Starting phenix.real_space_refine on Sun Apr 7 14:53:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq6_21317/04_2024/6vq6_21317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq6_21317/04_2024/6vq6_21317.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/6vq6_21317/04_2024/6vq6_21317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq6_21317/04_2024/6vq6_21317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq6_21317/04_2024/6vq6_21317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq6_21317/04_2024/6vq6_21317_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= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 337 5.16 5 C 39790 2.51 5 N 10670 2.21 5 O 11585 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 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "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 ARG 323": "NH1" <-> "NH2" 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 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ASP 436": "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 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 279": "OE1" <-> "OE2" 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 ARG 388": "NH1" <-> "NH2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 534": "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 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 454": "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 "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "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 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 TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F 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 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 458": "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 "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 214": "OE1" <-> "OE2" 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 PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 388": "OE1" <-> "OE2" Residue "a TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 118": "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 "b PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 82": "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 294": "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 "e PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 108": "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 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 62385 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: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1603 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 7, '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: 136 Chain: "J" 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: "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: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 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: "Q" 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: "R" 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: "S" 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: "a" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5030 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PTRANS': 31, 'TRANS': 718} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1126 Unresolved non-hydrogen angles: 1430 Unresolved non-hydrogen dihedrals: 922 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 23, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 19, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 652 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: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 621 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 480 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 88 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: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.91, per 1000 atoms: 0.38 Number of scatterers: 62385 At special positions: 0 Unit cell: (174.9, 174.9, 275.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 337 16.00 P 2 15.00 Mg 1 11.99 O 11585 8.00 N 10670 7.00 C 39790 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: 19.12 Conformation dependent library (CDL) restraints added in 8.8 seconds 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 288 helices and 40 sheets defined 58.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.31 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 320 through 340 removed outlier: 4.692A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (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 378 through 386 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: 4.321A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 removed outlier: 3.571A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.869A 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 557 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 587 removed outlier: 5.087A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.661A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 281 through 293 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 320 through 340 removed outlier: 4.568A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.746A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 438 through 441 No H-bonds generated for 'chain 'B' and resid 438 through 441' Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 472 through 496 removed outlier: 4.559A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 558 removed outlier: 3.894A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 586 removed outlier: 4.913A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 removed outlier: 4.043A pdb=" N LEU B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 281 through 293 Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 321 through 340 removed outlier: 3.637A pdb=" N SER C 326 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 331 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 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 376 through 388 removed outlier: 4.361A pdb=" N GLY C 379 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 383 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 384 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 387 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 458 through 468 removed outlier: 4.472A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 496 removed outlier: 4.191A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 585 removed outlier: 5.082A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 270 through 287 removed outlier: 3.636A pdb=" N THR D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 3.580A pdb=" N ALA D 278 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 280 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 287 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.970A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 382 through 385 No H-bonds generated for 'chain 'D' and resid 382 through 385' Processing helix chain 'D' and resid 400 through 403 removed outlier: 4.148A pdb=" N LYS D 403 " --> pdb=" O ARG D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 403' Processing helix chain 'D' and resid 415 through 439 removed outlier: 4.082A 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 Processing helix chain 'D' and resid 473 through 486 removed outlier: 3.861A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 253 through 256 Processing helix chain 'E' and resid 270 through 288 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 327 through 335 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 removed outlier: 3.839A pdb=" N ILE E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) 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 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 removed outlier: 3.683A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.088A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 removed outlier: 3.669A pdb=" N ARG F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 274 through 287 Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.997A pdb=" N ARG F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 405 removed outlier: 4.235A pdb=" N LYS F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 439 removed outlier: 4.293A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 446 through 461 removed outlier: 4.301A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 460 " --> pdb=" O GLN F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.162A 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 removed outlier: 5.038A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 19 removed outlier: 3.686A pdb=" N TRP G 19 " --> pdb=" O GLN G 16 " (cutoff:3.500A) 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 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: 5.308A pdb=" N ASN G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR G 201 " --> pdb=" O ILE G 198 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 removed outlier: 4.278A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG G 238 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 240 " --> pdb=" O PHE G 237 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 241 " --> pdb=" O ARG G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 310 Proline residue: G 278 - end of helix removed outlier: 3.628A pdb=" N ARG G 281 " --> pdb=" O GLY G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 343 removed outlier: 5.309A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP G 343 " --> pdb=" O TYR G 339 " (cutoff:3.500A) 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 removed outlier: 7.076A pdb=" N THR H 157 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 158 " --> pdb=" O SER H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 215 Processing helix chain 'I' and resid 5 through 106 removed outlier: 3.585A pdb=" N GLN I 67 " --> pdb=" O GLN I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 127 Processing helix chain 'I' and resid 138 through 159 Proline residue: I 142 - end of helix removed outlier: 3.707A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.696A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE I 157 " --> pdb=" O MET I 154 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR I 159 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 204 Processing helix chain 'I' and resid 208 through 216 removed outlier: 3.565A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 106 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: 3.684A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 150 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.655A pdb=" N LYS J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 Processing helix chain 'J' and resid 208 through 216 Processing helix chain 'K' and resid 5 through 106 Processing helix chain 'K' and resid 109 through 127 removed outlier: 4.593A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 158 Proline residue: K 142 - end of helix removed outlier: 3.751A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS K 150 " --> pdb=" O ALA K 147 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.606A pdb=" N LYS K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 216 removed outlier: 3.889A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 75 through 80 removed outlier: 3.607A pdb=" N ASP L 79 " --> pdb=" O HIS L 76 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA L 80 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'M' and resid 4 through 103 removed outlier: 3.668A pdb=" N ALA M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU M 93 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG M 94 " --> pdb=" O ARG M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 90 removed outlier: 3.577A pdb=" N GLY N 67 " --> pdb=" O MET N 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN N 68 " --> pdb=" O GLY N 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 104 Processing helix chain 'O' and resid 4 through 90 removed outlier: 3.892A pdb=" N ARG O 90 " --> pdb=" O SER O 86 " (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 55 removed outlier: 3.528A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) removed outlier: 5.070A 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 96 Processing helix chain 'Q' and resid 105 through 117 Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 125 through 142 removed outlier: 3.841A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 166 Processing helix chain 'Q' and resid 173 through 186 Processing helix chain 'Q' and resid 193 through 205 Processing helix chain 'Q' and resid 219 through 234 Processing helix chain 'R' and resid 15 through 36 removed outlier: 3.530A pdb=" N HIS R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 53 removed outlier: 3.666A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 71 Processing helix chain 'R' and resid 78 through 98 removed outlier: 3.982A pdb=" N ILE R 98 " --> pdb=" O LEU R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 116 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: 3.813A pdb=" N LEU R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 4.491A 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 194 through 206 Processing helix chain 'S' and resid 15 through 36 Processing helix chain 'S' and resid 43 through 48 Processing helix chain 'S' and resid 50 through 55 removed outlier: 5.034A pdb=" N TRP S 55 " --> pdb=" O ASP S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 70 Processing helix chain 'S' and resid 78 through 98 removed outlier: 3.929A pdb=" N LEU S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU S 91 " --> pdb=" O ILE S 87 " (cutoff:3.500A) removed outlier: 3.980A 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 125 through 141 removed outlier: 3.526A pdb=" N LYS S 141 " --> pdb=" O THR S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 Processing helix chain 'S' and resid 173 through 187 Processing helix chain 'S' and resid 193 through 204 Processing helix chain 'S' and resid 219 through 232 removed outlier: 3.528A pdb=" N MET S 229 " --> pdb=" O LEU S 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 32 removed outlier: 3.635A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) 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 removed outlier: 3.543A pdb=" N GLU a 71 " --> pdb=" O PHE a 67 " (cutoff:3.500A) 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 removed outlier: 3.544A pdb=" N GLU a 105 " --> pdb=" O GLU a 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN a 112 " --> pdb=" O LYS a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 180 through 190 removed outlier: 4.152A pdb=" N ARG a 185 " --> pdb=" O PRO a 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 227 through 239 Processing helix chain 'a' and resid 252 through 308 removed outlier: 3.526A pdb=" N ASN a 289 " --> pdb=" O ALA a 285 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 330 through 343 Processing helix chain 'a' and resid 371 through 379 Processing helix chain 'a' and resid 392 through 406 removed outlier: 4.707A 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 removed outlier: 3.534A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 482 through 487 removed outlier: 3.559A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 499 removed outlier: 3.736A pdb=" N SER a 498 " --> pdb=" O THR a 494 " (cutoff:3.500A) removed outlier: 5.128A 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: 4.344A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE a 536 " --> pdb=" O PHE a 532 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 4.020A 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: 4.398A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (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 666 removed outlier: 3.685A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.906A 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: 4.320A pdb=" N LEU a 740 " --> pdb=" O THR a 736 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG a 741 " --> pdb=" O ALA a 737 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU a 742 " --> pdb=" O SER a 738 " (cutoff:3.500A) removed outlier: 4.234A 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: 3.712A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 114 removed outlier: 3.674A pdb=" N LYS b 87 " --> pdb=" O PRO b 84 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN b 90 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU b 91 " --> pdb=" O THR b 88 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE b 96 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b 106 " --> pdb=" O TYR b 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN b 113 " --> pdb=" O VAL b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 168 removed outlier: 3.883A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 197 removed outlier: 4.089A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 417 through 441 Processing helix chain 'd' and resid 8 through 26 removed outlier: 3.705A pdb=" N ASP d 12 " --> pdb=" O PHE d 9 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN d 13 " --> pdb=" O ASN d 10 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY d 14 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR d 15 " --> pdb=" O ASP d 12 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL d 20 " --> pdb=" O GLU d 17 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG d 21 " --> pdb=" O GLY d 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 37 Processing helix chain 'd' and resid 42 through 51 removed outlier: 3.973A 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: 4.823A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.807A 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 157 Processing helix chain 'd' and resid 159 through 166 removed outlier: 4.180A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (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: 3.658A pdb=" N PHE d 228 " --> pdb=" O THR d 224 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLY d 229 " --> pdb=" O ILE d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 240 removed outlier: 3.670A 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: 3.921A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 272 through 280 removed outlier: 4.407A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 307 removed outlier: 4.063A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) removed outlier: 4.222A 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 59 removed outlier: 3.835A pdb=" N GLN e 59 " --> pdb=" O ALA e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 77 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: 4.152A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.567A pdb=" N VAL g 74 " --> pdb=" O VAL g 71 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE g 76 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.366A pdb=" N VAL g 129 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL g 148 " --> pdb=" O GLY g 145 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU g 152 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 3.887A pdb=" N PHE h 14 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA h 22 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE h 25 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER h 26 " --> pdb=" O MET h 23 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS h 36 " --> pdb=" O GLY h 33 " (cutoff:3.500A) removed outlier: 4.180A 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: 4.238A pdb=" N VAL h 129 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER h 153 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 47 removed outlier: 4.207A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.935A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 153 removed outlier: 4.037A pdb=" N VAL i 129 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR i 144 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 45 removed outlier: 3.791A pdb=" N PHE j 14 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA j 22 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE j 25 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS j 36 " --> pdb=" O GLY j 33 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER j 45 " --> pdb=" O ALA j 42 " (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: 3.669A pdb=" N MET j 61 " --> pdb=" O PRO j 58 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL