Starting phenix.real_space_refine on Sun Apr 7 14:13:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/04_2024/6vq7_21318_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/04_2024/6vq7_21318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/04_2024/6vq7_21318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/04_2024/6vq7_21318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/04_2024/6vq7_21318_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/04_2024/6vq7_21318_updated.pdb" } resolution = 4.0 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= 0.067 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 335 5.16 5 C 39740 2.51 5 N 10666 2.21 5 O 11581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 529": "OD1" <-> "OD2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B 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 GLU 279": "OE1" <-> "OE2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 323": "NH1" <-> "NH2" 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 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 531": "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 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 423": "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 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 248": "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 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F 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 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "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 PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 74": "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 155": "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 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 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 "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 197": "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 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 214": "OE1" <-> "OE2" Residue "S TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 370": "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 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 584": "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 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 GLU 98": "OE1" <-> "OE2" 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 415": "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 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 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 139": "OE1" <-> "OE2" 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 "h PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 139": "OE1" <-> "OE2" 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 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 139": "OE1" <-> "OE2" Residue "m TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 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 "n GLU 139": "OE1" <-> "OE2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 139": "OE1" <-> "OE2" Residue "p TYR 293": "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: 62325 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: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1716 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 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: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 866 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "O" Number of atoms: 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: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "R" 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: "S" 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: "a" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5009 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'PTRANS': 31, 'TRANS': 718} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1147 Unresolved non-hydrogen angles: 1454 Unresolved non-hydrogen dihedrals: 941 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 23, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 20, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 662 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: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "f" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 452 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 107 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: "B" 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: 24.11, per 1000 atoms: 0.39 Number of scatterers: 62325 At special positions: 0 Unit cell: (169.6, 174.9, 272.42, 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 335 16.00 P 2 15.00 Mg 1 11.99 O 11581 8.00 N 10666 7.00 C 39740 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: 19.82 Conformation dependent library (CDL) restraints added in 8.9 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: 287 helices and 41 sheets defined 58.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.48 Creating SS restraints... Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.657A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 281 through 293 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 320 through 340 removed outlier: 4.514A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 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 388 removed outlier: 3.707A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 438 through 441 No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 472 through 496 removed outlier: 4.595A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.832A pdb=" N THR A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 586 removed outlier: 4.877A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 removed outlier: 3.994A pdb=" N LEU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 281 through 293 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 321 through 340 removed outlier: 3.559A pdb=" N SER B 326 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 376 through 388 removed outlier: 4.365A pdb=" N GLY B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 383 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 384 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 387 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 458 through 468 removed outlier: 4.407A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 496 removed outlier: 4.088A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 585 removed outlier: 4.994A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 320 through 340 removed outlier: 4.646A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (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 378 through 386 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: 4.302A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 496 removed outlier: 3.594A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.920A 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 557 Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 587 removed outlier: 5.053A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 253 through 256 Processing helix chain 'D' and resid 270 through 288 Proline residue: D 275 - end of helix 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 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 removed outlier: 3.906A pdb=" N ILE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) 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 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 removed outlier: 3.665A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.130A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 209 removed outlier: 3.645A pdb=" N ARG E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 300 through 313 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 Processing helix chain 'E' and resid 381 through 386 removed outlier: 4.006A pdb=" N ARG E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) 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: 4.358A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 446 through 461 removed outlier: 4.374A pdb=" N TYR E 451 " --> pdb=" O ASP E 447 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.170A 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 removed outlier: 4.955A pdb=" N GLU E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 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 287 removed outlier: 3.547A pdb=" N THR F 274 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Proline residue: F 275 - end of helix removed outlier: 3.614A pdb=" N ALA F 278 " --> pdb=" O PRO F 275 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 279 " --> pdb=" O ARG F 276 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 280 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 removed outlier: 3.749A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) 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 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 400 through 403 removed outlier: 4.202A pdb=" N LYS F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 400 through 403' Processing helix chain 'F' and resid 415 through 439 removed outlier: 4.093A 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 Processing helix chain 'F' and resid 473 through 486 removed outlier: 3.805A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 28 through 31 No H-bonds generated for 'chain 'G' and resid 28 through 31' Processing helix chain 'G' and resid 48 through 79 Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 118 through 156 Processing helix chain 'G' and resid 191 through 203 removed outlier: 5.449A pdb=" N ASN G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP G 197 " --> pdb=" O HIS G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 removed outlier: 4.058A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG G 238 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS G 240 " --> pdb=" O PHE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 310 Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 328 through 343 removed outlier: 5.117A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU G 342 " --> pdb=" O LEU G 338 " (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 Processing helix chain 'H' and resid 176 through 215 Processing helix chain 