERT: l 131 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5805 (ptt) REVERT: l 134 ILE cc_start: 0.9023 (mp) cc_final: 0.8751 (tp) REVERT: m 23 MET cc_start: 0.6380 (tpt) cc_final: 0.5408 (mmm) REVERT: m 141 LEU cc_start: 0.6928 (mp) cc_final: 0.6195 (tp) REVERT: n 44 MET cc_start: 0.6112 (tpt) cc_final: 0.4952 (tpt) REVERT: n 47 MET cc_start: 0.8313 (ppp) cc_final: 0.7697 (pmm) REVERT: o 131 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8479 (ppp) REVERT: p 312 TRP cc_start: 0.8172 (m100) cc_final: 0.7397 (m100) outliers start: 195 outliers final: 157 residues processed: 950 average time/residue: 0.5234 time to fit residues: 868.0657 Evaluate side-chains 973 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 798 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 437 LYS Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 315 PHE Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain j residue 47 MET Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 44 MET Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 119 ARG Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 144 TYR Chi-restraints excluded: chain n residue 32 TYR Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain p residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 493 optimal weight: 6.9990 chunk 794 optimal weight: 40.0000 chunk 484 optimal weight: 0.8980 chunk 376 optimal weight: 8.9990 chunk 551 optimal weight: 50.0000 chunk 832 optimal weight: 8.9990 chunk 766 optimal weight: 9.9990 chunk 663 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 512 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 61638 Z= 0.364 Angle : 0.765 19.207 83673 Z= 0.384 Chirality : 0.045 0.342 9871 Planarity : 0.005 0.061 10900 Dihedral : 4.841 121.467 9025 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.54 % Favored : 95.45 % Rotamer: Outliers : 3.19 % Allowed : 19.17 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.65 (0.09), residues: 8369 helix: 1.22 (0.07), residues: 5008 sheet: -0.35 (0.21), residues: 663 loop : -0.76 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP b 49 HIS 0.005 0.001 HIS B 225 PHE 0.059 0.002 PHE m 25 TYR 0.037 0.002 TYR b 8 ARG 0.008 0.001 ARG Q 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 817 time to evaluate : 5.561 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: A 164 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8247 (t70) REVERT: A 193 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 254 CYS cc_start: 0.8396 (m) cc_final: 0.7835 (m) REVERT: A 318 MET cc_start: 0.9152 (mtt) cc_final: 0.8635 (mtp) REVERT: A 346 MET cc_start: 0.8946 (ttp) cc_final: 0.8688 (ttt) REVERT: A 491 GLU cc_start: 0.8927 (tt0) cc_final: 0.8720 (tm-30) REVERT: A 516 LYS cc_start: 0.9401 (mttt) cc_final: 0.9088 (tmtt) REVERT: A 574 MET cc_start: 0.8848 (mtt) cc_final: 0.8538 (mmt) REVERT: B 167 MET cc_start: 0.8717 (mtt) cc_final: 0.8474 (mtt) REVERT: B 306 MET cc_start: 0.8570 (ptm) cc_final: 0.8143 (tmm) REVERT: B 318 MET cc_start: 0.9412 (tpp) cc_final: 0.8317 (mpp) REVERT: B 340 MET cc_start: 0.8979 (ttm) cc_final: 0.8670 (tpp) REVERT: B 347 MET cc_start: 0.8855 (tpp) cc_final: 0.8591 (tpt) REVERT: B 458 MET cc_start: 0.8857 (mmt) cc_final: 0.8457 (mmt) REVERT: B 492 ILE cc_start: 0.9562 (mm) cc_final: 0.9308 (mm) REVERT: B 540 MET cc_start: 0.8852 (ptp) cc_final: 0.7856 (pmm) REVERT: C 39 MET cc_start: 0.8771 (tmm) cc_final: 0.8022 (tmm) REVERT: C 42 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8982 (mm) REVERT: C 56 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8739 (tpp80) REVERT: C 61 MET cc_start: 0.9165 (mmm) cc_final: 0.8636 (mmp) REVERT: C 234 LEU cc_start: 0.8960 (mp) cc_final: 0.8620 (tt) REVERT: C 458 MET cc_start: 0.9052 (mtp) cc_final: 0.8633 (mtt) REVERT: C 540 MET cc_start: 0.8846 (mmm) cc_final: 0.8037 (mmm) REVERT: C 541 LEU cc_start: 0.9685 (tp) cc_final: 0.9480 (tp) REVERT: C 550 MET cc_start: 0.9561 (mmp) cc_final: 0.9244 (mtt) REVERT: C 584 MET cc_start: 0.8857 (ptm) cc_final: 0.8168 (ptm) REVERT: C 608 MET cc_start: 0.8778 (tmm) cc_final: 0.8103 (tmm) REVERT: D 169 MET cc_start: 0.8818 (tmm) cc_final: 0.8560 (tmm) REVERT: D 254 MET cc_start: 0.8910 (tpp) cc_final: 0.8452 (mmm) REVERT: D 270 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8185 (tt0) REVERT: D 316 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8178 (mm-30) REVERT: D 382 GLN cc_start: 0.9372 (mp10) cc_final: 0.9119 (mp10) REVERT: D 402 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8709 (mtp) REVERT: D 410 MET cc_start: 0.8422 (mtm) cc_final: 0.8187 (mtp) REVERT: D 433 GLN cc_start: 0.9398 (tt0) cc_final: 0.9055 (tm-30) REVERT: E 234 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8883 (pmm) REVERT: E 254 MET cc_start: 0.8685 (mmm) cc_final: 0.8463 (mmm) REVERT: E 305 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8825 (mt-10) REVERT: E 309 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8492 (tm-30) REVERT: E 316 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7717 (mt-10) REVERT: E 330 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.8708 (t70) REVERT: E 356 MET cc_start: 0.9050 (mtm) cc_final: 0.8653 (pmm) REVERT: F 169 MET cc_start: 0.8921 (tmm) cc_final: 0.8635 (tmm) REVERT: F 171 GLN cc_start: 0.8920 (pt0) cc_final: 0.8295 (pt0) REVERT: F 180 MET cc_start: 0.8953 (mmm) cc_final: 0.8648 (mmm) REVERT: F 183 ILE cc_start: 0.9658 (mt) cc_final: 0.9303 (pt) REVERT: F 187 GLN cc_start: 0.9304 (pp30) cc_final: 0.8896 (pp30) REVERT: F 250 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8058 (mt-10) REVERT: F 300 MET cc_start: 0.9419 (mmm) cc_final: 0.8882 (mtm) REVERT: F 309 GLU cc_start: 0.9233 (tm-30) cc_final: 0.9024 (tm-30) REVERT: F 353 ILE cc_start: 0.9661 (mt) cc_final: 0.9439 (mm) REVERT: F 356 MET cc_start: 0.8801 (mtm) cc_final: 0.8339 (mtm) REVERT: F 410 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8103 (mtp) REVERT: F 435 MET cc_start: 0.9269 (tpp) cc_final: 0.8874 (tpt) REVERT: H 190 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9045 (mm-30) REVERT: H 193 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9011 (tm-30) REVERT: I 76 MET cc_start: 0.9487 (mpp) cc_final: 0.9245 (mpp) REVERT: I 129 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8364 (tp30) REVERT: I 182 GLU cc_start: 0.7809 (pt0) cc_final: 0.7534 (pt0) REVERT: I 196 LEU cc_start: 0.9838 (OUTLIER) cc_final: 0.9624 (mm) REVERT: I 207 MET cc_start: 0.9431 (mmt) cc_final: 0.9087 (mmm) REVERT: J 72 MET cc_start: 0.9209 (ppp) cc_final: 0.8834 (ppp) REVERT: J 182 GLU cc_start: 0.8562 (tt0) cc_final: 0.7772 (tt0) REVERT: J 194 ASN cc_start: 0.8647 (t0) cc_final: 0.8070 (t0) REVERT: J 207 MET cc_start: 0.9448 (mmp) cc_final: 0.8952 (mmm) REVERT: J 208 MET cc_start: 0.9186 (mmm) cc_final: 0.8779 (mmt) REVERT: K 129 GLU cc_start: 0.8236 (tt0) cc_final: 0.7739 (tt0) REVERT: K 194 ASN cc_start: 0.9202 (t0) cc_final: 0.8926 (t0) REVERT: K 207 MET cc_start: 0.8691 (tpp) cc_final: 0.8405 (tpp) REVERT: L 22 LEU cc_start: 0.9688 (mt) cc_final: 0.9446 (tp) REVERT: L 27 GLU cc_start: 0.9211 (pt0) cc_final: 0.8833 (pt0) REVERT: L 47 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9030 (mm-30) REVERT: M 99 LEU cc_start: 0.9718 (tt) cc_final: 0.9453 (tt) REVERT: M 102 MET cc_start: 0.9531 (mtt) cc_final: 0.9115 (mpp) REVERT: N 84 MET cc_start: 0.9104 (mtm) cc_final: 0.8763 (ptp) REVERT: N 102 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8592 (mtm) REVERT: Q 33 MET cc_start: 0.8743 (tmm) cc_final: 0.8255 (tmm) REVERT: Q 66 LEU cc_start: 0.9696 (tp) cc_final: 0.9258 (tt) REVERT: Q 109 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9104 (mm-30) REVERT: R 79 ASP cc_start: 0.9617 (OUTLIER) cc_final: 0.9328 (m-30) REVERT: R 139 TYR cc_start: 0.9074 (t80) cc_final: 0.8810 (t80) REVERT: R 229 MET cc_start: 0.9128 (mmm) cc_final: 0.8856 (mmm) REVERT: S 197 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: b 19 MET cc_start: 0.7371 (ppp) cc_final: 0.7116 (ppp) REVERT: b 70 TYR cc_start: 0.7578 (p90) cc_final: 0.7194 (p90) REVERT: b 100 VAL cc_start: 0.9105 (t) cc_final: 0.8739 (p) REVERT: b 157 ILE cc_start: 0.9156 (mt) cc_final: 0.8926 (mm) REVERT: c 421 MET cc_start: 0.8951 (mtp) cc_final: 0.8474 (mmm) REVERT: c 435 TYR cc_start: 0.9362 (t80) cc_final: 0.9111 (t80) REVERT: c 441 LEU cc_start: 0.9329 (mm) cc_final: 0.9006 (mt) REVERT: c 444 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7182 (tttm) REVERT: d 105 MET cc_start: 0.8938 (mmm) cc_final: 0.8652 (tpp) REVERT: d 138 MET cc_start: 0.8368 (mmp) cc_final: 0.8122 (mmm) REVERT: d 176 MET cc_start: 0.8316 (tpp) cc_final: 0.8080 (tmm) REVERT: d 307 LEU cc_start: 0.9110 (mp) cc_final: 0.8738 (tt) REVERT: d 334 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8643 (pt0) REVERT: h 28 MET cc_start: 0.9313 (mtp) cc_final: 0.9091 (tpt) REVERT: h 146 LEU cc_start: 0.8442 (mt) cc_final: 0.8191 (mt) REVERT: i 23 MET cc_start: 0.6414 (tpt) cc_final: 0.6023 (tpt) REVERT: i 61 MET cc_start: 0.5792 (ptp) cc_final: 0.5246 (ptp) REVERT: i 88 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7236 (ttp-170) REVERT: j 55 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8187 (p) REVERT: k 25 PHE cc_start: 0.8738 (m-80) cc_final: 0.8429 (m-80) REVERT: k 47 MET cc_start: 0.7665 (pmm) cc_final: 0.7305 (pmm) REVERT: k 78 ASN cc_start: 0.8398 (m-40) cc_final: 0.7905 (t0) REVERT: k 131 MET cc_start: 0.7869 (ppp) cc_final: 0.7294 (tpt) REVERT: l 13 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: l 134 ILE cc_start: 0.8990 (mp) cc_final: 0.8679 (tp) REVERT: m 53 MET cc_start: 0.5848 (mmp) cc_final: 0.5514 (mmp) REVERT: m 141 LEU cc_start: 0.6995 (mp) cc_final: 0.6279 (tp) REVERT: n 44 MET cc_start: 0.5961 (tpt) cc_final: 0.4832 (tpt) REVERT: n 47 MET cc_start: 0.8333 (ppp) cc_final: 0.7853 (pmm) REVERT: o 61 MET cc_start: 0.5518 (ptp) cc_final: 0.4924 (ptt) REVERT: o 131 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8366 (ppp) REVERT: p 312 TRP cc_start: 0.8142 (m100) cc_final: 0.7388 (m100) outliers start: 180 outliers final: 155 residues processed: 937 average time/residue: 0.5206 time to fit residues: 848.9322 Evaluate side-chains 959 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 790 time to evaluate : 5.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 437 LYS Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 132 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain S residue 10 MET Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 71 ASP Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 131 MET Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain i residue 55 SER Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 44 MET Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 119 ARG Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain n residue 32 TYR Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain p residue 330 ASN Chi-restraints excluded: chain p residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 526 optimal weight: 20.0000 chunk 706 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 611 optimal weight: 50.0000 chunk 97 optimal weight: 0.0670 chunk 184 optimal weight: 20.0000 chunk 664 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 682 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 HIS S 117 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.100214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.080423 restraints weight = 359039.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.081907 restraints weight = 165856.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.082678 restraints weight = 90768.185| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 61638 Z= 0.329 Angle : 0.753 17.025 83673 Z= 0.378 Chirality : 0.045 0.347 9871 Planarity : 0.005 0.059 10900 Dihedral : 4.820 122.272 9025 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.43 % Favored : 95.56 % Rotamer: Outliers : 3.06 % Allowed : 19.66 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.66 (0.09), residues: 8369 helix: 1.22 (0.07), residues: 4998 sheet: -0.35 (0.21), residues: 658 loop : -0.74 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP b 49 HIS 0.005 0.001 HIS B 225 PHE 0.056 0.002 PHE m 25 TYR 0.067 0.002 TYR j 144 ARG 0.016 0.001 ARG l 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15691.63 seconds wall clock time: 274 minutes 14.33 seconds (16454.33 seconds total)