j 74 " --> pdb=" O VAL j 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE j 76 " --> pdb=" O ALA j 73 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.956A pdb=" N VAL j 129 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU j 152 " --> pdb=" O ALA j 149 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER j 153 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 47 removed outlier: 4.490A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.063A 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: 3.531A pdb=" N ILE k 76 " --> pdb=" O ALA k 73 " (cutoff:3.500A) removed outlier: 3.556A 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: 4.219A pdb=" N VAL k 129 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER k 153 " --> pdb=" O LEU k 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 47 removed outlier: 3.685A pdb=" N PHE l 14 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER l 20 " --> pdb=" O MET l 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA l 22 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE l 25 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER l 26 " --> pdb=" O MET l 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS l 36 " --> pdb=" O GLY l 33 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 52 Processing helix chain 'l' and resid 54 through 79 Proline residue: l 58 - end of helix removed outlier: 3.594A pdb=" N ILE l 76 " --> pdb=" O ALA l 73 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 123 removed outlier: 3.932A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 154 removed outlier: 3.759A pdb=" N VAL l 129 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR l 154 " --> pdb=" O ILE l 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 46 removed outlier: 4.427A pdb=" N PHE m 25 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS m 36 " --> pdb=" O GLY m 33 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY m 38 " --> pdb=" O ALA m 35 " (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: 3.985A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 153 removed outlier: 3.869A pdb=" N VAL m 129 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER m 153 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 45 removed outlier: 4.139A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (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 78 Processing helix chain 'n' and resid 87 through 122 removed outlier: 3.624A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 153 removed outlier: 4.183A pdb=" N VAL n 129 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER n 153 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 47 removed outlier: 3.741A pdb=" N PHE o 14 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA o 22 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE o 25 " --> pdb=" O ALA o 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR o 34 " --> pdb=" O ALA o 31 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS o 36 " --> pdb=" O GLY o 33 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL o 46 " --> 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: 3.769A pdb=" N ILE o 57 " --> pdb=" O LYS o 54 " (cutoff:3.500A) Proline residue: o 58 - end of helix removed outlier: 3.614A pdb=" N VAL o 74 " --> pdb=" O VAL o 71 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE o 76 " --> pdb=" O ALA o 73 " (cutoff:3.500A) removed outlier: 3.630A 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 153 removed outlier: 4.259A pdb=" N VAL o 129 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR o 144 " --> pdb=" O LEU o 141 " (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 18 through 20 removed outlier: 6.899A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 185 removed outlier: 6.819A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.200A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 219 through 221 removed outlier: 4.077A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 245 through 247 removed outlier: 8.341A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.570A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.366A 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: 4.719A pdb=" N GLU B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.539A 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: 6.249A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 309 through 312 removed outlier: 6.297A pdb=" N ILE B 272 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL B 312 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR B 274 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL B 344 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER B 403 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N MET B 346 " --> pdb=" O SER B 403 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER B 405 " --> pdb=" O MET B 346 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA B 348 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= N, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.510A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 56 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN C 65 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE C 54 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS C 84 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG C 44 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR C 82 " --> pdb=" O ARG C 44 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= P, first strand: chain 'C' and resid 183 through 185 Processing sheet with id= Q, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.339A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 245 through 248 removed outlier: 8.619A pdb=" N THR C 246 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 248 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY C 408 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 272 through 277 Processing sheet with id= T, first strand: chain 'C' and resid 390 through 393 Processing sheet with id= U, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.777A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= W, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.442A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 191 through 193 Processing sheet with id= Y, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.676A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 94 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AA, first strand: chain 'E' and resid 131 through 133 removed outlier: 8.122A pdb=" N PHE E 132 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU E 259 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS E 292 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET E 234 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 298 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL E 236 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 191 through 194 Processing sheet with id= AC, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.800A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU F 88 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AE, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.035A pdb=" N PHE F 132 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU F 259 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE F 351 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 370 through 375 removed outlier: 3.529A pdb=" N VAL G 34 " --> pdb=" O GLN G 322 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 182 through 190 removed outlier: 6.412A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.774A 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 Processing sheet with id= AJ, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AK, first strand: chain 'K' and resid 164 through 167 removed outlier: 3.993A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.520A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE L 63 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE L 11 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.270A 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: 3.621A pdb=" N ILE a 351 " --> pdb=" O PHE a 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE a 16 " --> pdb=" O ILE a 351 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'a' and resid 197 through 202 removed outlier: 4.411A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) 3895 hydrogen bonds defined for protein. 9798 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: 20.24 Time building geometry restraints manager: 21.14 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: 10472 1.30 - 1.43: 15374 1.43 - 1.55: 37004 1.55 - 1.68: 3 1.68 - 1.81: 606 Bond restraints: 63459 Sorted by residual: bond pdb=" N PRO E 391 " pdb=" CA PRO E 391 " ideal model delta sigma weight residual 1.469 1.532 -0.063 7.40e-03 1.83e+04 7.28e+01 bond pdb=" C TYR D 504 " pdb=" N PRO D 505 " ideal model delta sigma weight residual 1.337 1.406 -0.070 1.06e-02 8.90e+03 4.34e+01 bond pdb=" C PRO H 107 " pdb=" O PRO H 107 " ideal model delta sigma weight residual 1.233 1.171 0.062 9.60e-03 1.09e+04 4.22e+01 bond pdb=" N PRO D 352 " pdb=" CA PRO D 352 " ideal model delta sigma weight residual 1.466 1.539 -0.073 1.24e-02 6.50e+03 3.42e+01 bond pdb=" N PRO E 396 " pdb=" CA PRO E 396 " ideal model delta sigma weight residual 1.469 1.539 -0.070 1.25e-02 6.40e+03 3.17e+01 ... (remaining 63454 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.01: 1503 105.01 - 112.33: 32346 112.33 - 119.65: 20723 119.65 - 126.97: 30996 126.97 - 134.29: 506 Bond angle restraints: 86074 Sorted by residual: angle pdb=" C ILE E 189 " pdb=" N PRO E 190 " pdb=" CA PRO E 190 " ideal model delta sigma weight residual 119.85 129.31 -9.46 1.01e+00 9.80e-01 8.77e+01 angle pdb=" C ARG C 215 " pdb=" N PRO C 216 " pdb=" CA PRO C 216 " ideal model delta sigma weight residual 119.76 129.26 -9.50 1.03e+00 9.43e-01 8.51e+01 angle pdb=" C SER A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta sigma weight residual 120.38 129.09 -8.71 1.03e+00 9.43e-01 7.15e+01 angle pdb=" N GLN d 171 " pdb=" CA GLN d 171 " pdb=" C GLN d 171 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.48e+01 angle pdb=" C LEU E 395 " pdb=" N PRO E 396 " pdb=" CA PRO E 396 " ideal model delta sigma weight residual 120.04 128.52 -8.48 1.08e+00 8.57e-01 6.16e+01 ... (remaining 86069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 37250 23.68 - 47.36: 691 47.36 - 71.04: 159 71.04 - 94.72: 55 94.72 - 118.41: 2 Dihedral angle restraints: 38157 sinusoidal: 13835 harmonic: 24322 Sorted by residual: dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.40 118.41 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.48 -98.48 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA ILE F 406 " pdb=" C ILE F 406 " pdb=" N GLY F 407 " pdb=" CA GLY F 407 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 38154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 7593 0.080 - 0.159: 2211 0.159 - 0.239: 217 0.239 - 0.318: 18 0.318 - 0.398: 1 Chirality restraints: 10040 Sorted by residual: chirality pdb=" CA GLU a 30 " pdb=" N GLU a 30 " pdb=" C GLU a 30 " pdb=" CB GLU a 30 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA TYR n 68 " pdb=" N TYR n 68 " pdb=" C TYR n 68 " pdb=" CB TYR n 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LEU M 69 " pdb=" N LEU M 69 " pdb=" C LEU M 69 " pdb=" CB LEU M 69 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 10037 not shown) Planarity restraints: 11108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+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 ASP G 236 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C ASP G 236 " 0.076 2.00e-02 2.50e+03 pdb=" O ASP G 236 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE G 237 " -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 4.26e-02 1.82e+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 " -0.024 2.00e-02 2.50e+03 ... (remaining 11105 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 23 2.43 - 3.05: 43150 3.05 - 3.66: 95260 3.66 - 4.28: 145563 4.28 - 4.90: 236324 Nonbonded interactions: 520320 Sorted by model distance: nonbonded pdb=" OG1 THR C 257 " pdb="MG MG C 702 " model vdw 1.809 2.170 nonbonded pdb=" OG SER b 136 " pdb=" O GLN b 197 " model vdw 2.305 2.440 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.319 2.520 nonbonded pdb=" O ARG a 179 " pdb=" N PHE a 183 " model vdw 2.327 2.520 nonbonded pdb=" O ASP G 196 " pdb=" N GLN G 200 " model vdw 2.342 2.520 ... (remaining 520315 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' selection = chain 'B' selection = (chain 'C' and resid 17 through 616) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = (chain 'J' and ((resid 2 through 66 and (name N or name CA or name C or name O o \ r name CB )) or resid 67 through 226)) selection = (chain 'K' and ((resid 2 through 66 and (name N or name CA or name C or name O o \ r name CB )) or resid 67 through 226)) } ncs_group { reference = chain 'M' selection = chain 'N' 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: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.050 Extract box with map and model: 10.250 Check model and map are aligned: 0.670 Set scattering table: 0.440 Process input model: 124.930 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.460 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 0.115 63459 Z= 0.604 Angle : 0.952 10.648 86074 Z= 0.696 Chirality : 0.063 0.398 10040 Planarity : 0.005 0.046 11108 Dihedral : 10.959 118.405 22533 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.57 % Favored : 97.16 % Rotamer: Outliers : 0.30 % Allowed : 1.21 % Favored : 98.49 % Cbeta Deviations : 0.01 % 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: 0.63 (0.09), residues: 8372 helix: 1.03 (0.07), residues: 4873 sheet: -0.21 (0.18), residues: 760 loop : -0.35 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 450 HIS 0.003 0.000 HIS E 199 PHE 0.011 0.000 PHE d 96 TYR 0.015 0.001 TYR F 389 ARG 0.003 0.000 ARG F 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2272 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2254 time to evaluate : 5.342 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 61 MET cc_start: 0.9001 (mtp) cc_final: 0.8565 (mtm) REVERT: A 95 MET cc_start: 0.8343 (mmm) cc_final: 0.8062 (tpp) REVERT: A 100 ASP cc_start: 0.8662 (t0) cc_final: 0.8391 (t0) REVERT: A 116 ILE cc_start: 0.9086 (pt) cc_final: 0.8581 (mm) REVERT: A 147 ILE cc_start: 0.9619 (pt) cc_final: 0.9408 (mm) REVERT: A 167 MET cc_start: 0.8781 (mtm) cc_final: 0.8508 (mtt) REVERT: A 205 MET cc_start: 0.9134 (mtm) cc_final: 0.8922 (mtm) REVERT: A 245 THR cc_start: 0.9260 (m) cc_final: 0.8993 (p) REVERT: A 291 PHE cc_start: 0.9058 (t80) cc_final: 0.8770 (t80) REVERT: A 306 MET cc_start: 0.8775 (ptm) cc_final: 0.8195 (ppp) REVERT: A 318 MET cc_start: 0.8990 (mmm) cc_final: 0.8073 (mpp) REVERT: A 331 ILE cc_start: 0.9689 (tp) cc_final: 0.9445 (tp) REVERT: A 345 SER cc_start: 0.9695 (t) cc_final: 0.9466 (p) REVERT: A 346 MET cc_start: 0.9016 (ttt) cc_final: 0.8289 (tmm) REVERT: A 362 SER cc_start: 0.9614 (t) cc_final: 0.9377 (p) REVERT: A 472 PHE cc_start: 0.8690 (t80) cc_final: 0.7886 (t80) REVERT: A 541 LEU cc_start: 0.9739 (tp) cc_final: 0.9512 (tp) REVERT: A 545 ILE cc_start: 0.9805 (mt) cc_final: 0.9569 (mt) REVERT: A 604 LEU cc_start: 0.9025 (mp) cc_final: 0.8653 (tp) REVERT: B 53 GLU cc_start: 0.8953 (pt0) cc_final: 0.8018 (pt0) REVERT: B 61 MET cc_start: 0.9180 (mtp) cc_final: 0.8751 (mmm) REVERT: B 168 LEU cc_start: 0.9255 (tp) cc_final: 0.9049 (tp) REVERT: B 203 LEU cc_start: 0.9022 (mt) cc_final: 0.8742 (pp) REVERT: B 254 CYS cc_start: 0.7754 (p) cc_final: 0.7239 (p) REVERT: B 318 MET cc_start: 0.8889 (mmm) cc_final: 0.8525 (mmm) REVERT: B 324 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8925 (tm-30) REVERT: B 346 MET cc_start: 0.9035 (ttp) cc_final: 0.8752 (ttp) REVERT: B 349 ASP cc_start: 0.8064 (t0) cc_final: 0.7711 (t0) REVERT: B 356 GLU cc_start: 0.9317 (tp30) cc_final: 0.8386 (tp30) REVERT: B 387 GLU cc_start: 0.8506 (tp30) cc_final: 0.8106 (tm-30) REVERT: B 422 THR cc_start: 0.9224 (m) cc_final: 0.8741 (m) REVERT: B 450 TRP cc_start: 0.5566 (m-10) cc_final: 0.5271 (m-10) REVERT: B 458 MET cc_start: 0.8797 (mtp) cc_final: 0.8362 (mtt) REVERT: B 544 MET cc_start: 0.9286 (mtt) cc_final: 0.8965 (mmm) REVERT: B 584 MET cc_start: 0.8948 (mtm) cc_final: 0.6955 (mtp) REVERT: C 50 LEU cc_start: 0.9500 (mt) cc_final: 0.9287 (mt) REVERT: C 95 MET cc_start: 0.8733 (mmm) cc_final: 0.7725 (mmt) REVERT: C 108 ASP cc_start: 0.9332 (m-30) cc_final: 0.9047 (t70) REVERT: C 162 ILE cc_start: 0.9376 (mm) cc_final: 0.9153 (mm) REVERT: C 166 ILE cc_start: 0.9479 (mm) cc_final: 0.9202 (tp) REVERT: C 173 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7325 (pmt100) REVERT: C 231 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8840 (mm-40) REVERT: C 232 ARG cc_start: 0.8500 (mtt90) cc_final: 0.8115 (mtm-85) REVERT: C 254 CYS cc_start: 0.9037 (m) cc_final: 0.8489 (m) REVERT: C 296 MET cc_start: 0.8554 (ttt) cc_final: 0.8305 (ttm) REVERT: C 318 MET cc_start: 0.9253 (mtt) cc_final: 0.8606 (mtp) REVERT: C 360 GLU cc_start: 0.9173 (tt0) cc_final: 0.8805 (tm-30) REVERT: C 487 GLU cc_start: 0.9383 (tp30) cc_final: 0.8821 (tm-30) REVERT: C 523 ASN cc_start: 0.9252 (t0) cc_final: 0.9025 (t0) REVERT: C 540 MET cc_start: 0.9095 (ptm) cc_final: 0.8862 (ptm) REVERT: C 541 LEU cc_start: 0.9773 (tp) cc_final: 0.9538 (tt) REVERT: C 550 MET cc_start: 0.9205 (mtm) cc_final: 0.8155 (mtt) REVERT: C 573 HIS cc_start: 0.8878 (t70) cc_final: 0.8637 (t-170) REVERT: C 608 MET cc_start: 0.9415 (mtm) cc_final: 0.9144 (ttt) REVERT: D 51 SER cc_start: 0.9048 (t) cc_final: 0.8811 (p) REVERT: D 113 GLU cc_start: 0.8799 (tt0) cc_final: 0.8340 (tm-30) REVERT: D 114 PHE cc_start: 0.9283 (m-80) cc_final: 0.8496 (m-80) REVERT: D 128 LEU cc_start: 0.9209 (mt) cc_final: 0.8999 (pt) REVERT: D 159 ASN cc_start: 0.8840 (t0) cc_final: 0.7982 (p0) REVERT: D 162 CYS cc_start: 0.7722 (p) cc_final: 0.6297 (p) REVERT: D 234 MET cc_start: 0.8041 (mtm) cc_final: 0.7561 (mtm) REVERT: D 238 MET cc_start: 0.9000 (tpp) cc_final: 0.8372 (tpt) REVERT: D 250 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8933 (tm-30) REVERT: D 262 ASN cc_start: 0.8684 (t0) cc_final: 0.8461 (t0) REVERT: D 268 THR cc_start: 0.8819 (p) cc_final: 0.8477 (t) REVERT: D 300 MET cc_start: 0.9441 (mmm) cc_final: 0.9238 (mmp) REVERT: D 410 MET cc_start: 0.8655 (mtt) cc_final: 0.8357 (mtm) REVERT: E 88 GLU cc_start: 0.8570 (tt0) cc_final: 0.8335 (tm-30) REVERT: E 90 SER cc_start: 0.9282 (t) cc_final: 0.8547 (p) REVERT: E 127 MET cc_start: 0.8912 (ptm) cc_final: 0.8558 (ptm) REVERT: E 180 MET cc_start: 0.8828 (mmm) cc_final: 0.8563 (mmm) REVERT: E 183 ILE cc_start: 0.9584 (mt) cc_final: 0.9299 (pt) REVERT: E 234 MET cc_start: 0.8808 (mpp) cc_final: 0.7869 (mpp) REVERT: E 238 MET cc_start: 0.9108 (tpt) cc_final: 0.8836 (tpp) REVERT: E 298 THR cc_start: 0.8902 (m) cc_final: 0.8547 (m) REVERT: E 353 ILE cc_start: 0.9334 (mt) cc_final: 0.9054 (mm) REVERT: E 355 THR cc_start: 0.8669 (m) cc_final: 0.8430 (p) REVERT: E 361 ILE cc_start: 0.9145 (tp) cc_final: 0.8878 (tp) REVERT: E 402 MET cc_start: 0.8563 (ttt) cc_final: 0.8276 (ttt) REVERT: E 484 LEU cc_start: 0.9243 (mt) cc_final: 0.9023 (mt) REVERT: F 87 LEU cc_start: 0.8917 (mt) cc_final: 0.8568 (mp) REVERT: F 88 GLU cc_start: 0.8687 (tt0) cc_final: 0.8415 (tm-30) REVERT: F 113 GLU cc_start: 0.9327 (pt0) cc_final: 0.9009 (pp20) REVERT: F 127 MET cc_start: 0.9217 (mtp) cc_final: 0.8890 (mtp) REVERT: F 159 ASN cc_start: 0.8676 (t0) cc_final: 0.8457 (t0) REVERT: F 180 MET cc_start: 0.8377 (mtp) cc_final: 0.8092 (mmm) REVERT: F 231 PHE cc_start: 0.8409 (t80) cc_final: 0.8042 (t80) REVERT: F 262 ASN cc_start: 0.8288 (t0) cc_final: 0.7571 (t0) REVERT: F 288 GLN cc_start: 0.9383 (mt0) cc_final: 0.8635 (mt0) REVERT: F 316 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8583 (mm-30) REVERT: F 360 ASP cc_start: 0.8631 (t0) cc_final: 0.8270 (t0) REVERT: F 417 ASP cc_start: 0.8995 (m-30) cc_final: 0.8771 (m-30) REVERT: H 78 ASP cc_start: 0.7532 (t0) cc_final: 0.7231 (t0) REVERT: H 137 ASN cc_start: 0.8345 (m-40) cc_final: 0.7978 (m-40) REVERT: H 187 ILE cc_start: 0.9599 (mt) cc_final: 0.9277 (mt) REVERT: H 192 ASP cc_start: 0.9144 (m-30) cc_final: 0.8560 (t0) REVERT: H 197 GLU cc_start: 0.8021 (pt0) cc_final: 0.7565 (pt0) REVERT: I 129 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8641 (mm-30) REVERT: I 164 ASP cc_start: 0.8848 (t0) cc_final: 0.8585 (t0) REVERT: I 198 SER cc_start: 0.9633 (m) cc_final: 0.8814 (p) REVERT: I 201 ASP