'I' and resid 5 through 106 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: 3.744A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS I 150 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.685A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR I 159 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 Processing helix chain 'I' and resid 208 through 216 Processing helix chain 'J' and resid 5 through 106 Processing helix chain 'J' and resid 109 through 127 removed outlier: 4.570A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 158 Proline residue: J 142 - end of helix removed outlier: 3.762A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 150 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.621A pdb=" N LYS J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 removed outlier: 3.919A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 5 through 106 removed outlier: 3.633A pdb=" N ALA K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 127 Processing helix chain 'K' and resid 138 through 159 Proline residue: K 142 - end of helix removed outlier: 3.741A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.768A pdb=" N LYS K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE K 157 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 204 Processing helix chain 'K' and resid 208 through 216 removed outlier: 3.631A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 75 through 80 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'M' and resid 4 through 90 Processing helix chain 'M' and resid 92 through 104 Processing helix chain 'N' and resid 4 through 90 removed outlier: 3.854A 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 103 removed outlier: 3.608A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 36 Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.628A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 78 through 98 removed outlier: 4.088A pdb=" N ILE Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'Q' and resid 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: 3.796A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 166 removed outlier: 3.551A pdb=" N GLN Q 165 " --> pdb=" O MET Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 186 Processing helix chain 'Q' and resid 194 through 206 Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 50 through 55 removed outlier: 4.943A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 78 through 98 removed outlier: 3.895A pdb=" N LEU R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 91 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 3.991A 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 125 through 141 removed outlier: 3.546A pdb=" N LYS R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 Processing helix chain 'R' and resid 173 through 187 Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 219 through 232 removed outlier: 3.587A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 36 Processing helix chain 'S' and resid 43 through 55 removed outlier: 3.610A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL S 52 " --> pdb=" O ASP S 48 " (cutoff:3.500A) removed outlier: 5.107A 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 96 Processing helix chain 'S' and resid 105 through 117 Processing helix chain 'S' and resid 121 through 123 No H-bonds generated for 'chain 'S' and resid 121 through 123' Processing helix chain 'S' and resid 125 through 142 removed outlier: 3.909A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 Processing helix chain 'S' and resid 173 through 186 Processing helix chain 'S' and resid 193 through 205 Processing helix chain 'S' and resid 219 through 234 Processing helix chain 'a' and resid 19 through 32 removed outlier: 3.589A 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 Processing helix chain 'a' and resid 92 through 131 removed outlier: 3.605A pdb=" N GLU a 98 " --> pdb=" O ILE a 95 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU a 116 " --> pdb=" O THR a 113 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR a 126 " --> pdb=" O LEU a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 180 through 190 Processing helix chain 'a' and resid 227 through 239 Processing helix chain 'a' and resid 252 through 308 removed outlier: 4.217A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 327 through 343 removed outlier: 4.599A pdb=" N ASP a 331 " --> pdb=" O THR a 328 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 379 Processing helix chain 'a' and resid 392 through 406 removed outlier: 4.914A 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: 3.519A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 482 through 487 Processing helix chain 'a' and resid 493 through 499 removed outlier: 3.607A pdb=" N SER a 498 " --> pdb=" O THR a 494 " (cutoff:3.500A) removed outlier: 5.029A 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: 4.567A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.976A 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: 4.304A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 3.518A 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: 3.706A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.751A 