cc_start: 0.9429 (m-30) cc_final: 0.9220 (p0) REVERT: J 88 ASP cc_start: 0.9282 (t70) cc_final: 0.8952 (t0) REVERT: J 92 THR cc_start: 0.9722 (m) cc_final: 0.9376 (p) REVERT: J 119 LEU cc_start: 0.9767 (mt) cc_final: 0.9548 (tp) REVERT: J 177 ILE cc_start: 0.9813 (mm) cc_final: 0.9337 (mm) REVERT: J 196 LEU cc_start: 0.9447 (tp) cc_final: 0.9189 (mt) REVERT: J 210 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8666 (mp0) REVERT: K 93 ASP cc_start: 0.9480 (m-30) cc_final: 0.9195 (m-30) REVERT: K 97 GLU cc_start: 0.9471 (tp30) cc_final: 0.9193 (tp30) REVERT: K 124 LEU cc_start: 0.9770 (mt) cc_final: 0.9570 (mm) REVERT: K 132 MET cc_start: 0.8332 (mmt) cc_final: 0.7950 (mmm) REVERT: K 175 GLU cc_start: 0.9314 (mp0) cc_final: 0.8712 (mm-30) REVERT: L 31 ASN cc_start: 0.8249 (p0) cc_final: 0.7952 (p0) REVERT: L 89 LEU cc_start: 0.8937 (mt) cc_final: 0.8451 (mt) REVERT: L 98 TYR cc_start: 0.6814 (t80) cc_final: 0.6135 (t80) REVERT: N 100 LEU cc_start: 0.9637 (mt) cc_final: 0.9389 (mm) REVERT: N 107 ARG cc_start: 0.8488 (mtt180) cc_final: 0.8269 (mmm-85) REVERT: O 96 LEU cc_start: 0.9662 (mt) cc_final: 0.9418 (tt) REVERT: O 103 VAL cc_start: 0.9831 (t) cc_final: 0.9548 (t) REVERT: Q 32 CYS cc_start: 0.9405 (m) cc_final: 0.8909 (m) REVERT: Q 42 LEU cc_start: 0.9631 (mt) cc_final: 0.9332 (mp) REVERT: Q 129 LYS cc_start: 0.9567 (mttt) cc_final: 0.9123 (mmmt) REVERT: Q 231 ASP cc_start: 0.8972 (m-30) cc_final: 0.8634 (m-30) REVERT: R 13 LEU cc_start: 0.9377 (mt) cc_final: 0.9138 (mt) REVERT: R 78 LEU cc_start: 0.9546 (tp) cc_final: 0.9213 (pt) REVERT: R 109 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9161 (mm-30) REVERT: R 125 ASP cc_start: 0.9250 (m-30) cc_final: 0.8911 (p0) REVERT: R 130 LEU cc_start: 0.9562 (mt) cc_final: 0.9145 (tp) REVERT: R 156 THR cc_start: 0.9636 (m) cc_final: 0.8948 (m) REVERT: R 169 THR cc_start: 0.7814 (p) cc_final: 0.5866 (p) REVERT: R 170 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8395 (mp0) REVERT: R 194 ASP cc_start: 0.9409 (m-30) cc_final: 0.9118 (p0) REVERT: S 10 MET cc_start: 0.8139 (ttm) cc_final: 0.7918 (ttm) REVERT: S 17 GLN cc_start: 0.8914 (tp40) cc_final: 0.8504 (tp40) REVERT: S 51 ASP cc_start: 0.8846 (p0) cc_final: 0.8424 (p0) REVERT: S 188 MET cc_start: 0.9022 (tpp) cc_final: 0.8661 (tpp) REVERT: S 192 LYS cc_start: 0.9388 (mttt) cc_final: 0.8948 (mtpp) REVERT: S 200 PHE cc_start: 0.9370 (t80) cc_final: 0.9134 (t80) REVERT: a 375 GLN cc_start: 0.8303 (tp40) cc_final: 0.8092 (tp-100) REVERT: a 379 ASP cc_start: 0.7687 (m-30) cc_final: 0.7033 (m-30) REVERT: a 453 MET cc_start: 0.7175 (mtm) cc_final: 0.6974 (mtm) REVERT: a 533 LEU cc_start: 0.9109 (tp) cc_final: 0.8812 (tt) REVERT: a 549 MET cc_start: 0.7952 (mtp) cc_final: 0.6080 (mtp) REVERT: a 594 LYS cc_start: 0.7980 (tttp) cc_final: 0.7637 (ttmt) REVERT: a 641 ILE cc_start: 0.8905 (mm) cc_final: 0.8635 (mm) REVERT: a 741 ARG cc_start: 0.8583 (mtt180) cc_final: 0.7900 (mtp180) REVERT: b 36 ASP cc_start: 0.7675 (t0) cc_final: 0.7201 (p0) REVERT: b 153 VAL cc_start: 0.8968 (t) cc_final: 0.8720 (p) REVERT: d 78 MET cc_start: 0.8782 (ptm) cc_final: 0.8309 (ptp) REVERT: d 149 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8581 (tt0) REVERT: d 221 PHE cc_start: 0.8155 (m-80) cc_final: 0.7939 (m-10) REVERT: d 224 THR cc_start: 0.8778 (m) cc_final: 0.8334 (p) REVERT: d 321 LEU cc_start: 0.8799 (mt) cc_final: 0.8508 (mt) REVERT: g 13 PHE cc_start: 0.8363 (t80) cc_final: 0.7741 (t80) REVERT: g 26 SER cc_start: 0.8226 (m) cc_final: 0.7979 (p) REVERT: g 32 TYR cc_start: 0.7985 (t80) cc_final: 0.7199 (t80) REVERT: h 13 PHE cc_start: 0.8072 (t80) cc_final: 0.7415 (t80) REVERT: h 32 TYR cc_start: 0.7831 (t80) cc_final: 0.7362 (t80) REVERT: h 53 MET cc_start: 0.7805 (mmp) cc_final: 0.7578 (pmm) REVERT: h 112 ILE cc_start: 0.8837 (mm) cc_final: 0.8612 (mm) REVERT: h 121 THR cc_start: 0.8336 (m) cc_final: 0.6623 (m) REVERT: i 32 TYR cc_start: 0.8997 (t80) cc_final: 0.8663 (t80) REVERT: i 112 ILE cc_start: 0.9447 (mt) cc_final: 0.9138 (mm) REVERT: j 37 SER cc_start: 0.8620 (m) cc_final: 0.8409 (p) REVERT: j 52 ILE cc_start: 0.8147 (tt) cc_final: 0.7878 (mt) REVERT: j 102 SER cc_start: 0.8904 (m) cc_final: 0.8597 (p) REVERT: j 121 THR cc_start: 0.8395 (m) cc_final: 0.7353 (m) REVERT: j 139 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7672 (tm-30) REVERT: k 61 MET cc_start: 0.8434 (mmp) cc_final: 0.8048 (mmt) REVERT: l 121 THR cc_start: 0.8503 (m) cc_final: 0.8203 (p) REVERT: m 25 PHE cc_start: 0.7589 (m-80) cc_final: 0.7222 (m-80) REVERT: m 61 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6864 (mtt) REVERT: m 121 THR cc_start: 0.7858 (m) cc_final: 0.6746 (p) REVERT: n 68 TYR cc_start: 0.8023 (m-10) cc_final: 0.7461 (m-80) REVERT: p 328 ILE cc_start: 0.9527 (mt) cc_final: 0.9248 (tt) outliers start: 18 outliers final: 4 residues processed: 2260 average time/residue: 0.5896 time to fit residues: 2246.6860 Evaluate side-chains 1298 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1292 time to evaluate : 5.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain n residue 139 GLU Chi-restraints excluded: chain o residue 139 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 706 optimal weight: 9.9990 chunk 634 optimal weight: 30.0000 chunk 352 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 427 optimal weight: 0.8980 chunk 338 optimal weight: 0.9990 chunk 656 optimal weight: 2.9990 chunk 253 optimal weight: 0.0970 chunk 398 optimal weight: 7.9990 chunk 488 optimal weight: 1.9990 chunk 760 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 261 GLN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN D 161 GLN D 456 GLN D 497 GLN E 181 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN H 27 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN R 17 GLN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN j 78 ASN k 92 GLN ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 7 ASN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 63459 Z= 0.237 Angle : 0.719 13.229 86074 Z= 0.369 Chirality : 0.045 0.247 10040 Planarity : 0.005 0.065 11108 Dihedral : 4.764 110.633 9075 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 2.36 % Allowed : 12.27 % Favored : 85.37 % 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: 1.20 (0.09), residues: 8372 helix: 1.55 (0.07), residues: 4908 sheet: -0.11 (0.18), residues: 739 loop : -0.22 (0.12), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 49 HIS 0.006 0.001 HIS E 363 PHE 0.040 0.002 PHE f 33 TYR 0.055 0.002 TYR b 70 ARG 0.019 0.001 ARG a 805 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1592 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1448 time to evaluate : 5.302 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: A 33 ASP cc_start: 0.8905 (t0) cc_final: 0.8613 (t70) REVERT: A 100 ASP cc_start: 0.8758 (t0) cc_final: 0.8551 (t0) REVERT: A 147 ILE cc_start: 0.9653 (pt) cc_final: 0.9407 (mm) REVERT: A 171 ARG cc_start: 0.8405 (ptp-110) cc_final: 0.8193 (mtt90) REVERT: A 263 LEU cc_start: 0.9563 (tt) cc_final: 0.9355 (pp) REVERT: A 306 MET cc_start: 0.8928 (ptm) cc_final: 0.8391 (ppp) REVERT: A 346 MET cc_start: 0.8893 (ttt) cc_final: 0.8639 (ttt) REVERT: A 347 MET cc_start: 0.7870 (tpp) cc_final: 0.7618 (tpp) REVERT: A 362 SER cc_start: 0.9710 (t) cc_final: 0.9360 (p) REVERT: A 540 MET cc_start: 0.8899 (mtp) cc_final: 0.8616 (mtp) REVERT: A 596 LYS cc_start: 0.9361 (tttm) cc_final: 0.9088 (tppt) REVERT: A 608 MET cc_start: 0.9466 (ttm) cc_final: 0.8752 (ttt) REVERT: B 53 GLU cc_start: 0.9019 (pt0) cc_final: 0.8467 (pt0) REVERT: B 61 MET cc_start: 0.9184 (mtp) cc_final: 0.8808 (mmm) REVERT: B 67 TYR cc_start: 0.8980 (m-10) cc_final: 0.7975 (m-10) REVERT: B 95 MET cc_start: 0.8336 (tpp) cc_final: 0.8109 (tpp) REVERT: B 167 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8614 (mtt) REVERT: B 168 LEU cc_start: 0.9186 (tp) cc_final: 0.8954 (tp) REVERT: B 275 VAL cc_start: 0.9495 (t) cc_final: 0.9209 (p) REVERT: B 306 MET cc_start: 0.9154 (mmt) cc_final: 0.8850 (mmt) REVERT: B 323 ARG cc_start: 0.9175 (mtm110) cc_final: 0.8349 (mtm110) REVERT: B 340 MET cc_start: 0.9147 (mtt) cc_final: 0.8528 (ttm) REVERT: B 367 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 387 GLU cc_start: 0.8676 (tp30) cc_final: 0.8168 (tm-30) REVERT: B 520 LEU cc_start: 0.9474 (mt) cc_final: 0.9223 (mp) REVERT: B 540 MET cc_start: 0.9171 (mtp) cc_final: 0.8966 (ptp) REVERT: B 544 MET cc_start: 0.9444 (mtt) cc_final: 0.9081 (mmm) REVERT: B 550 MET cc_start: 0.9452 (mmm) cc_final: 0.9074 (mmp) REVERT: B 584 MET cc_start: 0.8759 (mtm) cc_final: 0.7129 (mtp) REVERT: C 34 MET cc_start: 0.8905 (mmm) cc_final: 0.8525 (tpp) REVERT: C 54 ILE cc_start: 0.9367 (mt) cc_final: 0.8959 (tp) REVERT: C 65 GLN cc_start: 0.8826 (tt0) cc_final: 0.8585 (tt0) REVERT: C 95 MET cc_start: 0.8750 (mmm) cc_final: 0.7893 (mmt) REVERT: C 108 ASP cc_start: 0.9171 (m-30) cc_final: 0.8964 (t0) REVERT: C 166 ILE cc_start: 0.9483 (mm) cc_final: 0.9182 (tp) REVERT: C 173 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7245 (pmt100) REVERT: C 192 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8981 (tt) REVERT: C 231 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8835 (mm-40) REVERT: C 235 ASP cc_start: 0.9140 (t70) cc_final: 0.8924 (t0) REVERT: C 254 CYS cc_start: 0.9028 (m) cc_final: 0.8600 (m) REVERT: C 296 MET cc_start: 0.8484 (ttt) cc_final: 0.7802 (ttm) REVERT: C 346 MET cc_start: 0.9261 (ppp) cc_final: 0.8744 (tmm) REVERT: C 360 GLU cc_start: 0.9098 (tt0) cc_final: 0.8822 (tm-30) REVERT: C 367 GLU cc_start: 0.8607 (tp30) cc_final: 0.8249 (tp30) REVERT: C 368 MET cc_start: 0.9362 (mmm) cc_final: 0.8668 (tpp) REVERT: C 458 MET cc_start: 0.8316 (mmm) cc_final: 0.7999 (mmm) REVERT: C 487 GLU cc_start: 0.9382 (tp30) cc_final: 0.9099 (tm-30) REVERT: C 523 ASN cc_start: 0.9296 (t0) cc_final: 0.9059 (t0) REVERT: C 540 MET cc_start: 0.9072 (ptm) cc_final: 0.8781 (ptm) REVERT: C 573 HIS cc_start: 0.8920 (t70) cc_final: 0.8536 (t70) REVERT: C 608 MET cc_start: 0.9349 (mtm) cc_final: 0.9011 (mtp) REVERT: D 51 SER cc_start: 0.9116 (t) cc_final: 0.8883 (p) REVERT: D 113 GLU cc_start: 0.8830 (tt0) cc_final: 0.8276 (tm-30) REVERT: D 234 MET cc_start: 0.7875 (mtm) cc_final: 0.7217 (mtm) REVERT: D 238 MET cc_start: 0.8647 (tpp) cc_final: 0.8173 (tpt) REVERT: D 250 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8923 (tm-30) REVERT: D 254 MET cc_start: 0.8122 (mmm) cc_final: 0.7873 (mmm) REVERT: D 268 THR cc_start: 0.9006 (p) cc_final: 0.8727 (t) REVERT: D 270 GLU cc_start: 0.9257 (tt0) cc_final: 0.8808 (tt0) REVERT: D 300 MET cc_start: 0.9524 (mmm) cc_final: 0.8870 (mmm) REVERT: D 305 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8701 (mt-10) REVERT: D 358 ASN cc_start: 0.8875 (m-40) cc_final: 0.8657 (m110) REVERT: D 410 MET cc_start: 0.8582 (mtt) cc_final: 0.8271 (mtm) REVERT: D 430 LYS cc_start: 0.9648 (mmtt) cc_final: 0.9349 (tppt) REVERT: E 88 GLU cc_start: 0.8453 (tt0) cc_final: 0.8220 (tm-30) REVERT: E 90 SER cc_start: 0.9158 (t) cc_final: 0.8158 (p) REVERT: E 113 GLU cc_start: 0.9041 (tt0) cc_final: 0.8802 (tm-30) REVERT: E 183 ILE cc_start: 0.9548 (mt) cc_final: 0.9232 (pt) REVERT: E 187 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: E 207 CYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9070 (t) REVERT: E 234 MET cc_start: 0.8740 (mpp) cc_final: 0.7670 (mpp) REVERT: E 238 MET cc_start: 0.9014 (tpt) cc_final: 0.8748 (tpp) REVERT: E 293 VAL cc_start: 0.9692 (t) cc_final: 0.9366 (m) REVERT: E 355 THR cc_start: 0.8999 (m) cc_final: 0.8609 (p) REVERT: E 402 MET cc_start: 0.8459 (ttt) cc_final: 0.7969 (ttt) REVERT: F 85 GLN cc_start: 0.9180 (tt0) cc_final: 0.8810 (tp-100) REVERT: F 87 LEU cc_start: 0.9108 (mt) cc_final: 0.8855 (mt) REVERT: F 88 GLU cc_start: 0.8897 (tt0) cc_final: 0.8430 (tm-30) REVERT: F 127 MET cc_start: 0.9265 (mtp) cc_final: 0.8934 (mtp) REVERT: F 137 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9178 (mttt) REVERT: F 180 MET cc_start: 0.8522 (mtp) cc_final: 0.8301 (mmm) REVERT: F 234 MET cc_start: 0.7994 (ptt) cc_final: 0.7747 (ptt) REVERT: F 271 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7852 (ttm110) REVERT: F 283 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8787 (mt-10) REVERT: F 288 GLN cc_start: 0.9327 (mt0) cc_final: 0.8508 (mt0) REVERT: F 327 MET cc_start: 0.9378 (ttm) cc_final: 0.9152 (ttp) REVERT: F 360 ASP cc_start: 0.8838 (t0) cc_final: 0.8320 (t0) REVERT: F 417 ASP cc_start: 0.9070 (m-30) cc_final: 0.8670 (m-30) REVERT: F 494 ARG cc_start: 0.8678 (mmt90) cc_final: 0.8354 (mmm-85) REVERT: H 24 LYS cc_start: 0.9445 (tmmt) cc_final: 0.9215 (tmmt) REVERT: H 58 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7894 (tmm) REVERT: H 78 ASP cc_start: 0.7795 (t0) cc_final: 0.7479 (t0) REVERT: H 117 ASP cc_start: 0.6970 (t0) cc_final: 0.6758 (t0) REVERT: H 152 GLN cc_start: 0.8492 (mt0) cc_final: 0.8232 (mt0) REVERT: H 192 ASP cc_start: 0.9026 (m-30) cc_final: 0.8558 (t0) REVERT: I 68 LYS cc_start: 0.9534 (mttt) cc_final: 0.9310 (mttt) REVERT: I 76 MET cc_start: 0.9459 (mmp) cc_final: 0.9203 (mpp) REVERT: I 129 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8599 (tp30) REVERT: I 132 MET cc_start: 0.9016 (mtt) cc_final: 0.8758 (mtt) REVERT: J 154 MET cc_start: 0.9463 (mtt) cc_final: 0.9230 (ptp) REVERT: J 194 ASN cc_start: 0.8692 (t0) cc_final: 0.8454 (t0) REVERT: J 196 LEU cc_start: 0.9529 (tp) cc_final: 0.9328 (mt) REVERT: K 93 ASP cc_start: 0.9439 (m-30) cc_final: 0.9203 (m-30) REVERT: K 132 MET cc_start: 0.8170 (mmt) cc_final: 0.7466 (mmm) REVERT: K 175 GLU cc_start: 0.9318 (mp0) cc_final: 0.8748 (mm-30) REVERT: K 182 GLU cc_start: 0.7965 (tt0) cc_final: 0.7691 (tm-30) REVERT: K 208 MET cc_start: 0.9353 (mtt) cc_final: 0.8717 (mtt) REVERT: L 28 LEU cc_start: 0.8332 (tp) cc_final: 0.7380 (tp) REVERT: L 31 ASN cc_start: 0.8473 (p0) cc_final: 0.8016 (p0) REVERT: L 46 ASN cc_start: 0.8697 (p0) cc_final: 0.8381 (p0) REVERT: L 108 ARG cc_start: 0.9091 (tpp80) cc_final: 0.8787 (tpp80) REVERT: M 84 MET cc_start: 0.8847 (mtt) cc_final: 0.8527 (ttm) REVERT: Q 46 ARG cc_start: 0.9438 (mtp85) cc_final: 0.9018 (mtp85) REVERT: Q 62 PHE cc_start: 0.9209 (t80) cc_final: 0.8950 (t80) REVERT: Q 115 MET cc_start: 0.9463 (mtp) cc_final: 0.9257 (ptp) REVERT: Q 129 LYS cc_start: 0.9534 (mttt) cc_final: 0.9071 (mmmt) REVERT: Q 217 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9172 (mm) REVERT: R 33 MET cc_start: 0.9124 (tpp) cc_final: 0.8900 (tmm) REVERT: R 109 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9245 (mm-30) REVERT: R 115 MET cc_start: 0.9384 (mmm) cc_final: 0.9117 (tpp) REVERT: R 125 ASP cc_start: 0.9274 (m-30) cc_final: 0.9013 (p0) REVERT: R 130 LEU cc_start: 0.9442 (mt) cc_final: 0.8968 (tp) REVERT: R 185 LEU cc_start: 0.9493 (tp) cc_final: 0.9275 (tt) REVERT: R 188 MET cc_start: 0.7980 (tpt) cc_final: 0.6752 (tmm) REVERT: R 203 TYR cc_start: 0.9214 (t80) cc_final: 0.9012 (t80) REVERT: S 10 MET cc_start: 0.8164 (ttm) cc_final: 0.7931 (ttm) REVERT: S 109 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9092 (mm-30) REVERT: S 129 LYS cc_start: 0.9698 (mttt) cc_final: 0.9460 (ptpp) REVERT: S 159 LEU cc_start: 0.9434 (tp) cc_final: 0.9207 (mt) REVERT: S 188 MET cc_start: 0.9072 (tpp) cc_final: 0.8549 (tpp) REVERT: S 192 LYS cc_start: 0.9410 (mttt) cc_final: 0.8887 (mtpp) REVERT: a 375 GLN cc_start: 0.8237 (tp40) cc_final: 0.7764 (tp-100) REVERT: a 379 ASP cc_start: 0.7705 (m-30) cc_final: 0.6868 (m-30) REVERT: a 536 PHE cc_start: 0.7370 (m-80) cc_final: 0.7163 (m-80) REVERT: a 641 ILE cc_start: 0.8881 (mm) cc_final: 0.8590 (mm) REVERT: a 645 MET cc_start: 0.7529 (ptt) cc_final: 0.7237 (ppp) REVERT: a 651 MET cc_start: 0.6807 (mtm) cc_final: 0.5669 (tpt) REVERT: a 745 LEU cc_start: 0.9038 (mp) cc_final: 0.8750 (tp) REVERT: a 791 LEU cc_start: 0.7155 (mt) cc_final: 0.5325 (tp) REVERT: b 36 ASP cc_start: 0.7388 (t0) cc_final: 0.6964 (p0) REVERT: b 203 MET cc_start: 0.5269 (mmt) cc_final: 0.4995 (mmp) REVERT: c 448 ARG cc_start: 0.8067 (pmm-80) cc_final: 0.7564 (mtm110) REVERT: d 221 PHE cc_start: 0.8152 (m-80) cc_final: 0.7889 (m-80) REVERT: d 350 ILE cc_start: 0.8111 (pt) cc_final: 0.7901 (pt) REVERT: g 13 PHE cc_start: 0.8238 (t80) cc_final: 0.7393 (t80) REVERT: g 26 SER cc_start: 0.8331 (m) cc_final: 0.8099 (p) REVERT: g 144 TYR cc_start: 0.7538 (m-10) cc_final: 0.7303 (m-80) REVERT: h 32 TYR cc_start: 0.7836 (t80) cc_final: 0.7583 (t80) REVERT: h 53 MET cc_start: 0.7765 (mmp) cc_final: 0.7490 (pmm) REVERT: h 108 PHE cc_start: 0.8118 (m-80) cc_final: 0.7857 (m-80) REVERT: h 155 LYS cc_start: 0.6842 (tptm) cc_final: 0.6416 (tptm) REVERT: i 53 MET cc_start: 0.8346 (mmt) cc_final: 0.7393 (ttt) REVERT: i 78 ASN cc_start: 0.7991 (p0) cc_final: 0.7783 (p0) REVERT: j 60 VAL cc_start: 0.8935 (m) cc_final: 0.8716 (p) REVERT: j 76 ILE cc_start: 0.9035 (mm) cc_final: 0.8688 (tt) REVERT: k 25 PHE cc_start: 0.8866 (m-80) cc_final: 0.8382 (m-80) REVERT: k 28 MET cc_start: 0.8652 (mtp) cc_final: 0.8318 (ttt) REVERT: k 61 MET cc_start: 0.8383 (mmp) cc_final: 0.7672 (mmm) REVERT: k 68 TYR cc_start: 0.8634 (m-80) cc_final: 0.8418 (m-80) REVERT: k 108 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7433 (t80) REVERT: k 139 GLU cc_start: 0.8207 (tp30) cc_final: 0.7624 (tp30) REVERT: l 54 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7097 (ptpp) REVERT: l 68 TYR cc_start: 0.8889 (m-10) cc_final: 0.8675 (m-80) REVERT: m 25 PHE cc_start: 0.7774 (m-80) cc_final: 0.7506 (m-80) REVERT: m 121 THR cc_start: 0.6795 (m) cc_final: 0.6589 (p) REVERT: m 132 ILE cc_start: 0.7780 (mm) cc_final: 0.7537 (mt) REVERT: n 23 MET cc_start: 0.7039 (tpt) cc_final: 0.6661 (ppp) REVERT: n 32 TYR cc_start: 0.7478 (t80) cc_final: 0.6816 (t80) REVERT: o 104 LEU cc_start: 0.7844 (mt) cc_final: 0.7619 (mt) REVERT: o 137 PHE cc_start: 0.7455 (m-80) cc_final: 0.7147 (m-80) REVERT: o 144 TYR cc_start: 0.7366 (m-10) cc_final: 0.7027 (m-80) outliers start: 144 outliers final: 71 residues processed: 1532 average time/residue: 0.5528 time to fit residues: 1459.6505 Evaluate side-chains 1255 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1174 time to evaluate : 5.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 171 ASP Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 614 ILE Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain c residue 414 PHE Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 129 CYS Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 151 ILE Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 60 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 422 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 632 optimal weight: 0.9980 chunk 517 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 761 optimal weight: 2.9990 chunk 822 optimal weight: 6.9990 chunk 678 optimal weight: 6.9990 chunk 755 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 610 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 261 GLN D 156 GLN D 497 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 85 GLN H 137 ASN I 126 GLN K 74 ASN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN R 184 HIS ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 ASN ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 142 ASN ** d 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 330 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 63459 Z= 0.266 Angle : 0.689 12.921 86074 Z= 0.350 Chirality : 0.044 0.306 10040 Planarity : 0.005 0.108 11108 Dihedral : 4.551 116.229 9066 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.00 % Allowed : 14.45 % Favored : 82.55 % 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: 1.17 (0.09), residues: 8372 helix: 1.50 (0.07), residues: 4912 sheet: 0.08 (0.19), residues: 697 loop : -0.24 (0.12), residues: 2763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 49 HIS 0.006 0.001 HIS E 199 PHE 0.042 0.002 PHE R 62 TYR 0.028 0.002 TYR o 10 ARG 0.009 0.001 ARG h 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1396 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1213 time to evaluate : 5.320 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: A 34 MET cc_start: 0.8592 (mmm) cc_final: 0.8291 (mmm) REVERT: A 100 ASP cc_start: 0.8900 (t0) cc_final: 0.8587 (t0) REVERT: A 147 ILE cc_start: 0.9693 (pt) cc_final: 0.9357 (mm) REVERT: A 306 MET cc_start: 0.9018 (ptm) cc_final: 0.8495 (ppp) REVERT: A 346 MET cc_start: 0.8900 (ttt) cc_final: 0.8279 (tmm) REVERT: A 362 SER cc_start: 0.9755 (t) cc_final: 0.9373 (p) REVERT: A 439 LEU cc_start: 0.9375 (tp) cc_final: 0.8895 (tp) REVERT: A 540 MET cc_start: 0.8810 (mtp) cc_final: 0.8582 (mtp) REVERT: A 550 MET cc_start: 0.9344 (ttm) cc_final: 0.8803 (ttm) REVERT: A 596 LYS cc_start: 0.9348 (tttm) cc_final: 0.9123 (tppt) REVERT: A 608 MET cc_start: 0.9462 (ttm) cc_final: 0.9143 (ttt) REVERT: A 615 LEU cc_start: 0.8619 (tp) cc_final: 0.8335 (mt) REVERT: B 61 MET cc_start: 0.9225 (mtp) cc_final: 0.8868 (mmm) REVERT: B 167 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8444 (mtt) REVERT: B 168 LEU cc_start: 0.9199 (tp) cc_final: 0.8956 (tp) REVERT: B 340 MET cc_start: 0.9263 (mtt) cc_final: 0.8666 (ttm) REVERT: B 387 GLU cc_start: 0.8696 (tp30) cc_final: 0.8112 (tm-30) REVERT: B 450 TRP cc_start: 0.6462 (m-10) cc_final: 0.6225 (m-90) REVERT: B 544 MET cc_start: 0.9436 (mtt) cc_final: 0.9148 (mmm) REVERT: B 550 MET cc_start: 0.9501 (mmm) cc_final: 0.9244 (mmp) REVERT: B 584 MET cc_start: 0.8883 (mtm) cc_final: 0.7316 (mtp) REVERT: C 65 GLN cc_start: 0.8690 (tt0) cc_final: 0.8071 (pt0) REVERT: C 95 MET cc_start: 0.8901 (mmm) cc_final: 0.8060 (mmt) REVERT: C 166 ILE cc_start: 0.9467 (mm) cc_final: 0.9129 (tp) REVERT: C 173 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7214 (pmt100) REVERT: C 231 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8825 (mm-40) REVERT: C 254 CYS cc_start: 0.8961 (m) cc_final: 0.8574 (m) REVERT: C 296 MET cc_start: 0.8223 (ttt) cc_final: 0.7875 (ttm) REVERT: C 347 MET cc_start: 0.8947 (mpp) cc_final: 0.8708 (mpp) REVERT: C 360 GLU cc_start: 0.9158 (tt0) cc_final: 0.8870 (tm-30) REVERT: C 367 GLU cc_start: 0.8809 (tp30) cc_final: 0.8377 (tp30) REVERT: C 368 MET cc_start: 0.9388 (mmm) cc_final: 0.8790 (tpp) REVERT: C 401 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7842 (tm-30) REVERT: C 441 GLN cc_start: 0.9251 (mt0) cc_final: 0.8978 (mm-40) REVERT: C 487 GLU cc_start: 0.9446 (tp30) cc_final: 0.9099 (tm-30) REVERT: C 550 MET cc_start: 0.9009 (ttm) cc_final: 0.8706 (ttp) REVERT: C 573 HIS cc_start: 0.8942 (t70) cc_final: 0.8558 (t70) REVERT: C 608 MET cc_start: 0.9248 (mtm) cc_final: 0.9007 (ptp) REVERT: D 234 MET cc_start: 0.7949 (mtm) cc_final: 0.7021 (mtm) REVERT: D 238 MET cc_start: 0.8644 (tpp) cc_final: 0.8181 (tpt) REVERT: D 250 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8966 (tm-30) REVERT: D 268 THR cc_start: 0.9160 (p) cc_final: 0.8895 (t) REVERT: D 300 MET cc_start: 0.9473 (mmm) cc_final: 0.8786 (mmm) REVERT: D 305 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8753 (mt-10) REVERT: D 327 MET cc_start: 0.9100 (tpp) cc_final: 0.8741 (tpp) REVERT: D 351 ILE cc_start: 0.9530 (mt) cc_final: 0.9283 (mm) REVERT: D 410 MET cc_start: 0.8621 (mtt) cc_final: 0.8341 (mtm) REVERT: E 88 GLU cc_start: 0.8509 (tt0) cc_final: 0.8232 (tm-30) REVERT: E 90 SER cc_start: 0.9219 (t) cc_final: 0.8287 (p) REVERT: E 113 GLU cc_start: 0.9047 (tt0) cc_final: 0.8791 (tm-30) REVERT: E 183 ILE cc_start: 0.9482 (mt) cc_final: 0.9016 (pt) REVERT: E 234 MET cc_start: 0.8776 (mpp) cc_final: 0.8154 (mpp) REVERT: E 238 MET cc_start: 0.9077 (tpt) cc_final: 0.8829 (tpp) REVERT: E 355 THR cc_start: 0.9186 (m) cc_final: 0.8780 (p) REVERT: E 402 MET cc_start: 0.8550 (ttt) cc_final: 0.7898 (ttt) REVERT: F 85 GLN cc_start: 0.9210 (tt0) cc_final: 0.8807 (tp-100) REVERT: F 87 LEU cc_start: 0.9165 (mt) cc_final: 0.8890 (mt) REVERT: F 88 GLU cc_start: 0.8952 (tt0) cc_final: 0.8461 (tm-30) REVERT: F 127 MET cc_start: 0.9275 (mtp) cc_final: 0.8959 (mtp) REVERT: F 137 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9227 (mmmt) REVERT: F 180 MET cc_start: 0.8660 (mtp) cc_final: 0.8421 (mmm) REVERT: F 271 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8126 (ttm110) REVERT: F 283 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8790 (mt-10) REVERT: F 288 GLN cc_start: 0.9461 (mt0) cc_final: 0.8634 (mt0) REVERT: F 327 MET cc_start: 0.9448 (ttm) cc_final: 0.9150 (ttm) REVERT: F 360 ASP cc_start: 0.8871 (t0) cc_final: 0.8369 (t0) REVERT: F 367 ASP cc_start: 0.9019 (t70) cc_final: 0.8812 (t0) REVERT: F 402 MET cc_start: 0.9093 (ttm) cc_final: 0.8094 (ttm) REVERT: F 417 ASP cc_start: 0.9043 (m-30) cc_final: 0.8754 (m-30) REVERT: F 494 ARG cc_start: 0.8723 (mmt90) cc_final: 0.8453 (mmm-85) REVERT: H 58 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7788 (tmm) REVERT: H 78 ASP cc_start: 0.7941 (t0) cc_final: 0.7617 (t0) REVERT: H 152 GLN cc_start: 0.8712 (mt0) cc_final: 0.8324 (mt0) REVERT: H 192 ASP cc_start: 0.9035 (m-30) cc_final: 0.8538 (t0) REVERT: I 76 MET cc_start: 0.9558 (mmp) cc_final: 0.9295 (mmm) REVERT: I 132 MET cc_start: 0.9022 (mtt) cc_final: 0.8644 (mtt) REVERT: I 201 ASP cc_start: 0.9084 (m-30) cc_final: 0.8722 (p0) REVERT: I 207 MET cc_start: 0.9648 (mmm) cc_final: 0.9222 (mmm) REVERT: I 208 MET cc_start: 0.9154 (mmm) cc_final: 0.8675 (mmm) REVERT: J 129 GLU cc_start: 0.8067 (tt0) cc_final: 0.7013 (tt0) REVERT: J 132 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7728 (mpt) REVERT: J 175 GLU cc_start: 0.9229 (pm20) cc_final: 0.9023 (mm-30) REVERT: J 207 MET cc_start: 0.9174 (tpp) cc_final: 0.8798 (tpp) REVERT: J 210 GLU cc_start: 0.8528 (mp0) cc_final: 0.8275 (mp0) REVERT: K 73 SER cc_start: 0.9615 (t) cc_final: 0.9305 (p) REVERT: K 93 ASP cc_start: 0.9517 (m-30) cc_final: 0.9224 (m-30) REVERT: K 97 GLU cc_start: 0.9391 (tp30) cc_final: 0.9128 (tp30) REVERT: K 129 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8599 (tt0) REVERT: K 132 MET cc_start: 0.8068 (mmt) cc_final: 0.7332 (mmm) REVERT: K 175 GLU cc_start: 0.9329 (mp0) cc_final: 0.8787 (mm-30) REVERT: K 182 GLU cc_start: 0.7858 (tt0) cc_final: 0.7635 (tm-30) REVERT: K 208 MET cc_start: 0.9283 (mtt) cc_final: 0.8713 (mtt) REVERT: L 28 LEU cc_start: 0.8370 (tp) cc_final: 0.8125 (tp) REVERT: L 31 ASN cc_start: 0.8545 (p0) cc_final: 0.8083 (p0) REVERT: L 69 TYR cc_start: 0.7196 (p90) cc_final: 0.6574 (p90) REVERT: M 84 MET cc_start: 0.8936 (mtt) cc_final: 0.8664 (ttm) REVERT: N 72 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8807 (mm-30) REVERT: N 84 MET cc_start: 0.9244 (mmp) cc_final: 0.9032 (mtm) REVERT: N 105 ASP cc_start: 0.9260 (t0) cc_final: 0.8653 (p0) REVERT: Q 32 CYS cc_start: 0.9548 (m) cc_final: 0.9319 (m) REVERT: Q 115 MET cc_start: 0.9579 (mtp) cc_final: 0.9295 (ptp) REVERT: Q 129 LYS cc_start: 0.9605 (mttt) cc_final: 0.9115 (mmmt) REVERT: R 33 MET cc_start: 0.9186 (tpp) cc_final: 0.8911 (tmm) REVERT: R 109 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9261 (mm-30) REVERT: R 115 MET cc_start: 0.9451 (mmm) cc_final: 0.9115 (tpp) REVERT: R 130 LEU cc_start: 0.9392 (mt) cc_final: 0.9008 (tp) REVERT: R 166 TYR cc_start: 0.9112 (m-10) cc_final: 0.8465 (m-80) REVERT: R 188 MET cc_start: 0.8188 (tpt) cc_final: 0.7891 (tpp) REVERT: R 194 ASP cc_start: 0.9566 (OUTLIER) cc_final: 0.9243 (p0) REVERT: R 203 TYR cc_start: 0.9224 (t80) cc_final: 0.8970 (t80) REVERT: S 10 MET cc_start: 0.8213 (ttm) cc_final: 0.7874 (ttm) REVERT: S 109 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9091 (mm-30) REVERT: S 129 LYS cc_start: 0.9710 (mttt) cc_final: 0.9450 (ptpp) REVERT: S 188 MET cc_start: 0.9100 (tpp) cc_final: 0.8604 (tpp) REVERT: S 192 LYS cc_start: 0.9391 (mttt) cc_final: 0.8862 (mtpp) REVERT: a 406 MET cc_start: 0.6934 (mtt) cc_final: 0.6702 (mtm) REVERT: a 536 PHE cc_start: 0.7433 (m-80) cc_final: 0.7187 (m-80) REVERT: a 594 LYS cc_start: 0.8174 (tttp) cc_final: 0.7947 (ttmt) REVERT: a 651 MET cc_start: 0.6943 (mtm) cc_final: 0.5907 (mmm) REVERT: b 36 ASP cc_start: 0.7372 (t0) cc_final: 0.7013 (p0) REVERT: b 41 LEU cc_start: 0.8532 (mm) cc_final: 0.8082 (tp) REVERT: b 44 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8209 (p) REVERT: b 107 MET cc_start: 0.6749 (mmm) cc_final: 0.6416 (mmm) REVERT: c 421 MET cc_start: 0.8313 (ptt) cc_final: 0.7791 (mtp) REVERT: c 447 ASP cc_start: 0.8451 (p0) cc_final: 0.7761 (p0) REVERT: d 183 ASN cc_start: 0.8850 (m-40) cc_final: 0.7350 (m-40) REVERT: d 321 LEU cc_start: 0.8735 (mt) cc_final: 0.8370 (mt) REVERT: g 13 PHE cc_start: 0.8231 (t80) cc_final: 0.7061 (t80) REVERT: g 144 TYR cc_start: 0.7377 (m-10) cc_final: 0.7151 (m-80) REVERT: h 46 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.7760 (p) REVERT: h 53 MET cc_start: 0.7839 (mmp) cc_final: 0.7464 (pmm) REVERT: h 155 LYS cc_start: 0.6964 (tptm) cc_final: 0.6460 (tptm) REVERT: i 53 MET cc_start: 0.8208 (mmt) cc_final: 0.7212 (ttt) REVERT: i 78 ASN cc_start: 0.7813 (p0) cc_final: 0.7567 (p0) REVERT: i 108 PHE cc_start: 0.8516 (m-80) cc_final: 0.8191 (m-10) REVERT: i 137 PHE cc_start: 0.8329 (m-80) cc_final: 0.8047 (m-80) REVERT: i 152 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8913 (tp) REVERT: j 23 MET cc_start: 0.8633 (tmm) cc_final: 0.8096 (ppp) REVERT: j 32 TYR cc_start: 0.9137 (t80) cc_final: 0.8680 (t80) REVERT: j 76 ILE cc_start: 0.8938 (mm) cc_final: 0.8695 (tt) REVERT: j 131 MET cc_start: 0.7788 (ptm) cc_final: 0.7583 (ptm) REVERT: k 25 PHE cc_start: 0.8938 (m-80) cc_final: 0.8492 (m-80) REVERT: k 28 MET cc_start: 0.8679 (mtp) cc_final: 0.8423 (ttt) REVERT: k 44 MET cc_start: 0.7795 (tmm) cc_final: 0.7214 (tmm) REVERT: k 61 MET cc_start: 0.8281 (mmp) cc_final: 0.7701 (mtt) REVERT: k 108 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7386 (t80) REVERT: k 115 ASP cc_start: 0.7710 (t70) cc_final: 0.7485 (t0) REVERT: l 44 MET cc_start: 0.8076 (mmm) cc_final: 0.6519 (mmm) REVERT: m 25 PHE cc_start: 0.7876 (m-80) cc_final: 0.7577 (m-80) REVERT: m 121 THR cc_start: 0.6841 (m) cc_final: 0.6433 (p) REVERT: m 131 MET cc_start: 0.7099 (ptt) cc_final: 0.6785 (ptt) REVERT: m 132 ILE cc_start: 0.7853 (mm) cc_final: 0.7553 (mt) REVERT: n 23 MET cc_start: 0.7153 (tpt) cc_final: 0.6851 (tpt) REVERT: n 104 LEU cc_start: 0.8805 (mt) cc_final: 0.8542 (mt) REVERT: o 137 PHE cc_start: 0.7423 (m-80) cc_final: 0.7079 (m-80) outliers start: 183 outliers final: 100 residues processed: 1312 average time/residue: 0.5753 time to fit residues: 1309.9874 Evaluate side-chains 1174 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1065 time to evaluate : 5.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 171 ASP Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 592 PHE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 614 ILE Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain a residue 809 VAL Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain c residue 443 LEU Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 129 CYS Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 151 ILE Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 23 MET Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 306 VAL Chi-restraints excluded: chain p residue 319 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 752 optimal weight: 7.9990 chunk 572 optimal weight: 8.9990 chunk 395 optimal weight: 40.0000 chunk 84 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 511 optimal weight: 9.9990 chunk 764 optimal weight: 7.9990 chunk 809 optimal weight: 0.0270 chunk 399 optimal weight: 6.9990 chunk 724 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 overall best weight: 5.4046 ------------------------------------------------------------------------------- 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 484 GLN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN F 42 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 85 GLN H 137 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 GLN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN Q 160 GLN R 19 HIS S 198 HIS a 720 HIS ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 128 HIS b 197 GLN d 38 GLN ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 92 GLN ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 63459 Z= 0.359 Angle : 0.719 16.983 86074 Z= 0.369 Chirality : 0.044 0.274 10040 Planarity : 0.005 0.068 11108 Dihedral : 4.624 122.596 9065 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.46 % Allowed : 14.81 % Favored : 81.73 % 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: 1.09 (0.09), residues: 8372 helix: 1.43 (0.07), residues: 4928 sheet: 0.17 (0.20), residues: 686 loop : -0.32 (0.12), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP f 21 HIS 0.008 0.001 HIS E 199 PHE 0.044 0.002 PHE f 33 TYR 0.046 0.002 TYR h 144 ARG 0.028 0.001 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1078 time to evaluate : 5.452 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: A 95 MET cc_start: 0.8727 (tpp) cc_final: 0.8486 (tpp) REVERT: A 100 ASP cc_start: 0.8973 (t0) cc_final: 0.8513 (t0) REVERT: A 231 GLN cc_start: 0.9354 (mm-40) cc_final: 0.9052 (mm-40) REVERT: A 306 MET cc_start: 0.9079 (ptm) cc_final: 0.8586 (ppp) REVERT: A 318 MET cc_start: 0.9317 (mmt) cc_final: 0.8533 (mpp) REVERT: A 324 GLU cc_start: 0.9286 (tt0) cc_final: 0.8772 (tm-30) REVERT: A 346 MET cc_start: 0.8903 (ttt) cc_final: 0.8007 (tmm) REVERT: A 368 MET cc_start: 0.9287 (tpp) cc_final: 0.9068 (tpp) REVERT: A 399 GLU cc_start: 0.8713 (tp30) cc_final: 0.8275 (tp30) REVERT: A 437 LYS cc_start: 0.9602 (mmmm) cc_final: 0.9146 (tptp) REVERT: A 439 LEU cc_start: 0.9415 (tp) cc_final: 0.8953 (tp) REVERT: A 540 MET cc_start: 0.8831 (mtp) cc_final: 0.8617 (mtp) REVERT: A 541 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9439 (tt) REVERT: A 550 MET cc_start: 0.9383 (ttm) cc_final: 0.8934 (ttm) REVERT: A 570 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9316 (tp) REVERT: A 596 LYS cc_start: 0.9319 (tttm) cc_final: 0.9076 (tppt) REVERT: A 608 MET cc_start: 0.9533 (ttm) cc_final: 0.9133 (ttp) REVERT: B 61 MET cc_start: 0.9235 (mtp) cc_final: 0.8893 (mmm) REVERT: B 167 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8476 (mtt) REVERT: B 168 LEU cc_start: 0.9181 (tp) cc_final: 0.8962 (tp) REVERT: B 252 PHE cc_start: 0.6716 (m-80) cc_final: 0.6436 (m-80) REVERT: B 306 MET cc_start: 0.9125 (mmt) cc_final: 0.8829 (mmt) REVERT: B 340 MET cc_start: 0.9377 (mtt) cc_final: 0.8699 (ttm) REVERT: B 367 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: B 387 GLU cc_start: 0.8713 (tp30) cc_final: 0.8179 (tm-30) REVERT: B 544 MET cc_start: 0.9436 (mtt) cc_final: 0.9213 (mtp) REVERT: B 550 MET cc_start: 0.9513 (mmm) cc_final: 0.9294 (mmp) REVERT: C 65 GLN cc_start: 0.8657 (tt0) cc_final: 0.8080 (pt0) REVERT: C 166 ILE cc_start: 0.9511 (mm) cc_final: 0.9131 (tp) REVERT: C 173 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7597 (pmt100) REVERT: C 231 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8827 (mm-40) REVERT: C 254 CYS cc_start: 0.8772 (m) cc_final: 0.8486 (m) REVERT: C 296 MET cc_start: 0.8307 (ttt) cc_final: 0.8021 (ttm) REVERT: C 318 MET cc_start: 0.9104 (mtt) cc_final: 0.8320 (mtp) REVERT: C 360 GLU cc_start: 0.9166 (tt0) cc_final: 0.8923 (tm-30) REVERT: C 441 GLN cc_start: 0.9326 (mt0) cc_final: 0.9087 (mm-40) REVERT: C 487 GLU cc_start: 0.9496 (tp30) cc_final: 0.9090 (tm-30) REVERT: C 550 MET cc_start: 0.9004 (ttm) cc_final: 0.8771 (ttp) REVERT: C 573 HIS cc_start: 0.8972 (t70) cc_final: 0.8571 (t-90) REVERT: D 234 MET cc_start: 0.8205 (mtm) cc_final: 0.7685 (mtm) REVERT: D 238 MET cc_start: 0.8688 (tpp) cc_final: 0.8280 (tpt) REVERT: D 250 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9069 (tm-30) REVERT: D 254 MET cc_start: 0.8390 (mmm) cc_final: 0.7967 (mmm) REVERT: D 268 THR cc_start: 0.9306 (p) cc_final: 0.9078 (t) REVERT: D 300 MET cc_start: 0.9474 (mmm) cc_final: 0.8813 (mmm) REVERT: D 330 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8522 (t0) REVERT: D 351 ILE cc_start: 0.9495 (mt) cc_final: 0.9257 (mm) REVERT: D 402 MET cc_start: 0.8772 (tmm) cc_final: 0.8499 (tmm) REVERT: D 410 MET cc_start: 0.8787 (mtt) cc_final: 0.8547 (mtm) REVERT: E 88 GLU cc_start: 0.8449 (tt0) cc_final: 0.8071 (tm-30) REVERT: E 89 VAL cc_start: 0.9716 (OUTLIER) cc_final: 0.9269 (m) REVERT: E 90 SER cc_start: 0.9317 (t) cc_final: 0.8599 (p) REVERT: E 180 MET cc_start: 0.8716 (mmm) cc_final: 0.8502 (mmm) REVERT: E 234 MET cc_start: 0.8931 (mpp) cc_final: 0.7986 (mpp) REVERT: E 254 MET cc_start: 0.8950 (mmm) cc_final: 0.8351 (tpp) REVERT: E 355 THR cc_start: 0.9225 (m) cc_final: 0.8694 (p) REVERT: E 356 MET cc_start: 0.8160 (ttm) cc_final: 0.7865 (ttm) REVERT: E 402 MET cc_start: 0.8555 (ttt) cc_final: 0.7905 (ttt) REVERT: F 76 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9028 (mm) REVERT: F 85 GLN cc_start: 0.9253 (tt0) cc_final: 0.8808 (tp-100) REVERT: F 87 LEU cc_start: 0.9179 (mt) cc_final: 0.8931 (mt) REVERT: F 88 GLU cc_start: 0.9014 (tt0) cc_final: 0.8474 (tm-30) REVERT: F 127 MET cc_start: 0.9166 (mtp) cc_final: 0.8962 (mtp) REVERT: F 180 MET cc_start: 0.8901 (mtp) cc_final: 0.8333 (mmm) REVERT: F 247 ASP cc_start: 0.9330 (m-30) cc_final: 0.8192 (t0) REVERT: F 271 ARG cc_start: 0.8775 (mtt180) cc_final: 0.8225 (ttm110) REVERT: F 283 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8532 (mt-10) REVERT: F 327 MET cc_start: 0.9516 (ttm) cc_final: 0.9190 (ttm) REVERT: F 360 ASP cc_start: 0.8891 (t0) cc_final: 0.8419 (t0) REVERT: F 367 ASP cc_start: 0.9138 (t70) cc_final: 0.8896 (t0) REVERT: F 417 ASP cc_start: 0.9114 (m-30) cc_final: 0.8846 (m-30) REVERT: F 491 MET cc_start: 0.9208 (mtp) cc_final: 0.8955 (mtp) REVERT: F 494 ARG cc_start: 0.8814 (mmt90) cc_final: 0.8503 (mmm-85) REVERT: H 24 LYS cc_start: 0.9468 (tmmt) cc_final: 0.9232 (tmmt) REVERT: H 58 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7857 (tmm) REVERT: H 78 ASP cc_start: 0.7998 (t0) cc_final: 0.7665 (t0) REVERT: H 192 ASP cc_start: 0.9101 (m-30) cc_final: 0.8622 (t0) REVERT: I 76 MET cc_start: 0.9617 (mmp) cc_final: 0.9339 (mmm) REVERT: I 132 MET cc_start: 0.9233 (mtt) cc_final: 0.8861 (mtt) REVERT: J 72 MET cc_start: 0.9128 (mtp) cc_final: 0.8885 (ptp) REVERT: J 102 LEU cc_start: 0.9695 (mt) cc_final: 0.9420 (mt) REVERT: J 129 GLU cc_start: 0.8085 (tt0) cc_final: 0.7500 (tt0) REVERT: J 132 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: J 175 GLU cc_start: 0.9240 (pm20) cc_final: 0.8960 (mm-30) REVERT: J 207 MET cc_start: 0.9233 (tpp) cc_final: 0.8725 (tpp) REVERT: J 210 GLU cc_start: 0.8681 (mp0) cc_final: 0.8279 (mp0) REVERT: K 93 ASP cc_start: 0.9495 (m-30) cc_final: 0.9237 (m-30) REVERT: K 97 GLU cc_start: 0.9411 (tp30) cc_final: 0.9096 (tp30) REVERT: K 125 TYR cc_start: 0.8965 (m-10) cc_final: 0.8675 (m-10) REVERT: K 129 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8506 (tt0) REVERT: K 132 MET cc_start: 0.8042 (mmt) cc_final: 0.7548 (mmm) REVERT: K 175 GLU cc_start: 0.9381 (mp0) cc_final: 0.8784 (mm-30) REVERT: K 182 GLU cc_start: 0.7900 (tt0) cc_final: 0.7642 (tm-30) REVERT: L 14 GLU cc_start: 0.8201 (pp20) cc_final: 0.7925 (pp20) REVERT: L 15 ASP cc_start: 0.8439 (p0) cc_final: 0.8159 (p0) REVERT: L 22 LEU cc_start: 0.9029 (mt) cc_final: 0.8604 (tp) REVERT: L 31 ASN cc_start: 0.8448 (p0) cc_final: 0.8084 (p0) REVERT: L 69 TYR cc_start: 0.7494 (p90) cc_final: 0.7226 (p90) REVERT: L 108 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8500 (tpp80) REVERT: M 84 MET cc_start: 0.9008 (mtt) cc_final: 0.8730 (ttm) REVERT: N 72 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8787 (mm-30) REVERT: N 100 LEU cc_start: 0.9657 (mm) cc_final: 0.9277 (pp) REVERT: N 105 ASP cc_start: 0.9303 (t0) cc_final: 0.8748 (t0) REVERT: Q 32 CYS cc_start: 0.9585 (m) cc_final: 0.9365 (m) REVERT: Q 115 MET cc_start: 0.9606 (mtp) cc_final: 0.9311 (ptp) REVERT: Q 129 LYS cc_start: 0.9663 (mttt) cc_final: 0.9227 (mmmt) REVERT: Q 234 MET cc_start: 0.9044 (tmm) cc_final: 0.8436 (ppp) REVERT: R 33 MET cc_start: 0.9226 (tpp) cc_final: 0.8949 (tmm) REVERT: R 109 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9219 (mm-30) REVERT: R 115 MET cc_start: 0.9429 (mmm) cc_final: 0.9105 (mmm) REVERT: R 126 TYR cc_start: 0.9543 (m-80) cc_final: 0.9209 (m-80) REVERT: R 153 ARG cc_start: 0.8879 (tpm170) cc_final: 0.8621 (tpm170) REVERT: R 188 MET cc_start: 0.8339 (tpt) cc_final: 0.7945 (tpt) REVERT: R 194 ASP cc_start: 0.9575 (OUTLIER) cc_final: 0.9221 (p0) REVERT: R 203 TYR cc_start: 0.9309 (t80) cc_final: 0.9044 (t80) REVERT: S 10 MET cc_start: 0.8161 (ttm) cc_final: 0.7811 (ttm) REVERT: S 109 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9133 (mm-30) REVERT: S 129 LYS cc_start: 0.9718 (mttt) cc_final: 0.9483 (ptpp) REVERT: S 188 MET cc_start: 0.9136 (tpp) cc_final: 0.8567 (tpp) REVERT: S 192 LYS cc_start: 0.9349 (mttt) cc_final: 0.8723 (mtpp) REVERT: S 234 MET cc_start: 0.8025 (tmm) cc_final: 0.7764 (ppp) REVERT: a 375 GLN cc_start: 0.8643 (tt0) cc_final: 0.8107 (tp-100) REVERT: a 536 PHE cc_start: 0.7553 (m-80) cc_final: 0.7265 (m-80) REVERT: a 580 MET cc_start: 0.8250 (ptm) cc_final: 0.7372 (ptm) REVERT: a 616 MET cc_start: 0.8337 (mtt) cc_final: 0.7455 (tmm) REVERT: a 641 ILE cc_start: 0.8958 (mm) cc_final: 0.7904 (mm) REVERT: a 745 LEU cc_start: 0.9175 (mm) cc_final: 0.8626 (mm) REVERT: b 41 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8224 (tp) REVERT: b 107 MET cc_start: 0.7083 (mmm) cc_final: 0.6798 (mmm) REVERT: d 45 LEU cc_start: 0.9050 (mt) cc_final: 0.8764 (mt) REVERT: g 13 PHE cc_start: 0.8169 (t80) cc_final: 0.7650 (t80) REVERT: g 61 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: g 139 GLU cc_start: 0.7471 (tp30) cc_final: 0.6982 (mm-30) REVERT: h 53 MET cc_start: 0.7946 (mmp) cc_final: 0.6649 (tmm) REVERT: h 90 PHE cc_start: 0.8350 (m-80) cc_final: 0.7375 (m-80) REVERT: h 144 TYR cc_start: 0.7730 (m-80) cc_final: 0.7526 (m-80) REVERT: i 53 MET cc_start: 0.8246 (mmt) cc_final: 0.7315 (ttt) REVERT: i 64 ILE cc_start: 0.9492 (mm) cc_final: 0.9291 (mm) REVERT: i 68 TYR cc_start: 0.8659 (m-10) cc_final: 0.8157 (m-80) REVERT: i 131 MET cc_start: 0.8888 (ppp) cc_final: 0.8593 (ppp) REVERT: i 155 LYS cc_start: 0.7323 (mmtt) cc_final: 0.6976 (mttm) REVERT: j 23 MET cc_start: 0.8745 (tmm) cc_final: 0.8458 (ppp) REVERT: j 47 MET cc_start: 0.8969 (ppp) cc_final: 0.8475 (ppp) REVERT: j 65 ILE cc_start: 0.9475 (mm) cc_final: 0.9077 (mm) REVERT: j 68 TYR cc_start: 0.8758 (m-10) cc_final: 0.8067 (m-80) REVERT: j 139 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8108 (tm-30) REVERT: k 17 MET cc_start: 0.9052 (tpt) cc_final: 0.8580 (tpp) REVERT: k 25 PHE cc_start: 0.8897 (m-80) cc_final: 0.8679 (m-80) REVERT: k 61 MET cc_start: 0.8432 (mmp) cc_final: 0.8206 (mmm) REVERT: k 108 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7463 (t80) REVERT: l 68 TYR cc_start: 0.8935 (m-80) cc_final: 0.8571 (m-80) REVERT: m 25 PHE cc_start: 0.7820 (m-80) cc_final: 0.7558 (m-80) REVERT: m 121 THR cc_start: 0.6907 (m) cc_final: 0.5779 (p) REVERT: m 131 MET cc_start: 0.7199 (ptt) cc_final: 0.6577 (ptt) REVERT: m 144 TYR cc_start: 0.7857 (m-80) cc_final: 0.7655 (m-80) REVERT: n 23 MET cc_start: 0.7085 (tpt) cc_final: 0.6881 (tpt) REVERT: n 28 MET cc_start: 0.8793 (tpp) cc_final: 0.8166 (mmm) REVERT: n 53 MET cc_start: 0.7386 (mmt) cc_final: 0.7172 (mmp) REVERT: n 61 MET cc_start: 0.7984 (mmm) cc_final: 0.7137 (mmm) REVERT: n 139 GLU cc_start: 0.7315 (tp30) cc_final: 0.6225 (tp30) REVERT: p 340 TYR cc_start: 0.8128 (m-80) cc_final: 0.7740 (m-80) outliers start: 211 outliers final: 141 residues processed: 1201 average time/residue: 0.5518 time to fit residues: 1150.8787 Evaluate side-chains 1154 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 999 time to evaluate : 5.