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: 4.302A pdb=" N LEU a 740 " --> pdb=" O THR a 736 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG a 741 " --> pdb=" O ALA a 737 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU a 742 " --> pdb=" O SER a 738 " (cutoff:3.500A) removed outlier: 4.214A 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 removed outlier: 3.518A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) 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: 3.618A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 114 removed outlier: 3.648A pdb=" N LYS b 87 " --> pdb=" O PRO b 84 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN b 90 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU b 91 " --> pdb=" O THR b 88 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN b 113 " --> pdb=" O VAL b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 166 Processing helix chain 'b' and resid 173 through 197 removed outlier: 4.093A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.585A 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 9 through 26 removed outlier: 6.293A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY d 26 " --> pdb=" O GLY d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 37 Processing helix chain 'd' and resid 42 through 51 removed outlier: 3.935A 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: 4.715A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 128 Proline residue: d 127 - end of helix Processing helix chain 'd' and resid 147 through 156 Processing helix chain 'd' and resid 159 through 166 removed outlier: 4.209A 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: 3.598A pdb=" N PHE d 228 " --> pdb=" O THR d 224 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY d 229 " --> pdb=" O ILE d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 240 removed outlier: 3.608A 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: 3.957A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 272 through 280 removed outlier: 4.448A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 307 removed outlier: 4.128A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) removed outlier: 4.273A 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: 3.808A 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: 3.991A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.599A 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: 3.575A pdb=" N TYR g 68 " --> pdb=" O ILE g 65 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL g 74 " --> pdb=" O VAL g 71 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE g 76 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN g 78 " --> pdb=" O LEU g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 123 removed outlier: 3.544A pdb=" N ARG g 119 " --> pdb=" O ASP g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 154 removed outlier: 4.433A pdb=" N VAL g 129 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL g 148 " --> pdb=" O GLY g 145 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU g 152 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 44 removed outlier: 3.912A pdb=" N PHE h 14 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA h 22 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE h 25 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER h 26 " --> pdb=" O MET h 23 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS h 36 " --> pdb=" O GLY h 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY h 38 " --> pdb=" O ALA h 35 " (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 55 through 79 Proline residue: h 58 - end of helix removed outlier: 3.508A pdb=" N VAL h 71 " --> pdb=" O TYR h 68 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE h 76 " --> pdb=" O ALA h 73 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN h 78 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 123 Processing helix chain 'h' and resid 125 through 153 removed outlier: 4.012A pdb=" N VAL h 129 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER h 153 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 47 removed outlier: 3.776A pdb=" N ALA i 22 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE i 25 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER i 26 " --> pdb=" O MET i 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER i 37 " --> pdb=" O THR i 34 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER i 45 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL i 46 " --> 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: 3.829A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 153 removed outlier: 4.034A pdb=" N VAL i 129 " --> pdb=" O ARG i 126 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 47 removed outlier: 3.817A pdb=" N PHE j 14 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA j 22 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE j 25 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS j 36 " --> pdb=" O GLY j 33 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY j 38 " --> pdb=" O ALA j 35 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER j 45 