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O 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 199 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 171 ASP Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 543 ILE Chi-restraints excluded: chain a residue 592 PHE Chi-restraints excluded: chain a residue 614 ILE Chi-restraints excluded: chain a residue 637 GLN Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain a residue 809 VAL Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 41 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 110 VAL Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 420 TRP Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 33 TYR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 129 CYS Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 53 MET Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 151 ILE Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 60 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 23 MET Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 306 VAL Chi-restraints excluded: chain p residue 319 LEU Chi-restraints excluded: chain p residue 336 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 673 optimal weight: 0.0050 chunk 459 optimal weight: 0.0670 chunk 11 optimal weight: 8.9990 chunk 602 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 690 optimal weight: 20.0000 chunk 559 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 726 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 overall best weight: 4.2138 ------------------------------------------------------------------------------- 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 543 ASN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN R 177 GLN a 375 GLN a 762 HIS ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN ** n 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 63459 Z= 0.298 Angle : 0.684 12.090 86074 Z= 0.348 Chirality : 0.044 0.323 10040 Planarity : 0.004 0.078 11108 Dihedral : 4.567 122.399 9065 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.17 % Allowed : 16.16 % Favored : 80.68 % 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: 1.08 (0.09), residues: 8372 helix: 1.45 (0.07), residues: 4910 sheet: 0.15 (0.20), residues: 683 loop : -0.37 (0.12), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 39 HIS 0.007 0.001 HIS d 297 PHE 0.039 0.002 PHE f 33 TYR 0.038 0.002 TYR j 32 ARG 0.006 0.000 ARG M 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1064 time to evaluate : 5.451 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: A 34 MET cc_start: 0.8851 (mmm) cc_final: 0.8544 (mmm) REVERT: A 95 MET cc_start: 0.8696 (tpp) cc_final: 0.8492 (tpp) REVERT: A 100 ASP cc_start: 0.8987 (t0) cc_final: 0.8517 (t0) REVERT: A 231 GLN cc_start: 0.9332 (mm-40) cc_final: 0.9042 (mm-40) REVERT: A 279 GLU cc_start: 0.6795 (tt0) cc_final: 0.6549 (tt0) REVERT: A 284 MET cc_start: 0.9275 (tpt) cc_final: 0.9004 (mmm) REVERT: A 306 MET cc_start: 0.9082 (ptm) cc_final: 0.8520 (ppp) REVERT: A 318 MET cc_start: 0.9335 (mmt) cc_final: 0.8561 (mpp) REVERT: A 324 GLU cc_start: 0.9310 (tt0) cc_final: 0.8751 (tm-30) REVERT: A 346 MET cc_start: 0.8909 (ttt) cc_final: 0.8130 (tmm) REVERT: A 399 GLU cc_start: 0.8647 (tp30) cc_final: 0.8067 (tp30) REVERT: A 437 LYS cc_start: 0.9577 (OUTLIER) cc_final: 0.9129 (tptp) REVERT: A 439 LEU cc_start: 0.9440 (tp) cc_final: 0.8973 (tp) REVERT: A 540 MET cc_start: 0.8753 (mtp) cc_final: 0.8499 (mtp) REVERT: A 541 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9401 (tt) REVERT: A 550 MET cc_start: 0.9381 (ttm) cc_final: 0.8864 (ttm) REVERT: A 570 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9461 (tp) REVERT: A 596 LYS cc_start: 0.9350 (tttm) cc_final: 0.9083 (tppt) REVERT: A 608 MET cc_start: 0.9476 (ttm) cc_final: 0.9106 (ttp) REVERT: B 61 MET cc_start: 0.9224 (mtp) cc_final: 0.8901 (mmm) REVERT: B 167 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8499 (mtt) REVERT: B 168 LEU cc_start: 0.9195 (tp) cc_final: 0.8981 (tp) REVERT: B 252 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: B 306 MET cc_start: 0.9133 (mmt) cc_final: 0.8865 (mmt) REVERT: B 340 MET cc_start: 0.9402 (mtt) cc_final: 0.8687 (ttm) REVERT: B 349 ASP cc_start: 0.8029 (t0) cc_final: 0.7671 (m-30) REVERT: B 367 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: B 387 GLU cc_start: 0.8682 (tp30) cc_final: 0.8115 (tm-30) REVERT: B 550 MET cc_start: 0.9526 (mmm) cc_final: 0.9326 (mmp) REVERT: C 61 MET cc_start: 0.9295 (tpp) cc_final: 0.8851 (mmp) REVERT: C 65 GLN cc_start: 0.8684 (tt0) cc_final: 0.8251 (pt0) REVERT: C 166 ILE cc_start: 0.9481 (mm) cc_final: 0.9165 (tp) REVERT: C 173 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7561 (pmt100) REVERT: C 231 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8804 (mm-40) REVERT: C 232 ARG cc_start: 0.8825 (mtt90) cc_final: 0.8395 (mtm-85) REVERT: C 254 CYS cc_start: 0.8778 (m) cc_final: 0.8473 (m) REVERT: C 275 VAL cc_start: 0.9713 (t) cc_final: 0.9390 (m) REVERT: C 296 MET cc_start: 0.8347 (ttt) cc_final: 0.7974 (ttm) REVERT: C 360 GLU cc_start: 0.9165 (tt0) cc_final: 0.8895 (tm-30) REVERT: C 441 GLN cc_start: 0.9351 (mt0) cc_final: 0.9139 (mm-40) REVERT: C 487 GLU cc_start: 0.9450 (tp30) cc_final: 0.9110 (tm-30) REVERT: C 491 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8822 (tp30) REVERT: C 550 MET cc_start: 0.9060 (ttm) cc_final: 0.8704 (ttp) REVERT: C 573 HIS cc_start: 0.8940 (t70) cc_final: 0.8407 (t-170) REVERT: C 608 MET cc_start: 0.9252 (mtm) cc_final: 0.8953 (ptm) REVERT: D 234 MET cc_start: 0.8187 (mtm) cc_final: 0.7498 (mtm) REVERT: D 238 MET cc_start: 0.8679 (tpp) cc_final: 0.8271 (tpt) REVERT: D 250 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9053 (tm-30) REVERT: D 254 MET cc_start: 0.8507 (mmm) cc_final: 0.8228 (mmm) REVERT: D 268 THR cc_start: 0.9334 (p) cc_final: 0.9105 (t) REVERT: D 279 LEU cc_start: 0.9577 (mm) cc_final: 0.9138 (tp) REVERT: D 300 MET cc_start: 0.9421 (mmm) cc_final: 0.8661 (mmm) REVERT: D 351 ILE cc_start: 0.9500 (mt) cc_final: 0.9244 (mm) REVERT: D 410 MET cc_start: 0.8835 (mtt) cc_final: 0.8505 (mtm) REVERT: E 88 GLU cc_start: 0.8438 (tt0) cc_final: 0.7989 (tm-30) REVERT: E 89 VAL cc_start: 0.9710 (OUTLIER) cc_final: 0.9261 (m) REVERT: E 90 SER cc_start: 0.9321 (t) cc_final: 0.8563 (p) REVERT: E 113 GLU cc_start: 0.9045 (tt0) cc_final: 0.8751 (tm-30) REVERT: E 183 ILE cc_start: 0.9270 (mt) cc_final: 0.8889 (pt) REVERT: E 234 MET cc_start: 0.8780 (mpp) cc_final: 0.8149 (mpp) REVERT: E 250 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8555 (mt-10) REVERT: E 254 MET cc_start: 0.8994 (mmm) cc_final: 0.8380 (tpp) REVERT: E 333 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8839 (p) REVERT: E 356 MET cc_start: 0.8155 (ttm) cc_final: 0.7801 (ttm) REVERT: E 400 ARG cc_start: 0.8227 (tpm170) cc_final: 0.7977 (tpm170) REVERT: E 452 LEU cc_start: 0.9484 (tt) cc_final: 0.9103 (mt) REVERT: F 76 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8990 (mm) REVERT: F 85 GLN cc_start: 0.9250 (tt0) cc_final: 0.8691 (tp-100) REVERT: F 87 LEU cc_start: 0.9185 (mt) cc_final: 0.8845 (mp) REVERT: F 88 GLU cc_start: 0.8997 (tt0) cc_final: 0.8464 (tm-30) REVERT: F 127 MET cc_start: 0.9122 (mtp) cc_final: 0.8903 (mtp) REVERT: F 180 MET cc_start: 0.8868 (mtp) cc_final: 0.8469 (mmm) REVERT: F 254 MET cc_start: 0.8832 (mmm) cc_final: 0.8187 (mmm) REVERT: F 271 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8549 (ttm110) REVERT: F 283 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8628 (mt-10) REVERT: F 327 MET cc_start: 0.9510 (ttm) cc_final: 0.9226 (ttm) REVERT: F 360 ASP cc_start: 0.8922 (t0) cc_final: 0.8440 (t0) REVERT: F 367 ASP cc_start: 0.9141 (t70) cc_final: 0.8890 (t0) REVERT: F 410 MET cc_start: 0.8919 (mtp) cc_final: 0.8513 (ptp) REVERT: F 417 ASP cc_start: 0.9082 (m-30) cc_final: 0.8685 (m-30) REVERT: F 491 MET cc_start: 0.9174 (mtp) cc_final: 0.8949 (mtp) REVERT: F 494 ARG cc_start: 0.8882 (mmt90) cc_final: 0.8460 (mmm-85) REVERT: H 14 MET cc_start: 0.8974 (tpp) cc_final: 0.8182 (tpp) REVERT: H 24 LYS cc_start: 0.9455 (tmmt) cc_final: 0.9214 (tmmt) REVERT: H 58 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7859 (tmm) REVERT: H 78 ASP cc_start: 0.7950 (t0) cc_final: 0.7627 (t0) REVERT: H 192 ASP cc_start: 0.9095 (m-30) cc_final: 0.8603 (t0) REVERT: I 76 MET cc_start: 0.9620 (mmp) cc_final: 0.9337 (mmm) REVERT: I 129 GLU cc_start: 0.8906 (tp30) cc_final: 0.8572 (tp30) REVERT: I 132 MET cc_start: 0.9224 (mtt) cc_final: 0.8922 (mtt) REVERT: I 201 ASP cc_start: 0.9048 (m-30) cc_final: 0.8655 (p0) REVERT: J 72 MET cc_start: 0.9080 (mtp) cc_final: 0.8848 (ptp) REVERT: J 125 TYR cc_start: 0.9423 (m-80) cc_final: 0.9207 (m-80) REVERT: J 129 GLU cc_start: 0.8150 (tt0) cc_final: 0.7453 (tt0) REVERT: J 132 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8082 (mmm) REVERT: J 175 GLU cc_start: 0.9249 (pm20) cc_final: 0.8971 (mm-30) REVERT: J 207 MET cc_start: 0.9263 (tpp) cc_final: 0.8632 (tpp) REVERT: J 210 GLU cc_start: 0.8729 (mp0) cc_final: 0.8191 (mp0) REVERT: K 77 ASN cc_start: 0.9354 (m110) cc_final: 0.8737 (m110) REVERT: K 93 ASP cc_start: 0.9493 (m-30) cc_final: 0.9244 (m-30) REVERT: K 97 GLU cc_start: 0.9419 (tp30) cc_final: 0.9092 (tp30) REVERT: K 129 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8600 (tt0) REVERT: K 132 MET cc_start: 0.8021 (mmt) cc_final: 0.7147 (mmt) REVERT: K 175 GLU cc_start: 0.9376 (mp0) cc_final: 0.8779 (mm-30) REVERT: K 182 GLU cc_start: 0.7943 (tt0) cc_final: 0.7671 (tt0) REVERT: L 14 GLU cc_start: 0.8207 (pp20) cc_final: 0.7987 (pp20) REVERT: L 15 ASP cc_start: 0.8399 (p0) cc_final: 0.7885 (p0) REVERT: L 31 ASN cc_start: 0.8404 (p0) cc_final: 0.7963 (p0) REVERT: L 54 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8496 (tp-100) REVERT: L 108 ARG cc_start: 0.8972 (tpp80) cc_final: 0.8496 (tpp80) REVERT: M 84 MET cc_start: 0.9047 (mtt) cc_final: 0.8792 (ttm) REVERT: N 72 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8793 (mm-30) REVERT: N 100 LEU cc_start: 0.9671 (mm) cc_final: 0.9403 (mm) REVERT: Q 32 CYS cc_start: 0.9576 (m) cc_final: 0.9366 (m) REVERT: Q 129 LYS cc_start: 0.9614 (mttt) cc_final: 0.9253 (mmmt) REVERT: R 33 MET cc_start: 0.9207 (tpp) cc_final: 0.8887 (tmm) REVERT: R 109 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9182 (mm-30) REVERT: R 115 MET cc_start: 0.9397 (mmm) cc_final: 0.8956 (mmm) REVERT: R 188 MET cc_start: 0.8436 (tpt) cc_final: 0.8010 (tpt) REVERT: R 194 ASP cc_start: 0.9573 (OUTLIER) cc_final: 0.9223 (p0) REVERT: R 199 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9212 (mm) REVERT: R 203 TYR cc_start: 0.9386 (t80) cc_final: 0.9046 (t80) REVERT: S 10 MET cc_start: 0.8150 (ttm) cc_final: 0.7767 (ttm) REVERT: S 109 GLU cc_start: 0.9369 (mt-10) cc_final: 0.9114 (mm-30) REVERT: S 188 MET cc_start: 0.9090 (tpp) cc_final: 0.8534 (tpp) REVERT: S 192 LYS cc_start: 0.9334 (mttt) cc_final: 0.8731 (mtpp) REVERT: a 375 GLN cc_start: 0.8496 (tt0) cc_final: 0.7858 (tp-100) REVERT: a 406 MET cc_start: 0.7358 (mtm) cc_final: 0.7155 (mtm) REVERT: a 536 PHE cc_start: 0.7427 (m-80) cc_final: 0.7100 (m-80) REVERT: a 616 MET cc_start: 0.8396 (mtt) cc_final: 0.7624 (tmm) REVERT: a 730 LEU cc_start: 0.9257 (tt) cc_final: 0.9005 (pp) REVERT: a 745 LEU cc_start: 0.9160 (mm) cc_final: 0.8533 (mm) REVERT: a 757 TRP cc_start: 0.7641 (t60) cc_final: 0.7431 (t60) REVERT: a 808 TRP cc_start: 0.8811 (m-10) cc_final: 0.8462 (m-10) REVERT: b 19 MET cc_start: 0.9073 (tmm) cc_final: 0.8759 (tmm) REVERT: c 421 MET cc_start: 0.8375 (ptt) cc_final: 0.7937 (mtp) REVERT: d 45 LEU cc_start: 0.9048 (mt) cc_final: 0.8758 (mt) REVERT: d 224 THR cc_start: 0.8932 (m) cc_final: 0.8719 (p) REVERT: g 13 PHE cc_start: 0.8086 (t80) cc_final: 0.7779 (t80) REVERT: h 53 MET cc_start: 0.7958 (mmp) cc_final: 0.6622 (tmm) REVERT: h 90 PHE cc_start: 0.8313 (m-80) cc_final: 0.7352 (m-80) REVERT: h 144 TYR cc_start: 0.7798 (m-80) cc_final: 0.7552 (m-80) REVERT: i 47 MET cc_start: 0.8497 (ppp) cc_final: 0.8270 (ppp) REVERT: i 53 MET cc_start: 0.8180 (mmt) cc_final: 0.7219 (ttt) REVERT: i 68 TYR cc_start: 0.8785 (m-10) cc_final: 0.8160 (m-80) REVERT: i 131 MET cc_start: 0.9001 (ppp) cc_final: 0.8739 (ppp) REVERT: i 155 LYS cc_start: 0.7278 (mmtt) cc_final: 0.6995 (mttm) REVERT: j 23 MET cc_start: 0.8757 (tmm) cc_final: 0.8544 (tmm) REVERT: j 47 MET cc_start: 0.8969 (ppp) cc_final: 0.8631 (ppp) REVERT: k 25 PHE cc_start: 0.8868 (m-10) cc_final: 0.8324 (m-80) REVERT: k 28 MET cc_start: 0.8672 (mtp) cc_final: 0.8461 (ttt) REVERT: k 60 VAL cc_start: 0.8825 (t) cc_final: 0.8611 (p) REVERT: k 108 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7533 (t80) REVERT: l 47 MET cc_start: 0.7498 (ppp) cc_final: 0.7251 (ppp) REVERT: l 48 ARG cc_start: 0.6811 (ttp-110) cc_final: 0.6543 (ttm110) REVERT: l 68 TYR cc_start: 0.8880 (m-80) cc_final: 0.8552 (m-80) REVERT: l 115 ASP cc_start: 0.8213 (t0) cc_final: 0.7937 (t0) REVERT: m 25 PHE cc_start: 0.7902 (m-80) cc_final: 0.7638 (m-80) REVERT: m 121 THR cc_start: 0.6680 (m) cc_final: 0.5349 (p) REVERT: m 131 MET cc_start: 0.7257 (ptt) cc_final: 0.6738 (ptt) REVERT: n 23 MET cc_start: 0.7038 (tpt) cc_final: 0.6835 (tpt) REVERT: n 28 MET cc_start: 0.8812 (tpp) cc_final: 0.8181 (mmm) REVERT: n 61 MET cc_start: 0.7920 (mmm) cc_final: 0.6708 (mmm) REVERT: n 139 GLU cc_start: 0.7421 (tp30) cc_final: 0.6433 (tp30) REVERT: o 137 PHE cc_start: 0.7362 (m-80) cc_final: 0.7153 (m-80) REVERT: p 331 MET cc_start: 0.8038 (tpp) cc_final: 0.7800 (tmm) REVERT: p 340 TYR cc_start: 0.8020 (m-80) cc_final: 0.7627 (m-80) outliers start: 193 outliers final: 134 residues processed: 1171 average time/residue: 0.6068 time to fit residues: 1248.8483 Evaluate side-chains 1145 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 996 time to evaluate : 5.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O 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 199 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 171 ASP Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 543 ILE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 614 ILE Chi-restraints excluded: chain a residue 637 GLN Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 110 VAL Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 33 TYR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 129 CYS Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 151 ILE Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 108 PHE Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 306 VAL Chi-restraints excluded: chain p residue 319 LEU Chi-restraints excluded: chain p residue 336 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 272 optimal weight: 0.1980 chunk 728 optimal weight: 30.0000 chunk 159 optimal weight: 8.9990 chunk 475 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 809 optimal weight: 30.0000 chunk 672 optimal weight: 20.0000 chunk 374 optimal weight: 40.0000 chunk 67 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 425 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 85 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 GLN S 50 GLN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 87 ASN ** n 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 63459 Z= 0.240 Angle : 0.687 16.053 86074 Z= 0.342 Chirality : 0.044 0.322 10040 Planarity : 0.004 0.068 11108 Dihedral : 4.528 121.477 9065 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.99 % Allowed : 17.13 % Favored : 79.89 % 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: 1.09 (0.09), residues: 8372 helix: 1.46 (0.07), residues: 4911 sheet: 0.23 (0.21), residues: 666 loop : -0.40 (0.12), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP p 312 HIS 0.006 0.001 HIS B 164 PHE 0.045 0.002 PHE f 33 TYR 0.041 0.002 TYR j 32 ARG 0.011 0.000 ARG E 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1069 time to evaluate : 5.442 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: A 34 MET cc_start: 0.8922 (mmm) cc_final: 0.8592 (mmm) REVERT: A 100 ASP cc_start: 0.8946 (t0) cc_final: 0.8581 (t0) REVERT: A 231 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8969 (mm-40) REVERT: A 306 MET cc_start: 0.9056 (ptm) cc_final: 0.8519 (ppp) REVERT: A 324 GLU cc_start: 0.9301 (tt0) cc_final: 0.8777 (tm-30) REVERT: A 346 MET cc_start: 0.8921 (ttt) cc_final: 0.8119 (tmm) REVERT: A 399 GLU cc_start: 0.8691 (tp30) cc_final: 0.8054 (tp30) REVERT: A 437 LYS cc_start: 0.9581 (OUTLIER) cc_final: 0.9109 (tptp) REVERT: A 439 LEU cc_start: 0.9417 (tp) cc_final: 0.8965 (tp) REVERT: A 550 MET cc_start: 0.9401 (ttm) cc_final: 0.8847 (ttm) REVERT: A 552 ARG cc_start: 0.9391 (ttt180) cc_final: 0.9169 (ttm-80) REVERT: A 596 LYS cc_start: 0.9337 (tttm) cc_final: 0.9107 (tppt) REVERT: A 608 MET cc_start: 0.9468 (ttm) cc_final: 0.9108 (ttp) REVERT: B 34 MET cc_start: 0.8866 (tpt) cc_final: 0.8433 (tpt) REVERT: B 61 MET cc_start: 0.9224 (mtp) cc_final: 0.8990 (mmm) REVERT: B 168 LEU cc_start: 0.9164 (tp) cc_final: 0.8942 (tp) REVERT: B 340 MET cc_start: 0.9424 (mtt) cc_final: 0.8591 (ttm) REVERT: B 367 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: B 387 GLU cc_start: 0.8668 (tp30) cc_final: 0.8102 (tm-30) REVERT: B 550 MET cc_start: 0.9523 (mmm) cc_final: 0.9319 (mmp) REVERT: B 584 MET cc_start: 0.9075 (mtp) cc_final: 0.8819 (mpp) REVERT: C 61 MET cc_start: 0.9319 (tpp) cc_final: 0.8634 (mmm) REVERT: C 65 GLN cc_start: 0.8647 (tt0) cc_final: 0.8266 (pt0) REVERT: C 166 ILE cc_start: 0.9468 (mm) cc_final: 0.9177 (tp) REVERT: C 173 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7515 (pmt100) REVERT: C 231 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8722 (mm-40) REVERT: C 232 ARG cc_start: 0.8773 (mtt90) cc_final: 0.8380 (mtm-85) REVERT: C 254 CYS cc_start: 0.8779 (m) cc_final: 0.8467 (m) REVERT: C 275 VAL cc_start: 0.9698 (t) cc_final: 0.9361 (m) REVERT: C 296 MET cc_start: 0.8332 (ttt) cc_final: 0.7930 (ttm) REVERT: C 318 MET cc_start: 0.9120 (mtt) cc_final: 0.8863 (mtt) REVERT: C 360 GLU cc_start: 0.9152 (tt0) cc_final: 0.8880 (tm-30) REVERT: C 392 VAL cc_start: 0.9494 (OUTLIER) cc_final: 0.9120 (p) REVERT: C 487 GLU cc_start: 0.9436 (tp30) cc_final: 0.9099 (tm-30) REVERT: C 491 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8820 (tp30) REVERT: C 509 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9373 (pp) REVERT: C 550 MET cc_start: 0.9092 (ttm) cc_final: 0.8736 (ttp) REVERT: C 573 HIS cc_start: 0.8884 (t70) cc_final: 0.8464 (t70) REVERT: C 608 