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL j 46 " --> pdb=" O ALA j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 51 No H-bonds generated for 'chain 'j' and resid 49 through 51' Processing helix chain 'j' and resid 54 through 79 Proline residue: j 58 - end of helix removed outlier: 3.528A pdb=" N VAL j 74 " --> pdb=" O VAL j 71 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE j 76 " --> pdb=" O ALA j 73 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.944A pdb=" N VAL j 129 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER j 153 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 47 removed outlier: 4.395A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA k 43 " --> pdb=" O THR k 39 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 3.972A 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: 3.529A pdb=" N ILE k 76 " --> pdb=" O ALA k 73 " (cutoff:3.500A) removed outlier: 3.536A 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: 4.128A pdb=" N VAL k 129 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER k 153 " --> pdb=" O LEU k 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 47 removed outlier: 3.609A pdb=" N PHE l 14 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA l 22 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE l 25 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS l 36 " --> pdb=" O GLY l 33 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 51 No H-bonds generated for 'chain 'l' and resid 49 through 51' Processing helix chain 'l' and resid 54 through 79 Proline residue: l 58 - end of helix Processing helix chain 'l' and resid 87 through 123 removed outlier: 3.869A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 154 removed outlier: 3.910A pdb=" N VAL l 129 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 46 removed outlier: 3.608A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 51 No H-bonds generated for 'chain 'm' and resid 49 through 51' Processing helix chain 'm' and resid 53 through 55 No H-bonds generated for 'chain 'm' and resid 53 through 55' Processing helix chain 'm' and resid 57 through 79 Processing helix chain 'm' and resid 87 through 123 removed outlier: 3.944A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 154 removed outlier: 3.858A pdb=" N VAL m 129 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER m 153 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 45 removed outlier: 4.274A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET n 23 " --> pdb=" O ALA n 19 " (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: 3.621A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 153 removed outlier: 4.168A pdb=" N VAL n 129 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER n 153 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 47 removed outlier: 3.754A pdb=" N PHE o 14 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA o 22 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE o 25 " --> pdb=" O ALA o 22 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.729A pdb=" N ILE o 57 " --> pdb=" O LYS o 54 " (cutoff:3.500A) Proline residue: o 58 - end of helix removed outlier: 3.512A pdb=" N VAL o 72 " --> pdb=" O GLY o 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL o 74 " --> pdb=" O VAL o 71 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE o 76 " --> pdb=" O ALA o 73 " (cutoff:3.500A) removed outlier: 3.669A 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: 4.180A pdb=" N VAL o 129 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET o 131 " --> pdb=" O PHE o 128 " (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: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A 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: 4.702A pdb=" N GLU A 134 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.561A 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: 6.238A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 309 through 312 removed outlier: 6.344A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL A 344 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER A 403 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET A 346 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 405 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA A 348 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= G, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 56 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN B 65 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE B 54 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS B 84 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG B 44 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR B 82 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= I, first strand: chain 'B' and resid 133 through 135 Processing sheet with id= J, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.219A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.282A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.423A pdb=" N ILE B 406 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE B 248 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY B 408 " --> pdb=" O ILE B 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 