MET cc_start: 0.9220 (mtm) cc_final: 0.8920 (ptm) REVERT: D 234 MET cc_start: 0.8211 (mtm) cc_final: 0.7647 (mtm) REVERT: D 238 MET cc_start: 0.8667 (tpp) cc_final: 0.8239 (tpt) REVERT: D 250 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8948 (tm-30) REVERT: D 254 MET cc_start: 0.8534 (mmm) cc_final: 0.8211 (mmm) REVERT: D 268 THR cc_start: 0.9322 (p) cc_final: 0.9096 (t) REVERT: D 270 GLU cc_start: 0.9327 (tt0) cc_final: 0.9044 (tt0) REVERT: D 279 LEU cc_start: 0.9560 (mm) cc_final: 0.9071 (tp) REVERT: D 300 MET cc_start: 0.9512 (mmm) cc_final: 0.8680 (mmm) REVERT: D 351 ILE cc_start: 0.9484 (mt) cc_final: 0.9245 (mm) REVERT: D 410 MET cc_start: 0.8813 (mtt) cc_final: 0.8462 (mtm) REVERT: E 88 GLU cc_start: 0.8451 (tt0) cc_final: 0.7968 (tm-30) REVERT: E 89 VAL cc_start: 0.9698 (OUTLIER) cc_final: 0.9265 (m) REVERT: E 90 SER cc_start: 0.9307 (t) cc_final: 0.8551 (p) REVERT: E 113 GLU cc_start: 0.9052 (tt0) cc_final: 0.8654 (tm-30) REVERT: E 169 MET cc_start: 0.8888 (tmm) cc_final: 0.8612 (tmm) REVERT: E 180 MET cc_start: 0.8830 (mmm) cc_final: 0.8403 (mmm) REVERT: E 234 MET cc_start: 0.8800 (mpp) cc_final: 0.8320 (mpp) REVERT: E 254 MET cc_start: 0.9048 (mmm) cc_final: 0.8823 (mmm) REVERT: E 333 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8810 (p) REVERT: E 356 MET cc_start: 0.8140 (ttm) cc_final: 0.7469 (ttp) REVERT: E 402 MET cc_start: 0.9002 (ttm) cc_final: 0.8655 (ttm) REVERT: E 452 LEU cc_start: 0.9510 (tt) cc_final: 0.9129 (mt) REVERT: F 74 LEU cc_start: 0.9779 (pt) cc_final: 0.9120 (mp) REVERT: F 76 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8978 (mm) REVERT: F 85 GLN cc_start: 0.9237 (tt0) cc_final: 0.8680 (tp-100) REVERT: F 87 LEU cc_start: 0.9187 (mt) cc_final: 0.8841 (mp) REVERT: F 88 GLU cc_start: 0.8992 (tt0) cc_final: 0.8475 (tm-30) REVERT: F 180 MET cc_start: 0.8882 (mtp) cc_final: 0.8631 (mmm) REVERT: F 254 MET cc_start: 0.8731 (mmm) cc_final: 0.8390 (mmm) REVERT: F 271 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8540 (ttm110) REVERT: F 283 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8625 (mt-10) REVERT: F 300 MET cc_start: 0.9337 (mmm) cc_final: 0.9071 (mmm) REVERT: F 327 MET cc_start: 0.9511 (ttm) cc_final: 0.9250 (ttm) REVERT: F 333 THR cc_start: 0.9488 (m) cc_final: 0.9200 (p) REVERT: F 360 ASP cc_start: 0.8932 (t0) cc_final: 0.8486 (t0) REVERT: F 367 ASP cc_start: 0.9100 (t70) cc_final: 0.8858 (t0) REVERT: F 402 MET cc_start: 0.8868 (ttm) cc_final: 0.8015 (ttt) REVERT: F 410 MET cc_start: 0.8947 (mtp) cc_final: 0.8486 (ptp) REVERT: F 417 ASP cc_start: 0.9111 (m-30) cc_final: 0.8716 (m-30) REVERT: F 491 MET cc_start: 0.9185 (mtp) cc_final: 0.8896 (mtp) REVERT: F 494 ARG cc_start: 0.8885 (mmt90) cc_final: 0.8439 (mmm-85) REVERT: H 14 MET cc_start: 0.8901 (tpp) cc_final: 0.8102 (tpp) REVERT: H 24 LYS cc_start: 0.9451 (tmmt) cc_final: 0.9225 (tmmt) REVERT: H 58 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7948 (tmm) REVERT: H 67 PHE cc_start: 0.8558 (t80) cc_final: 0.8349 (t80) REVERT: H 78 ASP cc_start: 0.7924 (t0) cc_final: 0.7556 (t0) REVERT: H 192 ASP cc_start: 0.9097 (m-30) cc_final: 0.8562 (t0) REVERT: I 76 MET cc_start: 0.9573 (mmp) cc_final: 0.9249 (mmm) REVERT: I 129 GLU cc_start: 0.8874 (tp30) cc_final: 0.8516 (tp30) REVERT: I 132 MET cc_start: 0.9225 (mtt) cc_final: 0.8941 (mtt) REVERT: I 201 ASP cc_start: 0.9041 (m-30) cc_final: 0.8654 (p0) REVERT: J 72 MET cc_start: 0.9062 (mtp) cc_final: 0.8828 (ptp) REVERT: J 125 TYR cc_start: 0.9440 (m-80) cc_final: 0.9048 (m-80) REVERT: J 129 GLU cc_start: 0.8136 (tt0) cc_final: 0.7625 (tt0) REVERT: J 175 GLU cc_start: 0.9226 (pm20) cc_final: 0.8987 (mm-30) REVERT: J 207 MET cc_start: 0.9243 (tpp) cc_final: 0.8548 (tpp) REVERT: J 208 MET cc_start: 0.8661 (ppp) cc_final: 0.8379 (ppp) REVERT: J 210 GLU cc_start: 0.8762 (mp0) cc_final: 0.8156 (mp0) REVERT: K 93 ASP cc_start: 0.9487 (m-30) cc_final: 0.9244 (m-30) REVERT: K 97 GLU cc_start: 0.9417 (tp30) cc_final: 0.9058 (tp30) REVERT: K 129 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8975 (tt0) REVERT: K 175 GLU cc_start: 0.9365 (mp0) cc_final: 0.8796 (mm-30) REVERT: K 182 GLU cc_start: 0.8032 (tt0) cc_final: 0.7696 (tt0) REVERT: L 14 GLU cc_start: 0.8231 (pp20) cc_final: 0.8023 (pp20) REVERT: L 15 ASP cc_start: 0.8354 (p0) cc_final: 0.7895 (p0) REVERT: L 20 PHE cc_start: 0.8740 (m-80) cc_final: 0.8486 (m-80) REVERT: L 31 ASN cc_start: 0.8267 (p0) cc_final: 0.7811 (p0) REVERT: L 32 ARG cc_start: 0.8450 (mmp80) cc_final: 0.8146 (mmp80) REVERT: L 54 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8377 (tp-100) REVERT: L 108 ARG cc_start: 0.8986 (tpp80) cc_final: 0.8522 (tpp80) REVERT: M 78 ARG cc_start: 0.8695 (tpm170) cc_final: 0.8438 (tpm170) REVERT: M 84 MET cc_start: 0.9083 (mtt) cc_final: 0.8862 (ttm) REVERT: N 72 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8777 (mm-30) REVERT: N 84 MET cc_start: 0.9373 (mtm) cc_final: 0.8725 (ttm) REVERT: N 100 LEU cc_start: 0.9677 (mm) cc_final: 0.9395 (mm) REVERT: N 105 ASP cc_start: 0.9170 (t0) cc_final: 0.8488 (t70) REVERT: O 75 GLN cc_start: 0.9523 (tp-100) cc_final: 0.9059 (tp-100) REVERT: Q 32 CYS cc_start: 0.9565 (m) cc_final: 0.9348 (m) REVERT: Q 115 MET cc_start: 0.9573 (mtp) cc_final: 0.9280 (ptp) REVERT: R 33 MET cc_start: 0.9180 (tpp) cc_final: 0.8836 (tmm) REVERT: R 109 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9158 (mm-30) REVERT: R 115 MET cc_start: 0.9379 (mmm) cc_final: 0.8866 (mmm) REVERT: R 118 HIS cc_start: 0.8407 (t-90) cc_final: 0.7860 (t-90) REVERT: R 153 ARG cc_start: 0.8871 (tpm170) cc_final: 0.8636 (tpm170) REVERT: R 188 MET cc_start: 0.8449 (tpt) cc_final: 0.8020 (tpt) REVERT: R 194 ASP cc_start: 0.9572 (OUTLIER) cc_final: 0.9223 (p0) REVERT: R 199 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9223 (mm) REVERT: S 10 MET cc_start: 0.8176 (ttm) cc_final: 0.7810 (ttm) REVERT: S 109 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9123 (mm-30) REVERT: S 188 MET cc_start: 0.9077 (tpp) cc_final: 0.8529 (tpp) REVERT: S 192 LYS cc_start: 0.9350 (mttt) cc_final: 0.8755 (mtpp) REVERT: S 234 MET cc_start: 0.8044 (tmm) cc_final: 0.7741 (ppp) REVERT: a 406 MET cc_start: 0.7443 (mtm) cc_final: 0.7111 (mtm) REVERT: a 453 MET cc_start: 0.7660 (mmm) cc_final: 0.7363 (mmm) REVERT: a 536 PHE cc_start: 0.7474 (m-80) cc_final: 0.7081 (m-80) REVERT: a 540 MET cc_start: 0.8265 (ppp) cc_final: 0.8048 (ppp) REVERT: a 549 MET cc_start: 0.8215 (ppp) cc_final: 0.7925 (ppp) REVERT: a 616 MET cc_start: 0.8422 (mtt) cc_final: 0.7692 (tmm) REVERT: a 641 ILE cc_start: 0.9096 (mm) cc_final: 0.8083 (mm) REVERT: a 745 LEU cc_start: 0.9163 (mm) cc_final: 0.8457 (mm) REVERT: b 25 CYS cc_start: 0.9062 (m) cc_final: 0.8853 (m) REVERT: b 203 MET cc_start: 0.5452 (mmt) cc_final: 0.4179 (mmm) REVERT: c 421 MET cc_start: 0.8417 (ptt) cc_final: 0.8015 (mtp) REVERT: d 45 LEU cc_start: 0.9066 (mt) cc_final: 0.8755 (mt) REVERT: d 224 THR cc_start: 0.8930 (m) cc_final: 0.8698 (p) REVERT: g 13 PHE cc_start: 0.8159 (t80) cc_final: 0.7678 (t80) REVERT: h 53 MET cc_start: 0.7890 (mmp) cc_final: 0.6917 (tmm) REVERT: h 90 PHE cc_start: 0.8240 (m-80) cc_final: 0.7521 (m-80) REVERT: h 131 MET cc_start: 0.8382 (ppp) cc_final: 0.7940 (ppp) REVERT: i 13 PHE cc_start: 0.8726 (t80) cc_final: 0.8489 (t80) REVERT: i 53 MET cc_start: 0.8039 (mmt) cc_final: 0.7100 (ttt) REVERT: i 131 MET cc_start: 0.9000 (ppp) cc_final: 0.8756 (ppp) REVERT: i 155 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6826 (mttm) REVERT: j 47 MET cc_start: 0.8944 (ppp) cc_final: 0.8663 (ppp) REVERT: j 68 TYR cc_start: 0.8875 (m-10) cc_final: 0.8502 (m-10) REVERT: k 17 MET cc_start: 0.9011 (tpt) cc_final: 0.8577 (tpp) REVERT: k 25 PHE cc_start: 0.8844 (m-10) cc_final: 0.8381 (m-80) REVERT: k 108 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7608 (t80) REVERT: l 44 MET cc_start: 0.8224 (mmm) cc_final: 0.7842 (mmm) REVERT: l 47 MET cc_start: 0.7576 (ppp) cc_final: 0.7298 (ppp) REVERT: l 48 ARG cc_start: 0.6832 (ttp-110) cc_final: 0.6525 (ttm110) REVERT: l 61 MET cc_start: 0.8355 (mtm) cc_final: 0.8077 (mtm) REVERT: m 25 PHE cc_start: 0.7939 (m-80) cc_final: 0.7630 (m-80) REVERT: m 47 MET cc_start: 0.7848 (mmm) cc_final: 0.7604 (mmm) REVERT: m 121 THR cc_start: 0.6853 (m) cc_final: 0.5600 (p) REVERT: m 131 MET cc_start: 0.7252 (ptt) cc_final: 0.6656 (ptt) REVERT: n 13 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: n 17 MET cc_start: 0.7341 (mmt) cc_final: 0.7034 (mpp) REVERT: n 28 MET cc_start: 0.8803 (tpp) cc_final: 0.8090 (mmm) REVERT: n 61 MET cc_start: 0.7783 (mmm) cc_final: 0.6512 (mmm) REVERT: n 139 GLU cc_start: 0.7222 (tp30) cc_final: 0.6348 (tp30) REVERT: p 340 TYR cc_start: 0.8016 (m-80) cc_final: 0.7659 (m-80) outliers start: 182 outliers final: 125 residues processed: 1174 average time/residue: 0.5624 time to fit residues: 1155.7872 Evaluate side-chains 1125 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 987 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 GLU 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 C residue 24 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 171 ASP Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 592 PHE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 614 ILE Chi-restraints excluded: chain a residue 637 GLN Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 445 THR Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 33 TYR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 129 CYS Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain i residue 98 SER Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain n residue 13 PHE Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 53 MET Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 306 VAL Chi-restraints excluded: chain p residue 319 LEU Chi-restraints excluded: chain p residue 336 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 780 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 461 optimal weight: 9.9990 chunk 591 optimal weight: 50.0000 chunk 458 optimal weight: 4.9990 chunk 681 optimal weight: 0.0040 chunk 452 optimal weight: 8.9990 chunk 806 optimal weight: 0.8980 chunk 504 optimal weight: 20.0000 chunk 491 optimal weight: 20.0000 chunk 372 optimal weight: 9.9990 overall best weight: 4.3798 ------------------------------------------------------------------------------- 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** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN S 59 ASN a 375 GLN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 GLN ** n 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 63459 Z= 0.303 Angle : 0.713 13.824 86074 Z= 0.359 Chirality : 0.044 0.308 10040 Planarity : 0.004 0.059 11108 Dihedral : 4.590 120.373 9065 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.36 % Allowed : 18.29 % Favored : 78.35 % 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: 1.00 (0.09), residues: 8372 helix: 1.39 (0.07), residues: 4919 sheet: 0.13 (0.20), residues: 678 loop : -0.42 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 808 HIS 0.008 0.001 HIS E 363 PHE 0.045 0.002 PHE f 33 TYR 0.036 0.002 TYR j 32 ARG 0.009 0.000 ARG E 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1012 time to evaluate : 5.569 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: A 95 MET cc_start: 0.8829 (tpp) cc_final: 0.8614 (tpp) REVERT: A 100 ASP cc_start: 0.8978 (t0) cc_final: 0.8620 (t0) REVERT: A 231 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8949 (mm-40) REVERT: A 306 MET cc_start: 0.9031 (ptm) cc_final: 0.8510 (ppp) REVERT: A 324 GLU cc_start: 0.9291 (tt0) cc_final: 0.8783 (tm-30) REVERT: A 340 MET cc_start: 0.8839 (tpp) cc_final: 0.8611 (tpp) REVERT: A 346 MET cc_start: 0.8950 (ttt) cc_final: 0.8112 (tmm) REVERT: A 437 LYS cc_start: 0.9580 (OUTLIER) cc_final: 0.9176 (tptp) REVERT: A 439 LEU cc_start: 0.9430 (tp) cc_final: 0.8986 (tp) REVERT: A 550 MET cc_start: 0.9405 (ttm) cc_final: 0.8839 (ttm) REVERT: A 552 ARG cc_start: 0.9387 (ttt180) cc_final: 0.9169 (ttm-80) REVERT: A 570 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9412 (tp) REVERT: A 596 LYS cc_start: 0.9345 (tttm) cc_final: 0.9113 (tppt) REVERT: A 608 MET cc_start: 0.9517 (ttm) cc_final: 0.9131 (ttt) REVERT: B 34 MET cc_start: 0.8910 (tpt) cc_final: 0.8563 (tpt) REVERT: B 168 LEU cc_start: 0.9148 (tp) cc_final: 0.8924 (tp) REVERT: B 306 MET cc_start: 0.9117 (mmt) cc_final: 0.8809 (mmt) REVERT: B 340 MET cc_start: 0.9307 (mtt) cc_final: 0.9007 (mtt) REVERT: B 367 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: B 387 GLU cc_start: 0.8726 (tp30) cc_final: 0.8152 (tm-30) REVERT: B 392 VAL cc_start: 0.9367 (OUTLIER) cc_final: 0.9028 (p) REVERT: B 550 MET cc_start: 0.9533 (mmm) cc_final: 0.9323 (mmp) REVERT: C 65 GLN cc_start: 0.8656 (tt0) cc_final: 0.8223 (pt0) REVERT: C 95 MET cc_start: 0.8888 (mmm) cc_final: 0.8519 (mmm) REVERT: C 166 ILE cc_start: 0.9444 (mm) cc_final: 0.9103 (tp) REVERT: C 168 LEU cc_start: 0.9441 (tp) cc_final: 0.9055 (tt) REVERT: C 231 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8722 (mm-40) REVERT: C 232 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8489 (mtm-85) REVERT: C 254 CYS cc_start: 0.8668 (m) cc_final: 0.8309 (m) REVERT: C 275 VAL cc_start: 0.9702 (t) cc_final: 0.9365 (m) REVERT: C 296 MET cc_start: 0.8361 (ttt) cc_final: 0.7968 (ttm) REVERT: C 318 MET cc_start: 0.9065 (mtt) cc_final: 0.8627 (mtt) REVERT: C 360 GLU cc_start: 0.9182 (tt0) cc_final: 0.8905 (tm-30) REVERT: C 487 GLU cc_start: 0.9441 (tp30) cc_final: 0.9084 (tm-30) REVERT: C 491 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8846 (tp30) REVERT: C 509 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9378 (pp) REVERT: C 550 MET cc_start: 0.9116 (ttm) cc_final: 0.8758 (ttp) REVERT: C 573 HIS cc_start: 0.8771 (t70) cc_final: 0.8420 (t-90) REVERT: C 608 MET cc_start: 0.9233 (mtm) cc_final: 0.8942 (ptm) REVERT: D 238 MET cc_start: 0.8688 (tpp) cc_final: 0.8288 (tpt) REVERT: D 250 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9066 (tm-30) REVERT: D 254 MET cc_start: 0.8601 (mmm) cc_final: 0.8322 (mmm) REVERT: D 270 GLU cc_start: 0.9341 (tt0) cc_final: 0.9055 (tt0) REVERT: D 300 MET cc_start: 0.9517 (mmm) cc_final: 0.8632 (mmm) REVERT: D 330 ASP cc_start: 0.9068 (m-30) cc_final: 0.8788 (t0) REVERT: D 351 ILE cc_start: 0.9497 (mt) cc_final: 0.9263 (mm) REVERT: D 410 MET cc_start: 0.8840 (mtt) cc_final: 0.8493 (mtm) REVERT: E 88 GLU cc_start: 0.8442 (tt0) cc_final: 0.7922 (tm-30) REVERT: E 89 VAL cc_start: 0.9683 (OUTLIER) cc_final: 0.9268 (m) REVERT: E 90 SER cc_start: 0.9358 (t) cc_final: 0.8594 (p) REVERT: E 113 GLU cc_start: 0.9019 (tt0) cc_final: 0.8758 (tm-30) REVERT: E 234 MET cc_start: 0.8780 (mpp) cc_final: 0.8367 (mpp) REVERT: E 250 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8519 (mt-10) REVERT: E 254 MET cc_start: 0.9080 (mmm) cc_final: 0.8856 (mmm) REVERT: E 333 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8836 (p) REVERT: E 356 MET cc_start: 0.8250 (ttm) cc_final: 0.7580 (ttp) REVERT: E 402 MET cc_start: 0.9034 (ttm) cc_final: 0.8797 (ttm) REVERT: E 410 MET cc_start: 0.9083 (mtm) cc_final: 0.8146 (ptp) REVERT: E 452 LEU cc_start: 0.9511 (tt) cc_final: 0.9128 (mt) REVERT: E 453 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8772 (tm-30) REVERT: F 74 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9070 (mp) REVERT: F 76 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8970 (mm) REVERT: F 85 GLN cc_start: 0.9238 (tt0) cc_final: 0.8730 (tp-100) REVERT: F 88 GLU cc_start: 0.9013 (tt0) cc_final: 0.8465 (tm-30) REVERT: F 180 MET cc_start: 0.8943 (mtp) cc_final: 0.8674 (mmm) REVERT: F 254 MET cc_start: 0.8804 (mmm) cc_final: 0.8520 (mmm) REVERT: F 271 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8542 (ttm110) REVERT: F 283 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8626 (mt-10) REVERT: F 300 MET cc_start: 0.9345 (mmm) cc_final: 0.9014 (mmm) REVERT: F 327 MET cc_start: 0.9531 (ttm) cc_final: 0.9234 (ttm) REVERT: F 333 THR cc_start: 0.9492 (m) cc_final: 0.9198 (p) REVERT: F 360 ASP cc_start: 0.8959 (t0) cc_final: 0.8536 (t0) REVERT: F 367 ASP cc_start: 0.9197 (t70) cc_final: 0.8959 (t0) REVERT: F 402 MET cc_start: 0.8931 (ttm) cc_final: 0.8018 (ttt) REVERT: F 410 MET cc_start: 0.8936 (mtp) cc_final: 0.8477 (ptp) REVERT: F 417 ASP cc_start: 0.9147 (m-30) cc_final: 0.8822 (m-30) REVERT: F 491 MET cc_start: 0.9221 (mtp) cc_final: 0.8911 (mtp) REVERT: H 14 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8021 (tpp) REVERT: H 58 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7956 (tmm) REVERT: H 78 ASP cc_start: 0.7876 (t0) cc_final: 0.7490 (t0) REVERT: H 190 GLU cc_start: 0.9179 (tp30) cc_final: 0.8646 (tp30) REVERT: H 192 ASP cc_start: 0.9130 (m-30) cc_final: 0.8736 (t70) REVERT: I 76 MET cc_start: 0.9613 (mmp) cc_final: 0.9293 (mmm) REVERT: I 129 GLU cc_start: 0.8855 (tp30) cc_final: 0.8520 (tp30) REVERT: I 132 MET cc_start: 0.9189 (mtt) cc_final: 0.8935 (mtt) REVERT: I 201 ASP cc_start: 0.9119 (m-30) cc_final: 0.8748 (p0) REVERT: I 202 LEU cc_start: 0.9731 (mt) cc_final: 0.9438 (mm) REVERT: J 125 TYR cc_start: 0.9490 (m-80) cc_final: 0.9064 (m-80) REVERT: J 129 GLU cc_start: 0.7993 (tt0) cc_final: 0.7325 (tt0) REVERT: J 132 MET cc_start: 0.8025 (mmt) cc_final: 0.7180 (mmm) REVERT: J 175 GLU cc_start: 0.9246 (pm20) cc_final: 0.8998 (mm-30) REVERT: J 207 MET cc_start: 0.9284 (tpp) cc_final: 0.8551 (tpp) REVERT: J 210 GLU cc_start: 0.8798 (mp0) cc_final: 0.8124 (mp0) REVERT: K 93 ASP cc_start: 0.9506 (m-30) cc_final: 0.9227 (m-30) REVERT: K 97 GLU cc_start: 0.9423 (tp30) cc_final: 0.9083 (tp30) REVERT: K 129 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8812 (tt0) REVERT: K 132 MET cc_start: 0.8161 (mmt) cc_final: 0.7802 (mmm) REVERT: K 175 GLU cc_start: 0.9386 (mp0) cc_final: 0.8795 (mm-30) REVERT: K 182 GLU cc_start: 0.8073 (tt0) cc_final: 0.7771 (tt0) REVERT: K 207 MET cc_start: 0.9522 (mmp) cc_final: 0.9321 (mmp) REVERT: L 31 ASN cc_start: 0.8226 (p0) cc_final: 0.7730 (p0) REVERT: L 32 ARG cc_start: 0.8444 (mmp80) cc_final: 0.8235 (mmp80) REVERT: L 54 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8388 (tp-100) REVERT: L 108 ARG cc_start: 0.8962 (tpp80) cc_final: 0.8595 (tpp80) REVERT: M 84 MET cc_start: 0.9118 (mtt) cc_final: 0.8908 (ttm) REVERT: N 72 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8761 (mm-30) REVERT: N 84 MET cc_start: 0.9420 (mtm) cc_final: 0.8752 (ttm) REVERT: N 100 LEU cc_start: 0.9671 (mm) cc_final: 0.9410 (mm) REVERT: N 105 ASP cc_start: 0.9133 (t0) cc_final: 0.8436 (t70) REVERT: Q 32 CYS cc_start: 0.9550 (m) cc_final: 0.9326 (m) REVERT: Q 115 MET cc_start: 0.9579 (mtp) cc_final: 0.9263 (ptp) REVERT: R 33 MET cc_start: 0.9204 (tpp) cc_final: 0.8872 (tmm) REVERT: R 109 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9195 (mm-30) REVERT: R 115 MET cc_start: 0.9398 (mmm) cc_final: 0.8905 (mmm) REVERT: R 118 HIS cc_start: 0.8457 (t-90) cc_final: 0.7907 (t-90) REVERT: R 188 MET cc_start: 0.8497 (tpt) cc_final: 0.8119 (tpt) REVERT: R 194 ASP cc_start: 0.9575 (OUTLIER) cc_final: 0.9224 (p0) REVERT: R 199 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9231 (mm) REVERT: S 10 MET cc_start: 0.8213 (ttm) cc_final: 0.7845 (ttm) REVERT: S 109 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9098 (mm-30) REVERT: S 161 MET cc_start: 0.9481 (tmm) cc_final: 0.9278 (tmm) REVERT: S 188 MET cc_start: 0.9096 (tpp) cc_final: 0.8527 (tpp) REVERT: S 192 LYS cc_start: 0.9357 (mttt) cc_final: 0.8775 (mtpp) REVERT: S 234 MET cc_start: 0.8137 (tmm) cc_final: 0.7927 (ppp) REVERT: a 363 THR cc_start: 0.7603 (m) cc_final: 0.7245 (p) REVERT: a 453 MET cc_start: 0.7593 (mmm) cc_final: 0.7350 (mmm) REVERT: a 536 PHE cc_start: 0.7438 (m-80) cc_final: 0.7067 (m-80) REVERT: a 540 MET cc_start: 0.8300 (ppp) cc_final: 0.8057 (ppp) REVERT: a 616 MET cc_start: 0.8476 (mtt) cc_final: 0.7660 (tmm) REVERT: a 641 ILE cc_start: 0.9143 (mm) cc_final: 0.8205 (mm) REVERT: b 19 MET cc_start: 0.9025 (tmm) cc_final: 0.8752 (tmm) REVERT: b 25 CYS cc_start: 0.9072 (m) cc_final: 0.8850 (m) REVERT: b 69 ILE cc_start: 0.8061 (mt) cc_final: 0.7833 (mm) REVERT: c 421 MET cc_start: 0.8376 (ptt) cc_final: 0.8031 (mtp) REVERT: d 45 LEU cc_start: 0.9087 (mt) cc_final: 0.8772 (mt) REVERT: d 105 MET cc_start: 0.8317 (mmm) cc_final: 0.8116 (mmm) REVERT: g 13 PHE cc_start: 0.8153 (t80) cc_final: 0.7810 (t80) REVERT: h 53 MET cc_start: 0.7934 (mmp) cc_final: 0.7319 (ttt) REVERT: h 90 PHE cc_start: 0.8237 (m-80) cc_final: 0.7411 (m-80) REVERT: h 131 MET cc_start: 0.8418 (ppp) cc_final: 0.7928 (ppp) REVERT: i 13 PHE cc_start: 0.8600 (t80) cc_final: 0.8332 (t80) REVERT: i 53 MET cc_start: 0.8051 (mmt) cc_final: 0.7071 (ttt) REVERT: i 131 MET cc_start: 0.9004 (ppp) cc_final: 0.8774 (ppp) REVERT: i 155 LYS cc_start: 0.6977 (mmtt) cc_final: 0.6745 (mttm) REVERT: j 68 TYR cc_start: 0.9008 (m-10) cc_final: 0.8711 (m-80) REVERT: k 17 MET cc_start: 0.9050 (tpt) cc_final: 0.8606 (tpp) REVERT: k 25 PHE cc_start: 0.8681 (m-10) cc_final: 0.8387 (m-80) REVERT: k 108 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7732 (t80) REVERT: l 44 MET cc_start: 0.8302 (mmm) cc_final: 0.8069 (mmm) REVERT: l 47 MET cc_start: 0.7628 (ppp) cc_final: 0.7325 (ppp) REVERT: l 48 ARG cc_start: 0.6846 (ttp-110) cc_final: 0.6528 (ttm110) REVERT: m 25 PHE cc_start: 0.8040 (m-80) cc_final: 0.7682 (m-80) REVERT: m 121 THR cc_start: 0.6854 (m) cc_final: 0.5351 (p) REVERT: m 131 MET cc_start: 0.7292 (ptt) cc_final: 0.6733 (ptt) REVERT: n 13 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: n 28 MET cc_start: 0.8768 (tpp) cc_final: 0.8144 (mmt) REVERT: p 340 TYR cc_start: 0.8087 (m-80) cc_final: 0.7701 (m-80) outliers start: 205 outliers final: 146 residues processed: 1133 average time/residue: 0.5399 time to fit residues: 1072.6552 Evaluate side-chains 1126 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 964 time to evaluate : 5.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 GLU 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 C residue 24 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O 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 85 SER Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 171 ASP Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 543 ILE Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 579 PHE Chi-restraints excluded: chain a residue 587 LEU Chi-restraints excluded: chain a residue 592 PHE Chi-restraints excluded: chain a residue 609 LEU Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 614 ILE Chi-restraints excluded: chain a residue 637 GLN Chi-restraints excluded: chain a residue 807 HIS Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 33 TYR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 129 CYS Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 72 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain n residue 13 PHE Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 306 VAL Chi-restraints excluded: chain p residue 319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 499 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 481 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 512 optimal weight: 3.9990 chunk 549 optimal weight: 50.0000 chunk 398 optimal weight: 30.0000 chunk 75 optimal weight: 2.9990 chunk 634 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 85 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 524 ASN ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 63459 Z= 0.216 Angle : 0.704 14.823 86074 Z= 0.349 Chirality : 0.044 0.319 10040 Planarity : 0.004 0.058 11108 Dihedral : 4.552 118.788 9065 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.71 % Allowed : 18.96 % Favored : 78.33 % 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: 1.02 (0.09), residues: 8372 helix: 1.41 (0.07), residues: 4942 sheet: 0.18 (0.20), residues: 676 loop : -0.45 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP a 808 HIS 0.006 0.001 HIS a 749 PHE 0.047 0.002 PHE f 33 TYR 0.033 0.002 TYR b 70 ARG 0.008 0.000 ARG E 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1037 time to evaluate : 5.393 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: A 95 MET cc_start: 0.8742 (tpp) cc_final: 0.8482 (tpp) REVERT: A 100 ASP cc_start: 0.8949 (t0) cc_final: 0.8617 (t0) REVERT: A 231 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8861 (mm-40) REVERT: A 306 MET cc_start: 0.8982 (ptm) cc_final: 0.8517 (ppp) REVERT: A 324 GLU cc_start: 0.9303 (tt0) cc_final: 0.8755 (tm-30) REVERT: A 331 ILE cc_start: 0.9519 (tp) cc_final: 0.9307 (tt) REVERT: A 437 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9146 (tptp) REVERT: A 439 LEU cc_start: 0.9412 (tp) cc_final: 0.8954 (tp) REVERT: A 540 MET cc_start: 0.8872 (ptm) cc_final: 0.8416 (ptp) REVERT: A 550 MET cc_start: 0.9388 (ttm) cc_final: 0.8795 (ttp) REVERT: A 552 ARG cc_start: 0.9364 (ttt180) cc_final: 0.9023 (mtp-110) REVERT: A 596 LYS cc_start: 0.9337 (tttm) cc_final: 0.9120 (tppt) REVERT: A 608 MET cc_start: 0.9490 (ttm) cc_final: 0.9012 (ttp) REVERT: B 61 MET cc_start: 0.9188 (mmm) cc_final: 0.8898 (mmp) REVERT: B 168 LEU cc_start: 0.9124 (tp) cc_final: 0.8913 (tp) REVERT: B 306 MET cc_start: 0.9114 (mmt) cc_final: 0.8844 (mmt) REVERT: B 316 SER cc_start: 0.9653 (p) cc_final: 0.9390 (m) REVERT: B 340 MET cc_start: 0.9184 (mtt) cc_final: 0.8439 (ttm) REVERT: B 367 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: B 387 GLU cc_start: 0.8682 (tp30) cc_final: 0.8133 (tm-30) REVERT: B 392 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.8999 (p) REVERT: B 550 MET cc_start: 0.9506 (mmm) cc_final: 0.9297 (mmp) REVERT: C 65 GLN cc_start: 0.8635 (tt0) cc_final: 0.8306 (pt0) REVERT: C 95 MET cc_start: 0.8811 (mmm) cc_final: 0.8488 (mmm) REVERT: C 166 ILE cc_start: 0.9429 (mm) cc_final: 0.9108 (tp) REVERT: C 168 LEU cc_start: 0.9450 (tp) cc_final: 0.9051 (tt) REVERT: C 173 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7624 (pmt100) REVERT: C 231 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8749 (mp10) REVERT: C 232 ARG cc_start: 0.8718 (mtt90) cc_final: 0.8348 (mtm-85) REVERT: C 254 CYS cc_start: 0.8684 (m) cc_final: 0.8206 (m) REVERT: C 283 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8855 (mm-30) REVERT: C 296 MET cc_start: 0.8305 (ttt) cc_final: 0.7935 (ttm) REVERT: C 318 MET cc_start: 0.9079 (mtt) cc_final: 0.8623 (mtt) REVERT: C 360 GLU cc_start: 0.9145 (tt0) cc_final: 0.8882 (tm-30) REVERT: C 392 VAL cc_start: 0.9474 (OUTLIER) cc_final: 0.9221 (p) REVERT: C 487 GLU cc_start: 0.9432 (tp30) cc_final: 0.9049 (tm-30) REVERT: C 491 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8760 (tp30) REVERT: C 509 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9371 (pp) REVERT: C 550 MET cc_start: 0.9132 (ttm) cc_final: 0.8753 (ttp) REVERT: C 573 HIS cc_start: 0.8790 (t70) cc_final: 0.8291 (t70) REVERT: C 608 MET cc_start: 0.9173 (mtm) cc_final: 0.8901 (ptm) REVERT: D 169 MET cc_start: 0.8529 (tmm) cc_final: 0.8277 (tmm) REVERT: D 238 MET cc_start: 0.8651 (tpp) cc_final: 0.8244 (tpt) REVERT: D 254 MET cc_start: 0.8598 (mmm) cc_final: 0.8214 (mmm) REVERT: D 300 MET cc_start: 0.9482 (mmm) cc_final: 0.8590 (mmm) REVERT: D 330 ASP cc_start: 0.9027 (m-30) cc_final: 0.8730 (t0) REVERT: D 351 ILE cc_start: 0.9500 (mt) cc_final: 0.9272 (mm) REVERT: D 410 MET cc_start: 0.8877 (mtt) cc_final: 0.8528 (mtm) REVERT: E 90 SER cc_start: 0.9358 (t) cc_final: 0.9148 (p) REVERT: E 113 GLU cc_start: 0.9049 (tt0) cc_final: 0.8648 (tm-30) REVERT: E 169 MET cc_start: 0.8881 (tmm) cc_final: 0.8610 (tmm) REVERT: E 183 ILE cc_start: 0.9301 (mt) cc_final: 0.8998 (pt) REVERT: E 254 MET cc_start: 0.9085 (mmm) cc_final: 0.8859 (mmm) REVERT: E 356 MET cc_start: 0.8195 (ttm) cc_final: 0.7576 (ttp) REVERT: E 402 MET cc_start: 0.8975 (ttm) cc_final: 0.8510 (ttt) REVERT: E 410 MET cc_start: 0.9016 (mtm) cc_final: 0.8007 (ptp) REVERT: E 452 LEU cc_start: 0.9513 (tt) cc_final: 0.9120 (mt) REVERT: F 74 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9140 (mp) REVERT: F 76 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8950 (mm) REVERT: F 88 GLU cc_start: 0.8990 (tt0) cc_final: 0.8442 (tm-30) REVERT: F 180 MET cc_start: 0.8891 (mtp) cc_final: 0.8680 (mmm) REVERT: F 254 MET cc_start: 0.8775 (mmm) cc_final: 0.8500 (mmm) REVERT: F 271 ARG cc_start: 0.8935 (mtt180) cc_final: 0.8509 (ttm110) REVERT: F 281 THR cc_start: 0.9687 (m) cc_final: 0.9461 (p) REVERT: F 283 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8632 (mt-10) REVERT: F 300 MET cc_start: 0.9351 (mmm) cc_final: 0.8979 (mmm) REVERT: F 327 MET cc_start: 0.9556 (ttm) cc_final: 0.9284 (ttm) REVERT: F 333 THR cc_start: 0.9456 (m) cc_final: 0.9159 (p) REVERT: F 360 ASP cc_start: 0.8991 (t0) cc_final: 0.8579 (t0) REVERT: F 367 ASP cc_start: 0.9099 (t70) cc_final: 0.8855 (t0) REVERT: F 402 MET cc_start: 0.8819 (ttm) cc_final: 0.7993 (ttt) REVERT: F 410 MET cc_start: 0.9093 (mtp) cc_final: 0.8563 (ptp) REVERT: F 417 ASP cc_start: 0.9145 (m-30) cc_final: 0.8809 (m-30) REVERT: F 491 MET cc_start: 0.9213 (mtp) cc_final: 0.8897 (mtp) REVERT: H 14 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8077 (tpp) REVERT: H 58 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7975 (tmm) REVERT: H 78 ASP cc_start: 0.7799 (t0) cc_final: 0.7446 (t0) REVERT: H 190 GLU cc_start: 0.9182 (tp30) cc_final: 0.8500 (tm-30) REVERT: H 192 ASP cc_start: 0.9102 (m-30) cc_final: 0.8804 (t70) REVERT: I 76 MET cc_start: 0.9589 (mmp) cc_final: 0.9262 (mmm) REVERT: I 129 GLU cc_start: 0.8836 (tp30) cc_final: 0.8530 (tp30) REVERT: I 182 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: I 201 ASP cc_start: 0.9076 (m-30) cc_final: 0.8695 (p0) REVERT: I 202 LEU cc_start: 0.9720 (mt) cc_final: 0.9243 (mt) REVERT: J 175 GLU cc_start: 0.9222 (pm20) cc_final: 0.9021 (mm-30) REVERT: J 207 MET cc_start: 0.9286 (tpp) cc_final: 0.8597 (tpp) REVERT: J 208 MET cc_start: 0.8664 (ppp) cc_final: 0.8371 (ppp) REVERT: J 210 GLU cc_start: 0.8801 (mp0) cc_final: 0.8102 (mp0) REVERT: K 93 ASP cc_start: 0.9494 (m-30) cc_final: 0.9209 (m-30) REVERT: K 97 GLU cc_start: 0.9411 (tp30) cc_final: 0.9054 (tp30) REVERT: K 129 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8790 (tt0) REVERT: K 132 MET cc_start: 0.8191 (mmt) cc_final: 0.7816 (mmm) REVERT: K 175 GLU cc_start: 0.9375 (mp0) cc_final: 0.8792 (mm-30) REVERT: K 182 GLU cc_start: 0.8024 (tt0) cc_final: 0.7689 (tt0) REVERT: K 207 MET cc_start: 0.9553 (mmp) cc_final: 0.9258 (mmp) REVERT: L 31 ASN cc_start: 0.8225 (p0) cc_final: 0.7715 (p0) REVERT: L 54 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8294 (tp-100) REVERT: N 72 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8757 (mm-30) REVERT: N 84 MET cc_start: 0.9411 (mtm) cc_final: 0.8756 (ttm) REVERT: N 100 LEU cc_start: 0.9674 (mm) cc_final: 0.9347 (mm) REVERT: N 105 ASP cc_start: 0.9084 (t0) cc_final: 0.8410 (t70) REVERT: O 75 GLN cc_start: 0.9531 (tp-100) cc_final: 0.9142 (tp-100) REVERT: Q 32 CYS cc_start: 0.9525 (m) cc_final: 0.9288 (m) REVERT: Q 115 MET cc_start: 0.9535 (mtp) cc_final: 0.9230 (ptp) REVERT: R 33 MET cc_start: 0.9151 (tpp) cc_final: 0.8806 (tmm) REVERT: R 109 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9185 (mm-30) REVERT: R 115 MET cc_start: 0.9342 (mmm) cc_final: 0.8813 (mmm) REVERT: R 118 HIS cc_start: 0.8449 (t-90) cc_final: 0.7975 (t-90) REVERT: R 126 TYR cc_start: 0.9604 (m-80) cc_final: 0.9215 (m-80) REVERT: R 188 MET cc_start: 0.8569 (tpt) cc_final: 0.8137 (tpt) REVERT: R 194 ASP cc_start: 0.9571 (OUTLIER) cc_final: 0.9229 (p0) REVERT: R 199 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9229 (mm) REVERT: S 10 MET cc_start: 0.8202 (ttm) cc_final: 0.7842 (ttm) REVERT: S 109 GLU cc_start: 0.9381 (mt-10) cc_final: 0.8993 (mm-30) REVERT: S 115 MET cc_start: 0.9734 (mtp) cc_final: 0.9518 (mtm) REVERT: S 161 MET cc_start: 0.9485 (tmm) cc_final: 0.9252 (tmm) REVERT: S 188 MET cc_start: 0.9065 (tpp) cc_final: 0.8475 (tpp) REVERT: S 192 LYS cc_start: 0.9352 (mttt) cc_final: 0.8789 (mtpp) REVERT: a 363 THR cc_start: 0.7589 (m) cc_final: 0.7215 (p) REVERT: a 453 MET cc_start: 0.7606 (mmm) cc_final: 0.7357 (mmm) REVERT: a 536 PHE cc_start: 0.7421 (m-80) cc_final: 0.7045 (m-80) REVERT: a 540 MET cc_start: 0.8293 (ppp) cc_final: 0.8033 (ppp) REVERT: a 574 ILE cc_start: 0.8897 (mt) cc_final: 0.8565 (mm) REVERT: a 616 MET cc_start: 0.8442 (mtt) cc_final: 0.7715 (tmm) REVERT: a 641 ILE cc_start: 0.9158 (mm) cc_final: 0.8291 (mm) REVERT: a 730 LEU cc_start: 0.9187 (tt) cc_final: 0.8986 (pp) REVERT: a 745 LEU cc_start: 0.9145 (mm) cc_final: 0.8729 (mm) REVERT: b 19 MET cc_start: 0.9058 (tmm) cc_final: 0.8763 (tmm) REVERT: b 25 CYS cc_start: 0.9032 (m) cc_final: 0.8815 (m) REVERT: b 69 ILE cc_start: 0.8042 (mt) cc_final: 0.7824 (mm) REVERT: c 421 MET cc_start: 0.8423 (ptt) cc_final: 0.8204 (mtm) REVERT: d 45 LEU cc_start: 0.9073 (mt) cc_final: 0.8750 (mt) REVERT: g 13 PHE cc_start: 0.8100 (t80) cc_final: 0.7706 (t80) REVERT: h 53 MET cc_start: 0.7844 (mmp) cc_final: 0.7259 (ttt) REVERT: h 90 PHE cc_start: 0.8096 (m-80) cc_final: 0.7523 (m-80) REVERT: i 53 MET cc_start: 0.8030 (mmt) cc_final: 0.6965 (ttt) REVERT: i 131 MET cc_start: 0.8938 (ppp) cc_final: 0.8720 (ppp) REVERT: j 68 TYR cc_start: 0.9007 (m-10) cc_final: 0.8698 (m-80) REVERT: k 17 MET cc_start: 0.9068 (tpt) cc_final: 0.8856 (tpp) REVERT: k 21 SER cc_start: 0.9255 (m) cc_final: 0.8572 (p) REVERT: k 25 PHE cc_start: 0.8638 (m-10) cc_final: 0.8262 (m-80) REVERT: l 47 MET cc_start: 0.7641 (ppp) cc_final: 0.7307 (ppp) REVERT: l 48 ARG cc_start: 0.6856 (ttp-110) cc_final: 0.6495 (ttp-110) REVERT: m 25 PHE cc_start: 0.8110 (m-80) cc_final: 0.7767 (m-80) REVERT: m 47 MET cc_start: 0.7843 (mmm) cc_final: 0.7585 (mmm) REVERT: m 121 THR cc_start: 0.6767 (m) cc_final: 0.5452 (p) REVERT: m 131 MET cc_start: 0.7284 (ptt) cc_final: 0.6813 (ptt) REVERT: n 13 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: n 28 MET cc_start: 0.8756 (tpp) cc_final: 0.8177 (mmt) REVERT: n 110 ILE cc_start: 0.8751 (mm) cc_final: 0.8526 (mm) REVERT: p 331 MET cc_start: 0.7660 (tmm) cc_final: 0.7364 (tmm) REVERT: p 336 ASP cc_start: 0.7674 (m-30) cc_final: 0.7416 (m-30) outliers start: 165 outliers final: 117 residues processed: 1133 average time/residue: 0.5505 time to fit residues: 1097.7211 Evaluate side-chains 1118 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 987 time to evaluate : 5.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 543 ILE Chi-restraints excluded: chain a residue 587 LEU Chi-restraints excluded: chain a residue 592 PHE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 637 GLN Chi-restraints excluded: chain a residue 786 LEU Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 93 SER Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 33 TYR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 92 GLN Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 72 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain n residue 13 PHE Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 53 MET Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 733 optimal weight: 7.9990 chunk 772 optimal weight: 30.0000 chunk 705 optimal weight: 20.0000 chunk 751 optimal weight: 0.7980 chunk 452 optimal weight: 40.0000 chunk 327 optimal weight: 40.0000 chunk 590 optimal weight: 30.0000 chunk 230 optimal weight: 1.9990 chunk 679 optimal weight: 9.9990 chunk 711 optimal weight: 9.9990 chunk 749 optimal weight: 0.8980 overall best weight: 4.3386 ------------------------------------------------------------------------------- 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** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN a 504 ASN ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 812 GLN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 226 ASN i 92 GLN k 7 ASN ** n 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 63459 Z= 0.308 Angle : 0.754 15.374 86074 Z= 0.377 Chirality : 0.045 0.342 10040 Planarity : 0.005 0.077 11108 Dihedral : 4.634 116.663 9063 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.76 % Allowed : 19.55 % Favored : 77.69 % 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: 0.86 (0.09), residues: 8372 helix: 1.31 (0.07), residues: 4920 sheet: 0.11 (0.21), residues: 666 loop : -0.56 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP a 808 HIS 0.009 0.001 HIS E 363 PHE 0.050 0.002 PHE f 33 TYR 0.028 0.002 TYR k 144 ARG 0.018 0.001 ARG O 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 992 time to evaluate : 5.391 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: A 61 MET cc_start: 0.9069 (mtp) cc_final: 0.8594 (tpp) REVERT: A 95 MET cc_start: 0.8785 (tpp) cc_final: 0.8545 (tpp) REVERT: A 100 ASP cc_start: 0.9024 (t0) cc_final: 0.8683 (t0) REVERT: A 231 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8909 (mm-40) REVERT: A 306 MET cc_start: 0.8996 (ptm) cc_final: 0.8507 (ppp) REVERT: A 324 GLU cc_start: 0.9298 (tt0) cc_final: 0.8829 (tm-30) REVERT: A 331 ILE cc_start: 0.9367 (tp) cc_final: 0.8986 (tt) REVERT: A 340 MET cc_start: 0.8828 (tpp) cc_final: 0.8580 (tpp) REVERT: A 437 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9150 (tptp) REVERT: A 439 LEU cc_start: 0.9433 (tp) cc_final: 0.8985 (tp) REVERT: A 550 MET cc_start: 0.9396 (ttm) cc_final: 0.8806 (ttm) REVERT: A 552 ARG cc_start: 0.9375 (ttt180) cc_final: 0.9173 (ttm-80) REVERT: A 570 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9343 (tp) REVERT: A 596 LYS cc_start: 0.9319 (tttm) cc_final: 0.9106 (tppt) REVERT: A 608 MET cc_start: 0.9491 (ttm) cc_final: 0.9124 (ttp) REVERT: B 34 MET cc_start: 0.8629 (tpt) cc_final: 0.8361 (tpt) REVERT: B 168 LEU cc_start: 0.9156 (tp) cc_final: 0.8946 (tp) REVERT: B 252 PHE cc_start: 0.6575 (t80) cc_final: 0.6326 (t80) REVERT: B 306 MET cc_start: 0.9174 (mmt) cc_final: 0.8657 (mmt) REVERT: B 318 MET cc_start: 0.9162 (mmm) cc_final: 0.8941 (mmm) REVERT: B 340 MET cc_start: 0.9196 (mtt) cc_final: 0.8435 (ttm) REVERT: B 367 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: B 387 GLU cc_start: 0.8806 (tp30) cc_final: 0.8371 (tm-30) REVERT: C 61 MET cc_start: 0.9304 (tpp) cc_final: 0.8931 (mmp) REVERT: C 65 GLN cc_start: 0.8666 (tt0) cc_final: 0.8258 (pt0) REVERT: C 168 LEU cc_start: 0.9444 (tp) cc_final: 0.9226 (tp) REVERT: C 231 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8754 (mm-40) REVERT: C 232 ARG cc_start: 0.8830 (mtt90) cc_final: 0.8583 (mtm-85) REVERT: C 254 CYS cc_start: 0.8718 (m) cc_final: 0.8438 (m) REVERT: C 283 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8886 (mm-30) REVERT: C 296 MET cc_start: 0.8340 (ttt) cc_final: 0.7933 (ttm) REVERT: C 360 GLU cc_start: 0.9179 (tt0) cc_final: 0.8885 (tm-30) REVERT: C 487 GLU cc_start: 0.9461 (tp30) cc_final: 0.9051 (tm-30) REVERT: C 491 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8900 (tp30) REVERT: C 509 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9385 (pp) REVERT: C 550 MET cc_start: 0.9140 (ttm) cc_final: 0.8700 (ttp) REVERT: C 573 HIS cc_start: 0.8730 (t70) cc_final: 0.8327 (t-90) REVERT: C 608 MET cc_start: 0.9217 (mtm) cc_final: 0.8955 (ptm) REVERT: D 238 MET cc_start: 0.8672 (tpp) cc_final: 0.8290 (tpt) REVERT: D 254 MET cc_start: 0.8671 (mmm) cc_final: 0.8343 (mmm) REVERT: D 270 GLU cc_start: 0.9360 (tt0) cc_final: 0.9047 (tt0) REVERT: D 300 MET cc_start: 0.9470 (mmm) cc_final: 0.8580 (mmm) REVERT: D 330 ASP cc_start: 0.9074 (m-30) cc_final: 0.8820 (t0) REVERT: D 351 ILE cc_start: 0.9499 (mt) cc_final: 0.9259 (mm) REVERT: D 354 LEU cc_start: 0.9397 (mm) cc_final: 0.9145 (tp) REVERT: D 410 MET cc_start: 0.8977 (mtt) cc_final: 0.8642 (mtm) REVERT: E 90 SER cc_start: 0.9413 (t) cc_final: 0.9195 (p) REVERT: E 113 GLU cc_start: 0.9019 (tt0) cc_final: 0.8640 (tm-30) REVERT: E 180 MET cc_start: 0.8993 (mmm) cc_final: 0.8698 (mmm) REVERT: E 254 MET cc_start: 0.9121 (mmm) cc_final: 0.8882 (mmm) REVERT: E 333 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8861 (p) REVERT: E 356 MET cc_start: 0.8238 (ttm) cc_final: 0.7653 (ttp) REVERT: E 400 ARG cc_start: 0.7875 (tpm170) cc_final: 0.7279 (tpm170) REVERT: E 402 MET cc_start: 0.8922 (ttm) cc_final: 0.8477 (ttt) REVERT: E 410 MET cc_start: 0.9055 (mtm) cc_final: 0.8108 (ptp) REVERT: E 453 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8892 (tm-30) REVERT: F 74 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9067 (mp) REVERT: F 76 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8980 (mm) REVERT: F 88 GLU cc_start: 0.9020 (tt0) cc_final: 0.8444 (tm-30) REVERT: F 180 MET cc_start: 0.8965 (mtp) cc_final: 0.8692 (mmm) REVERT: F 254 MET cc_start: 0.8883 (mmm) cc_final: 0.8607 (mmm) REVERT: F 271 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8580 (ttm-80) REVERT: F 283 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8655 (mt-10) REVERT: F 300 MET cc_start: 0.9385 (mmm) cc_final: 0.8988 (mmm) REVERT: F 327 MET cc_start: 0.9546 (ttm) cc_final: 0.9220 (ttm) REVERT: F 333 THR cc_start: 0.9482 (m) cc_final: 0.9187 (p) REVERT: F 360 ASP cc_start: 0.9000 (t0) cc_final: 0.8563 (t0) REVERT: F 367 ASP cc_start: 0.9178 (t70) cc_final: 0.8940 (t0) REVERT: F 402 MET cc_start: 0.8923 (ttm) cc_final: 0.8038 (ttt) REVERT: F 410 MET cc_start: 0.8933 (mtp) cc_final: 0.8453 (ptp) REVERT: F 417 ASP cc_start: 0.9180 (m-30) cc_final: 0.8838 (m-30) REVERT: F 491 MET cc_start: 0.9219 (mtp) cc_final: 0.8886 (mtp) REVERT: H 14 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8678 (tpp) REVERT: H 58 