272 through 277 Processing sheet with id= N, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (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 98 through 100 removed outlier: 6.807A pdb=" N LEU C 311 " --> pdb=" O PHE C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 183 through 185 removed outlier: 6.946A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.158A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 219 through 221 removed outlier: 4.097A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 245 through 247 removed outlier: 8.360A pdb=" N THR C 246 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= V, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.655A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= X, first strand: chain 'D' and resid 131 through 133 removed outlier: 8.147A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N CYS D 258 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS D 292 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL D 230 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU D 294 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA D 232 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 296 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET D 234 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR D 298 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL D 236 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 191 through 194 Processing sheet with id= Z, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AB, first strand: chain 'E' and resid 131 through 133 removed outlier: 8.101A pdb=" N PHE E 132 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU E 259 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE E 351 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.742A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU F 88 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AE, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.638A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 191 through 193 Processing sheet with id= AG, first strand: chain 'G' and resid 370 through 374 removed outlier: 3.555A pdb=" N VAL G 370 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN G 317 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA G 318 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 182 through 190 removed outlier: 3.567A pdb=" N SER G 217 " --> pdb=" O LEU G 224 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 93 through 99 Processing sheet with id= AJ, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= AK, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AL, first strand: chain 'K' and resid 164 through 167 Processing sheet with id= AM, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.521A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE L 63 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE L 11 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU L 65 " --> pdb=" O ILE L 11 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'a' and resid 352 through 354 Processing sheet with id= AO, first strand: chain 'a' and resid 197 through 202 3915 hydrogen bonds defined for protein. 9795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.62 Time building geometry restraints manager: 21.86 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: 10471 1.30 - 1.43: 15343 1.43 - 1.56: 36976 1.56 - 1.68: 3 1.68 - 1.81: 602 Bond restraints: 63395 Sorted by residual: bond pdb=" C ASP C 290 " pdb=" N PHE C 291 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.81e+01 bond pdb=" N PRO D 391 " pdb=" CA PRO D 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.16e+01 bond pdb=" C TYR F 504 " pdb=" N PRO F 505 " ideal model delta sigma weight residual 1.337 1.406 -0.069 1.06e-02 8.90e+03 4.29e+01 bond pdb=" C ARG C 104 " pdb=" N PRO C 105 " ideal model delta sigma weight residual 1.333 1.393 -0.060 1.01e-02 9.80e+03 3.48e+01 bond pdb=" N PRO F 352 " pdb=" CA PRO F 352 " ideal model delta sigma weight residual 1.466 1.538 -0.071 1.24e-02 6.50e+03 3.32e+01 ... (remaining 63390 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.46: 1806 106.46 - 113.39: 34589 113.39 - 120.32: 26187 120.32 - 127.25: 22970 127.25 - 134.18: 445 Bond angle restraints: 85997 Sorted by residual: angle pdb=" C ILE D 189 " pdb=" N PRO D 190 " pdb=" CA PRO D 190 " ideal model delta sigma weight residual 119.85 129.28 -9.43 1.01e+00 9.80e-01 8.72e+01 angle pdb=" C ARG B 215 " pdb=" N PRO B 216 " pdb=" CA PRO B 216 " ideal model delta sigma weight residual 119.76 129.26 -9.50 1.03e+00 9.43e-01 8.50e+01 angle pdb=" C SER C 411 " pdb=" N PRO C 412 " pdb=" CA PRO C 412 " ideal model delta sigma weight residual 120.38 129.04 -8.66 1.03e+00 9.43e-01 7.07e+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 6.47e+01 angle pdb=" C LEU D 395 " pdb=" N PRO D 396 " pdb=" CA PRO D 396 " ideal model delta sigma weight residual 120.04 128.55 -8.51 1.08e+00 8.57e-01 6.21e+01 ... (remaining 85992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 37198 23.67 - 47.33: 703 47.33 - 71.00: 158 71.00 - 94.66: 62 94.66 - 118.33: 2 Dihedral angle restraints: 38123 sinusoidal: 13801 harmonic: 