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8051 (tmm) REVERT: H 78 ASP cc_start: 0.7894 (t0) cc_final: 0.7503 (t0) REVERT: H 192 ASP cc_start: 0.9188 (m-30) cc_final: 0.8833 (t70) REVERT: I 76 MET cc_start: 0.9607 (mmp) cc_final: 0.9280 (mmm) REVERT: I 129 GLU cc_start: 0.8851 (tp30) cc_final: 0.8505 (tp30) REVERT: I 132 MET cc_start: 0.9249 (mtt) cc_final: 0.8896 (mtt) REVERT: I 201 ASP cc_start: 0.9176 (m-30) cc_final: 0.8790 (p0) REVERT: I 202 LEU cc_start: 0.9739 (mt) cc_final: 0.9461 (mm) REVERT: J 129 GLU cc_start: 0.8167 (tt0) cc_final: 0.7344 (tt0) REVERT: J 132 MET cc_start: 0.8170 (mmt) cc_final: 0.7176 (mmm) REVERT: J 207 MET cc_start: 0.9308 (tpp) cc_final: 0.8746 (tpp) REVERT: J 208 MET cc_start: 0.8781 (ppp) cc_final: 0.8520 (ppp) REVERT: J 210 GLU cc_start: 0.8861 (mp0) cc_final: 0.8518 (mp0) REVERT: K 93 ASP cc_start: 0.9505 (m-30) cc_final: 0.9214 (m-30) REVERT: K 97 GLU cc_start: 0.9434 (tp30) cc_final: 0.9079 (tp30) REVERT: K 129 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8712 (tt0) REVERT: K 132 MET cc_start: 0.8097 (mmt) cc_final: 0.7790 (mmm) REVERT: K 175 GLU cc_start: 0.9392 (mp0) cc_final: 0.8818 (mm-30) REVERT: K 177 ILE cc_start: 0.9045 (mm) cc_final: 0.8832 (mm) REVERT: K 182 GLU cc_start: 0.8009 (tt0) cc_final: 0.7665 (tt0) REVERT: K 207 MET cc_start: 0.9567 (mmp) cc_final: 0.9345 (mmp) REVERT: L 31 ASN cc_start: 0.8269 (p0) cc_final: 0.7787 (p0) REVERT: L 54 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8362 (tp-100) REVERT: L 108 ARG cc_start: 0.8941 (tpp80) cc_final: 0.8536 (tpp80) REVERT: M 84 MET cc_start: 0.9038 (ttm) cc_final: 0.8772 (ttm) REVERT: N 72 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8771 (mm-30) REVERT: N 84 MET cc_start: 0.9438 (mtm) cc_final: 0.8808 (ttm) REVERT: N 100 LEU cc_start: 0.9668 (mm) cc_final: 0.9402 (mm) REVERT: N 105 ASP cc_start: 0.9099 (t0) cc_final: 0.8424 (t70) REVERT: O 78 ARG cc_start: 0.9176 (tmm160) cc_final: 0.8882 (ttp80) REVERT: Q 32 CYS cc_start: 0.9547 (m) cc_final: 0.9302 (m) REVERT: Q 103 MET cc_start: 0.7747 (tpt) cc_final: 0.7547 (tpp) REVERT: Q 115 MET cc_start: 0.9573 (mtp) cc_final: 0.9286 (ptp) REVERT: R 33 MET cc_start: 0.9187 (tpp) cc_final: 0.8848 (tmm) REVERT: R 109 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9181 (mm-30) REVERT: R 115 MET cc_start: 0.9382 (mmm) cc_final: 0.8975 (mmm) REVERT: R 118 HIS cc_start: 0.8487 (t-90) cc_final: 0.8013 (t-90) REVERT: R 126 TYR cc_start: 0.9623 (m-80) cc_final: 0.9328 (m-80) REVERT: R 188 MET cc_start: 0.8565 (tpt) cc_final: 0.8174 (tpt) REVERT: R 194 ASP cc_start: 0.9580 (OUTLIER) cc_final: 0.9301 (p0) REVERT: R 199 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9206 (mm) REVERT: S 10 MET cc_start: 0.8234 (ttm) cc_final: 0.7865 (ttm) REVERT: S 109 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9001 (mm-30) REVERT: S 161 MET cc_start: 0.9538 (tmm) cc_final: 0.9290 (tmm) REVERT: S 188 MET cc_start: 0.9073 (tpp) cc_final: 0.8482 (tpp) REVERT: S 192 LYS cc_start: 0.9363 (mttt) cc_final: 0.8811 (mtpp) REVERT: a 10 MET cc_start: 0.7060 (tmm) cc_final: 0.6379 (tmm) REVERT: a 363 THR cc_start: 0.7434 (m) cc_final: 0.7110 (p) REVERT: a 423 MET cc_start: 0.7827 (mmt) cc_final: 0.7607 (mmt) REVERT: a 536 PHE cc_start: 0.7439 (m-80) cc_final: 0.6995 (m-80) REVERT: a 540 MET cc_start: 0.8332 (ppp) cc_final: 0.8056 (ppp) REVERT: a 592 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: a 616 MET cc_start: 0.8483 (mtt) cc_final: 0.7747 (tmm) REVERT: a 641 ILE cc_start: 0.9186 (mm) cc_final: 0.8307 (mm) REVERT: b 19 MET cc_start: 0.9101 (tmm) cc_final: 0.8794 (tmm) REVERT: b 25 CYS cc_start: 0.9061 (m) cc_final: 0.8833 (m) REVERT: b 41 LEU cc_start: 0.8492 (mp) cc_final: 0.7943 (tp) REVERT: b 203 MET cc_start: 0.5787 (mmt) cc_final: 0.4625 (mmm) REVERT: c 421 MET cc_start: 0.8394 (ptt) cc_final: 0.8127 (mtp) REVERT: g 13 PHE cc_start: 0.8173 (t80) cc_final: 0.7718 (t80) REVERT: h 53 MET cc_start: 0.7969 (mmp) cc_final: 0.7405 (ttt) REVERT: h 90 PHE cc_start: 0.8138 (m-80) cc_final: 0.7564 (m-80) REVERT: i 13 PHE cc_start: 0.8740 (t80) cc_final: 0.8029 (t80) REVERT: i 17 MET cc_start: 0.8949 (ttm) cc_final: 0.8218 (mtm) REVERT: i 53 MET cc_start: 0.8092 (mmt) cc_final: 0.6930 (ttt) REVERT: i 68 TYR cc_start: 0.8728 (m-10) cc_final: 0.8363 (m-80) REVERT: i 131 MET cc_start: 0.8941 (ppp) cc_final: 0.8718 (ppp) REVERT: i 155 LYS cc_start: 0.6689 (mmtt) cc_final: 0.6397 (mttm) REVERT: j 68 TYR cc_start: 0.9060 (m-10) cc_final: 0.8573 (m-80) REVERT: k 21 SER cc_start: 0.9280 (m) cc_final: 0.8630 (p) REVERT: l 47 MET cc_start: 0.7660 (ppp) cc_final: 0.7428 (ppp) REVERT: l 48 ARG cc_start: 0.6909 (ttp-110) cc_final: 0.6522 (ttm110) REVERT: m 23 MET cc_start: 0.7484 (ppp) cc_final: 0.6768 (ppp) REVERT: m 25 PHE cc_start: 0.8145 (m-80) cc_final: 0.7750 (m-80) REVERT: m 47 MET cc_start: 0.7925 (mmm) cc_final: 0.7692 (mmm) REVERT: m 121 THR cc_start: 0.6743 (m) cc_final: 0.5477 (p) REVERT: m 131 MET cc_start: 0.7286 (ptt) cc_final: 0.6956 (ptt) REVERT: n 13 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: n 61 MET cc_start: 0.7213 (mmm) cc_final: 0.6980 (mtp) REVERT: n 110 ILE cc_start: 0.8798 (mm) cc_final: 0.8588 (mm) outliers start: 168 outliers final: 131 residues processed: 1089 average time/residue: 0.5461 time to fit residues: 1038.7721 Evaluate side-chains 1105 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 960 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 543 ILE Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 579 PHE Chi-restraints excluded: chain a residue 592 PHE Chi-restraints excluded: chain a residue 609 LEU Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 637 GLN Chi-restraints excluded: chain a residue 786 LEU Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 93 SER Chi-restraints excluded: chain c residue 445 THR Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 33 TYR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 118 VAL Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 92 GLN Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 72 VAL Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain n residue 13 PHE Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 53 MET Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 493 optimal weight: 2.9990 chunk 794 optimal weight: 20.0000 chunk 485 optimal weight: 5.9990 chunk 377 optimal weight: 50.0000 chunk 552 optimal weight: 50.0000 chunk 833 optimal weight: 5.9990 chunk 767 optimal weight: 20.0000 chunk 664 optimal weight: 20.0000 chunk 68 optimal weight: 0.0980 chunk 512 optimal weight: 9.9990 chunk 407 optimal weight: 6.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- 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** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN S 59 ASN ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 721 GLN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 GLN n 7 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 63459 Z= 0.310 Angle : 0.762 14.007 86074 Z= 0.382 Chirality : 0.045 0.368 10040 Planarity : 0.004 0.058 11108 Dihedral : 4.668 115.932 9063 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.64 % Allowed : 19.96 % Favored : 77.40 % 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: 0.81 (0.09), residues: 8372 helix: 1.28 (0.07), residues: 4898 sheet: 0.11 (0.21), residues: 640 loop : -0.58 (0.12), residues: 2834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP a 808 HIS 0.008 0.001 HIS E 363 PHE 0.052 0.002 PHE f 33 TYR 0.042 0.002 TYR j 32 ARG 0.014 0.001 ARG O 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 989 time to evaluate : 5.422 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: 0.8778 (tpp) cc_final: 0.8544 (tpp) REVERT: A 100 ASP cc_start: 0.9055 (t0) cc_final: 0.8710 (t0) REVERT: A 306 MET cc_start: 0.8985 (ptm) cc_final: 0.8547 (ppp) REVERT: A 324 GLU cc_start: 0.9312 (tt0) cc_final: 0.8878 (tm-30) REVERT: A 340 MET cc_start: 0.8844 (tpp) cc_final: 0.8550 (tpp) REVERT: A 347 MET cc_start: 0.8591 (tpp) cc_final: 0.8186 (tpp) REVERT: A 439 LEU cc_start: 0.9437 (tp) cc_final: 0.9002 (tp) REVERT: A 540 MET cc_start: 0.8936 (ptm) cc_final: 0.8357 (ptp) REVERT: A 550 MET cc_start: 0.9402 (ttm) cc_final: 0.8773 (ttm) REVERT: A 552 ARG cc_start: 0.9361 (ttt180) cc_final: 0.9116 (ttm-80) REVERT: A 570 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9316 (tp) REVERT: A 596 LYS cc_start: 0.9322 (tttm) cc_final: 0.9111 (tppt) REVERT: A 608 MET cc_start: 0.9499 (ttm) cc_final: 0.9112 (ttt) REVERT: B 34 MET cc_start: 0.8602 (tpt) cc_final: 0.8350 (tpt) REVERT: B 168 LEU cc_start: 0.9145 (tp) cc_final: 0.8911 (tp) REVERT: B 252 PHE cc_start: 0.6764 (t80) cc_final: 0.6539 (t80) REVERT: B 306 MET cc_start: 0.9257 (mmt) cc_final: 0.9024 (mmt) REVERT: B 340 MET cc_start: 0.9180 (mtt) cc_final: 0.8394 (ttm) REVERT: B 367 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: B 387 GLU cc_start: 0.8801 (tp30) cc_final: 0.8175 (tm-30) REVERT: B 550 MET cc_start: 0.9394 (mmp) cc_final: 0.8972 (mtp) REVERT: C 61 MET cc_start: 0.9294 (tpp) cc_final: 0.8926 (mmp) REVERT: C 65 GLN cc_start: 0.8683 (tt0) cc_final: 0.8306 (pt0) REVERT: C 168 LEU cc_start: 0.9418 (tp) cc_final: 0.9199 (tp) REVERT: C 231 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8722 (mm-40) REVERT: C 232 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8487 (mtm-85) REVERT: C 235 ASP cc_start: 0.9357 (t0) cc_final: 0.8977 (m-30) REVERT: C 254 CYS cc_start: 0.8735 (m) cc_final: 0.8438 (m) REVERT: C 283 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8925 (mm-30) REVERT: C 296 MET cc_start: 0.8330 (ttt) cc_final: 0.7923 (ttm) REVERT: C 318 MET cc_start: 0.9115 (mtt) cc_final: 0.8339 (mtp) REVERT: C 360 GLU cc_start: 0.9175 (tt0) cc_final: 0.8883 (tm-30) REVERT: C 487 GLU cc_start: 0.9481 (tp30) cc_final: 0.9040 (tm-30) REVERT: C 491 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8899 (tp30) REVERT: C 509 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9383 (pp) REVERT: C 550 MET cc_start: 0.9148 (ttm) cc_final: 0.8718 (ttp) REVERT: C 573 HIS cc_start: 0.8801 (t70) cc_final: 0.8399 (t-90) REVERT: C 608 MET cc_start: 0.9208 (mtm) cc_final: 0.8949 (ptm) REVERT: D 169 MET cc_start: 0.8372 (tmm) cc_final: 0.8074 (tmm) REVERT: D 238 MET cc_start: 0.8645 (tpp) cc_final: 0.8266 (tpt) REVERT: D 254 MET cc_start: 0.8686 (mmm) cc_final: 0.8338 (mmm) REVERT: D 270 GLU cc_start: 0.9366 (tt0) cc_final: 0.9068 (tt0) REVERT: D 300 MET cc_start: 0.9457 (mmm) cc_final: 0.8640 (mmm) REVERT: D 330 ASP cc_start: 0.9055 (m-30) cc_final: 0.8799 (t0) REVERT: D 351 ILE cc_start: 0.9501 (mt) cc_final: 0.9270 (mm) REVERT: D 410 MET cc_start: 0.8970 (mtt) cc_final: 0.8628 (mtm) REVERT: E 180 MET cc_start: 0.8971 (mmm) cc_final: 0.8757 (mmm) REVERT: E 183 ILE cc_start: 0.9333 (mt) cc_final: 0.8983 (pt) REVERT: E 254 MET cc_start: 0.9133 (mmm) cc_final: 0.8884 (mmm) REVERT: E 333 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8867 (p) REVERT: E 356 MET cc_start: 0.8233 (ttm) cc_final: 0.7660 (ttp) REVERT: E 400 ARG cc_start: 0.7953 (tpm170) cc_final: 0.7275 (tpm170) REVERT: E 402 MET cc_start: 0.8940 (ttm) cc_final: 0.8511 (ttt) REVERT: E 410 MET cc_start: 0.9027 (mtm) cc_final: 0.8120 (ptp) REVERT: E 452 LEU cc_start: 0.9520 (tt) cc_final: 0.9164 (mt) REVERT: E 453 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8772 (tm-30) REVERT: F 74 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.8956 (mp) REVERT: F 76 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9006 (mm) REVERT: F 88 GLU cc_start: 0.9023 (tt0) cc_final: 0.8439 (tm-30) REVERT: F 254 MET cc_start: 0.8898 (mmm) cc_final: 0.8622 (mmm) REVERT: F 271 ARG cc_start: 0.9073 (mtt180) cc_final: 0.8604 (ttm-80) REVERT: F 283 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8680 (mt-10) REVERT: F 300 MET cc_start: 0.9375 (mmm) cc_final: 0.8977 (mmm) REVERT: F 327 MET cc_start: 0.9549 (ttm) cc_final: 0.9254 (ttm) REVERT: F 333 THR cc_start: 0.9493 (m) cc_final: 0.9194 (p) REVERT: F 360 ASP cc_start: 0.8985 (t0) cc_final: 0.8583 (t0) REVERT: F 367 ASP cc_start: 0.9173 (t70) cc_final: 0.8932 (t0) REVERT: F 402 MET cc_start: 0.8962 (ttm) cc_final: 0.8085 (ttt) REVERT: F 417 ASP cc_start: 0.9182 (m-30) cc_final: 0.8843 (m-30) REVERT: F 491 MET cc_start: 0.9215 (mtp) cc_final: 0.8883 (mtp) REVERT: H 14 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8671 (tpp) REVERT: H 58 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8112 (tmm) REVERT: H 78 ASP cc_start: 0.7900 (t0) cc_final: 0.7602 (t0) REVERT: H 192 ASP cc_start: 0.9211 (m-30) cc_final: 0.8853 (t70) REVERT: I 76 MET cc_start: 0.9623 (mmp) cc_final: 0.9300 (mmm) REVERT: I 129 GLU cc_start: 0.8841 (tp30) cc_final: 0.8507 (tp30) REVERT: I 132 MET cc_start: 0.9261 (mtt) cc_final: 0.8945 (mtt) REVERT: I 182 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: I 201 ASP cc_start: 0.9189 (m-30) cc_final: 0.8794 (p0) REVERT: I 202 LEU cc_start: 0.9737 (mt) cc_final: 0.9460 (mm) REVERT: J 129 GLU cc_start: 0.8165 (tt0) cc_final: 0.7424 (tm-30) REVERT: J 132 MET cc_start: 0.8246 (mmt) cc_final: 0.7582 (mmm) REVERT: J 207 MET cc_start: 0.9281 (tpp) cc_final: 0.8695 (tpp) REVERT: J 208 MET cc_start: 0.8782 (ppp) cc_final: 0.8514 (ppp) REVERT: J 210 GLU cc_start: 0.8886 (mp0) cc_final: 0.8544 (mp0) REVERT: K 93 ASP cc_start: 0.9510 (m-30) cc_final: 0.9217 (m-30) REVERT: K 97 GLU cc_start: 0.9429 (tp30) cc_final: 0.9077 (tp30) REVERT: K 129 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8763 (tt0) REVERT: K 132 MET cc_start: 0.8096 (mmt) cc_final: 0.7723 (mmm) REVERT: K 175 GLU cc_start: 0.9399 (mp0) cc_final: 0.8816 (mm-30) REVERT: K 182 GLU cc_start: 0.8067 (tt0) cc_final: 0.7693 (tt0) REVERT: K 207 MET cc_start: 0.9587 (mmp) cc_final: 0.9330 (mmp) REVERT: L 31 ASN cc_start: 0.8235 (p0) cc_final: 0.7750 (p0) REVERT: L 54 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8349 (tp-100) REVERT: L 98 TYR cc_start: 0.7161 (t80) cc_final: 0.6677 (t80) REVERT: L 108 ARG cc_start: 0.8941 (tpp80) cc_final: 0.8544 (tpp80) REVERT: M 84 MET cc_start: 0.9016 (ttm) cc_final: 0.8748 (ttm) REVERT: N 72 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8652 (mm-30) REVERT: N 75 GLN cc_start: 0.9439 (mt0) cc_final: 0.9070 (mt0) REVERT: N 84 MET cc_start: 0.9434 (mtm) cc_final: 0.8810 (ttm) REVERT: N 100 LEU cc_start: 0.9680 (mm) cc_final: 0.9421 (mm) REVERT: N 105 ASP cc_start: 0.9098 (t0) cc_final: 0.8422 (t70) REVERT: N 109 GLN cc_start: 0.9397 (tt0) cc_final: 0.8955 (tp40) REVERT: Q 32 CYS cc_start: 0.9549 (m) cc_final: 0.9295 (m) REVERT: Q 115 MET cc_start: 0.9589 (mtp) cc_final: 0.9302 (ptp) REVERT: R 33 MET cc_start: 0.9162 (tpp) cc_final: 0.8816 (tmm) REVERT: R 109 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9236 (mm-30) REVERT: R 115 MET cc_start: 0.9378 (mmm) cc_final: 0.8984 (mmm) REVERT: R 118 HIS cc_start: 0.8491 (t-90) cc_final: 0.8017 (t-90) REVERT: R 122 TRP cc_start: 0.8107 (t-100) cc_final: 0.7699 (t60) REVERT: R 126 TYR cc_start: 0.9626 (m-80) cc_final: 0.9364 (m-80) REVERT: R 188 MET cc_start: 0.8653 (tpt) cc_final: 0.8234 (tpt) REVERT: R 194 ASP cc_start: 0.9601 (OUTLIER) cc_final: 0.9304 (p0) REVERT: R 199 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9216 (mm) REVERT: S 10 MET cc_start: 0.8247 (ttm) cc_final: 0.7878 (ttm) REVERT: S 109 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9011 (mm-30) REVERT: S 161 MET cc_start: 0.9528 (tmm) cc_final: 0.9275 (tmm) REVERT: S 188 MET cc_start: 0.9073 (tpp) cc_final: 0.8470 (tpp) REVERT: S 192 LYS cc_start: 0.9360 (mttt) cc_final: 0.8769 (mtpp) REVERT: a 10 MET cc_start: 0.7069 (tmm) cc_final: 0.6450 (tmm) REVERT: a 363 THR cc_start: 0.7468 (m) cc_final: 0.7148 (p) REVERT: a 423 MET cc_start: 0.7867 (mmt) cc_final: 0.7638 (mmt) REVERT: a 536 PHE cc_start: 0.7439 (m-80) cc_final: 0.6998 (m-80) REVERT: a 540 MET cc_start: 0.8340 (ppp) cc_final: 0.8055 (ppp) REVERT: a 592 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: a 616 MET cc_start: 0.8487 (mtt) cc_final: 0.7731 (tmm) REVERT: a 641 ILE cc_start: 0.9232 (mm) cc_final: 0.8383 (mm) REVERT: b 19 MET cc_start: 0.9099 (tmm) cc_final: 0.8795 (tmm) REVERT: b 25 CYS cc_start: 0.9058 (m) cc_final: 0.8818 (m) REVERT: b 41 LEU cc_start: 0.8516 (mp) cc_final: 0.7906 (tp) REVERT: b 107 MET cc_start: 0.6758 (mmm) cc_final: 0.6526 (mmm) REVERT: b 203 MET cc_start: 0.5848 (mmt) cc_final: 0.4701 (mmm) REVERT: c 421 MET cc_start: 0.8423 (ptt) cc_final: 0.8031 (mtp) REVERT: d 128 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9095 (mtpp) REVERT: d 321 LEU cc_start: 0.8736 (mt) cc_final: 0.8449 (mt) REVERT: g 26 SER cc_start: 0.8876 (m) cc_final: 0.8528 (p) REVERT: g 47 MET cc_start: 0.7232 (ppp) cc_final: 0.6903 (mmm) REVERT: g 131 MET cc_start: 0.7791 (ppp) cc_final: 0.7544 (ppp) REVERT: h 53 MET cc_start: 0.7996 (mmp) cc_final: 0.7444 (ttt) REVERT: h 90 PHE cc_start: 0.8156 (m-80) cc_final: 0.7541 (m-80) REVERT: i 53 MET cc_start: 0.8097 (mmt) cc_final: 0.6978 (ttt) REVERT: i 68 TYR cc_start: 0.8698 (m-10) cc_final: 0.8333 (m-80) REVERT: j 68 TYR cc_start: 0.9081 (m-10) cc_final: 0.8615 (m-80) REVERT: j 108 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7787 (t80) REVERT: l 47 MET cc_start: 0.7770 (ppp) cc_final: 0.7559 (ppp) REVERT: l 48 ARG cc_start: 0.6956 (ttp-110) cc_final: 0.6572 (ttm110) REVERT: m 23 MET cc_start: 0.7733 (ppp) cc_final: 0.7111 (ppp) REVERT: m 25 PHE cc_start: 0.8120 (m-80) cc_final: 0.7761 (m-80) REVERT: m 47 MET cc_start: 0.7791 (mmm) cc_final: 0.7575 (mmm) REVERT: m 121 THR cc_start: 0.6686 (m) cc_final: 0.5453 (p) REVERT: m 131 MET cc_start: 0.7224 (ptt) cc_final: 0.6765 (ptt) REVERT: n 13 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: n 28 MET cc_start: 0.8761 (tpp) cc_final: 0.8143 (mmm) REVERT: n 110 ILE cc_start: 0.8749 (mm) cc_final: 0.8522 (mm) outliers start: 161 outliers final: 137 residues processed: 1081 average time/residue: 0.5420 time to fit residues: 1028.9104 Evaluate side-chains 1109 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 957 time to evaluate : 5.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain a residue 385 THR Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 543 ILE Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 592 PHE Chi-restraints excluded: chain a residue 609 LEU Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 637 GLN Chi-restraints excluded: chain a residue 786 LEU Chi-restraints excluded: chain a residue 824 LEU Chi-restraints excluded: chain b residue 90 ASN Chi-restraints excluded: chain b residue 93 SER Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 445 THR Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 33 TYR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 129 CYS Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain h residue 7 ASN Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 92 GLN Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 92 GLN Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain l residue 72 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 55 SER Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain n residue 7 ASN Chi-restraints excluded: chain n residue 13 PHE Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 53 MET Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 527 optimal weight: 1.9990 chunk 707 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 612 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 665 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 682 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 484 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** a 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS i 92 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.079527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.055541 restraints weight = 293814.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057174 restraints weight = 143462.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.058264 restraints weight = 87034.372| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 63459 Z= 0.218 Angle : 0.760 17.894 86074 Z= 0.374 Chirality : 0.045 0.366 10040 Planarity : 0.004 0.057 11108 Dihedral : 4.629 115.311 9063 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.17 % Allowed : 20.64 % Favored : 77.20 % 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: 8372 helix: 1.32 (0.07), residues: 4950 sheet: 0.09 (0.21), residues: 640 loop : -0.51 (0.12), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP a 808 HIS 0.007 0.001 HIS B 164 PHE 0.049 0.002 PHE f 33 TYR 0.045 0.002 TYR b 103 ARG 0.012 0.000 ARG O 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17739.29 seconds wall clock time: 309 minutes 5.35 seconds (18545.35 seconds total)