24322 Sorted by residual: dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.33 118.33 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" CA LYS I 59 " pdb=" C LYS I 59 " pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta harmonic sigma weight residual 180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.43 -98.42 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 38120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 7321 0.071 - 0.142: 2348 0.142 - 0.213: 272 0.213 - 0.284: 85 0.284 - 0.355: 10 Chirality restraints: 10036 Sorted by residual: chirality pdb=" CA PHE H 155 " pdb=" N PHE H 155 " pdb=" C PHE H 155 " pdb=" CB PHE H 155 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA TYR h 68 " pdb=" N TYR h 68 " pdb=" C TYR h 68 " pdb=" CB TYR h 68 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LEU H 48 " pdb=" N LEU H 48 " pdb=" C LEU H 48 " pdb=" CB LEU H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 10033 not shown) Planarity restraints: 11103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C LEU o 86 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU o 86 " 0.030 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 4.47e-02 2.00e+01 pdb=" C ASP G 236 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP G 236 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE G 237 " -0.026 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 4.34e-02 1.88e+01 pdb=" C ASN k 7 " 0.075 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 ... (remaining 11100 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9618 2.76 - 3.29: 66960 3.29 - 3.83: 104913 3.83 - 4.36: 127896 4.36 - 4.90: 209409 Nonbonded interactions: 518796 Sorted by model distance: nonbonded pdb=" OG SER a 738 " pdb=" NH1 ARG a 741 " model vdw 2.219 2.520 nonbonded pdb=" O TYR G 181 " pdb=" N LYS G 231 " model vdw 2.271 2.520 nonbonded pdb=" OG SER B 269 " pdb=" OG SER B 345 " model vdw 2.303 2.440 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 103 " model vdw 2.331 2.520 nonbonded pdb=" O VAL G 307 " pdb=" N GLY G 311 " model vdw 2.346 2.520 ... (remaining 518791 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' and resid 17 through 616) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 1.980 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: 10.660 Check model and map are aligned: 0.670 Set scattering table: 0.440 Process input model: 129.000 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 63395 Z= 0.608 Angle : 0.981 10.952 85997 Z= 0.724 Chirality : 0.065 0.355 10036 Planarity : 0.005 0.046 11103 Dihedral : 10.857 118.330 22499 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.46 % Favored : 97.34 % Rotamer: Outliers : 0.61 % Allowed : 0.81 % Favored : 98.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8372 helix: 0.94 (0.07), residues: 4967 sheet: -0.08 (0.18), residues: 707 loop : -0.19 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 55 HIS 0.003 0.000 HIS D 199 PHE 0.011 0.000 PHE n 137 TYR 0.016 0.000 TYR E 389 ARG 0.004 0.000 ARG E 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 1941 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1904 time to evaluate : 5.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.9198 (tp40) cc_final: 0.8314 (tm-30) REVERT: A 106 LEU cc_start: 0.9713 (mt) cc_final: 0.9390 (mm) REVERT: A 203 LEU cc_start: 0.9264 (mt) cc_final: 0.9051 (mp) REVERT: A 263 LEU cc_start: 0.9603 (tp) cc_final: 0.9253 (pp) REVERT: A 264 SER cc_start: 0.9493 (p) cc_final: 0.9240 (p) REVERT: A 328 TYR cc_start: 0.9315 (m-80) cc_final: 0.9092 (m-10) REVERT: A 329 THR cc_start: 0.9509 (m) cc_final: 0.9131 (p) REVERT: A 331 ILE cc_start: 0.9812 (tt) cc_final: 0.9530 (tt) REVERT: A 356 GLU cc_start: 0.9362 (tp30) cc_final: 0.8925 (tp30) REVERT: A 399 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 422 THR cc_start: 0.9651 (m) cc_final: 0.9338 (m) REVERT: A 520 LEU cc_start: 0.9507 (mt) cc_final: 0.9120 (tt) REVERT: A 540 MET cc_start: 0.9290 (mtp) cc_final: 0.9041 (mtp) REVERT: A 550 MET cc_start: 0.9020 (mmm) cc_final: 0.8661 (mmm) REVERT: A 567 TRP cc_start: 0.9337 (t-100) cc_final: 0.9010 (t-100) REVERT: A 590 VAL cc_start: 0.8845 (t) cc_final: 0.8297 (p) REVERT: B 54 ILE cc_start: 0.9654 (mt) cc_final: 0.9448 (mm) REVERT: B 61 MET cc_start: 0.9293 (mtp) cc_final: 0.8919 (mtt) REVERT: B 66 VAL cc_start: 0.9677 (t) cc_final: 0.9451 (m) REVERT: B 117 TYR cc_start: 0.8575 (m-80) cc_final: 0.8256 (m-80) REVERT: B 147 ILE cc_start: 0.9558 (pt) cc_final: 0.9159 (mm) REVERT: B 273 ILE cc_start: 0.9745 (mm) cc_final: 0.9408 (mt) REVERT: B 293 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8833 (mm-30) REVERT: B 306 MET cc_start: 0.8694 (tpp) cc_final: 0.8334 (tpp) REVERT: B 331 ILE cc_start: 0.9711 (tp) cc_final: 0.9426 (tt) REVERT: B 433 TRP cc_start: 0.9413 (m-10) cc_final: 0.8962 (m-10) REVERT: B 447 SER cc_start: 0.8708 (p) cc_final: 0.8141 (p) REVERT: B 458 MET cc_start: 0.8797 (mtp) cc_final: 0.8397 (mmm) REVERT: B 523 ASN cc_start: 0.9351 (t0) cc_final: 0.9144 (t0) REVERT: B 540 MET cc_start: 0.8831 (ptm) cc_final: 0.8163 (ttm) REVERT: B 590 VAL cc_start: 0.9312 (t) cc_final: 0.8893 (p) REVERT: C 50 LEU cc_start: 0.9668 (mt) cc_final: 0.9461 (mt) REVERT: C 65 GLN cc_start: 0.8924 (tp40) cc_final: 0.7888 (tp-100) REVERT: C 99 PHE cc_start: 0.8911 (m-80) cc_final: 0.8595 (m-80) REVERT: C 106 LEU cc_start: 0.9475 (mt) cc_final: 0.9260 (mp) REVERT: C 108 ASP cc_start: 0.9451 (m-30) cc_final: 0.9180 (t0) REVERT: C 147 ILE cc_start: 0.9642 (pt) cc_final: 0.9283 (mm) REVERT: C 237 LEU cc_start: 0.9724 (mt) cc_final: 0.9360 (mt) REVERT: C 282 ASN cc_start: 0.8524 (m-40) cc_final: 0.8175 (m-40) REVERT: C 318 MET cc_start: 0.9528 (mmm) cc_final: 0.9063 (mmm) REVERT: C 324 GLU cc_start: 0.9138 (tt0) cc_final: 0.8909 (tm-30) REVERT: C 327 ILE cc_start: 0.9560 (mm) cc_final: 0.9246 (mt) REVERT: C 328 TYR cc_start: 0.9361 (m-80) cc_final: 0.9039 (m-10) REVERT: C 345 SER cc_start: 0.9373 (t) cc_final: 0.9048 (t) REVERT: C 356 GLU cc_start: 0.9412 (tp30) cc_final: 0.9193 (mm-30) REVERT: C 385 PHE cc_start: 0.9562 (t80) cc_final: 0.9352 (t80) REVERT: C 436 ASP cc_start: 0.8433 (t70) cc_final: 0.8120 (t0) REVERT: C 520 LEU cc_start: 0.9730 (mt) cc_final: 0.9472 (mt) REVERT: C 550 MET cc_start: 0.9435 (mtm) cc_final: 0.8985 (mtp) REVERT: D 97 GLN cc_start: 0.9399 (tt0) cc_final: 0.9187 (tm-30) REVERT: D 153 ILE cc_start: 0.9456 (pt) cc_final: 0.9216 (pt) REVERT: D 234 MET cc_start: 0.8259 (mpp) cc_final: 0.7557 (mtm) REVERT: D 254 MET cc_start: 0.8043 (tpp) cc_final: 0.7817 (mmm) REVERT: D 299 ASP cc_start: 0.8956 (m-30) cc_final: 0.8611 (m-30) REVERT: D 300 MET cc_start: 0.9177 (mmm) cc_final: 0.8939 (mmm) REVERT: D 302 SER cc_start: 0.9582 (m) cc_final: 0.9335 (t) REVERT: D 435 MET cc_start: 0.9405 (tpp) cc_final: 0.9173 (tpp) REVERT: E 57 LEU cc_start: 0.9536 (mt) cc_final: 0.9235 (mt) REVERT: E 74 LEU cc_start: 0.9709 (pt) cc_final: 0.9314 (pp) REVERT: E 87 LEU cc_start: 0.9126 (mt) cc_final: 0.8819 (mm) REVERT: E 127 MET cc_start: 0.9178 (mtp) cc_final: 0.8731 (mtt) REVERT: E 154 MET cc_start: 0.9350 (mmm) cc_final: 0.9115 (mmm) REVERT: E 170 ILE cc_start: 0.9517 (mt) cc_final: 0.9188 (mm) REVERT: E 183 ILE cc_start: 0.9252 (mm) cc_final: 0.8793 (tt) REVERT: E 288 GLN cc_start: 0.9062 (mt0) cc_final: 0.8296 (mp10) REVERT: E 305 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9083 (tm-30) REVERT: E 352 PRO cc_start: 0.8853 (Cg_exo) cc_final: 0.8500 (Cg_endo) REVERT: E 360 ASP cc_start: 0.8431 (t0) cc_final: 0.7983 (t0) REVERT: E 410 MET cc_start: 0.7931 (mmm) cc_final: 0.7635 (mmm) REVERT: E 417 ASP cc_start: 0.8942 (m-30) cc_final: 0.8640 (m-30) REVERT: F 112 CYS cc_start: 0.8969 (m) cc_final: 0.8629 (p) REVERT: F 127 MET cc_start: 0.8972 (mtp) cc_final: 0.8604 (mtp) REVERT: F 183 ILE cc_start: 0.9609 (mt) cc_final: 0.9268 (mt) REVERT: F 205 GLN cc_start: 0.9396 (tt0) cc_final: 0.9030 (tt0) REVERT: F 249 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9092 (mt-10) REVERT: F 262 ASN cc_start: 0.9080 (t0) cc_final: 0.8046 (t0) REVERT: F 268 THR cc_start: 0.9205 (p) cc_final: 0.8829 (t) REVERT: F 305 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9138 (mt-10) REVERT: F 309 GLU cc_start: 0.9153 (tt0) cc_final: 0.8929 (tt0) REVERT: F 316 GLU cc_start: 0.9183 (tp30) cc_final: 0.8852 (tp30) REVERT: F 342 GLU cc_start: 0.8503 (tt0) cc_final: 0.8213 (pp20) REVERT: F 359 ASP cc_start: 0.8603 (m-30) cc_final: 0.8388 (t0) REVERT: F 425 CYS cc_start: 0.9500 (m) cc_final: 0.9241 (m) REVERT: F 453 GLU cc_start: 0.9297 (tt0) cc_final: 0.9030 (tp30) REVERT: F 481 TRP cc_start: 0.8823 (m100) cc_final: 0.8451 (m100) REVERT: H 14 MET cc_start: 0.8746 (tpt) cc_final: 0.8308 (tpt) REVERT: H 20 LYS cc_start: 0.9187 (mttt) cc_final: 0.8959 (ptpp) REVERT: H 23 LEU cc_start: 0.9565 (tp) cc_final: 0.9318 (tt) REVERT: H 24 LYS cc_start: 0.9681 (tttt) cc_final: 0.9422 (ptpp) REVERT: H 58 MET cc_start: 0.7741 (tmm) cc_final: 0.7253 (tmm) REVERT: H 81 THR cc_start: 0.9258 (m) cc_final: 0.8893 (p) REVERT: H 91 GLN cc_start: 0.9097 (tt0) cc_final: 0.8601 (tt0) REVERT: H 99 ASP cc_start: 0.9069 (t0) cc_final: 0.8665 (p0) REVERT: H 138 TYR cc_start: 0.8840 (m-80) cc_final: 0.8328 (m-80) REVERT: H 190 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8891 (tm-30) REVERT: H 197 GLU cc_start: 0.8719 (pt0) cc_final: 0.8337 (pt0) REVERT: I 76 MET cc_start: 0.9292 (mtm) cc_final: 0.8538 (ptm) REVERT: I 127 LEU cc_start: 0.9441 (tp) cc_final: 0.9106 (tp) REVERT: I 132 MET cc_start: 0.8803 (mtt) cc_final: 0.8527 (mtt) REVERT: I 177 ILE cc_start: 0.9718 (mt) cc_final: 0.9144 (mp) REVERT: I 198 SER cc_start: 0.9649 (m) cc_final: 0.9379 (p) REVERT: I 203 ILE cc_start: 0.9691 (mp) cc_final: 0.9354 (tt) REVERT: J 76 MET cc_start: 0.9135 (mmm) cc_final: 0.8928 (mmp) REVERT: J 97 GLU cc_start: 0.9543 (tp30) cc_final: 0.9190 (tp30) REVERT: J 127 LEU cc_start: 0.9647 (mt) cc_final: 0.9420 (mt) REVERT: J 203 ILE cc_start: 0.9799 (mt) cc_final: 0.9498 (tp) REVERT: K 76 MET cc_start: 0.9579 (mtm) cc_final: 0.9326 (ptp) REVERT: K 96 ASN cc_start: 0.9703 (m-40) cc_final: 0.9498 (m-40) REVERT: K 115 LEU cc_start: 0.9840 (tp) cc_final: 0.9616 (pp) REVERT: K 127 LEU cc_start: 0.9633 (mt) cc_final: 0.9137 (mt) REVERT: K 132 MET cc_start: 0.8187 (mtt) cc_final: 0.7616 (mtt) REVERT: K 197 GLU cc_start: 0.8804 (mp0) cc_final: 0.8463 (mp0) REVERT: L 18 THR cc_start: 0.9491 (m) cc_final: 0.9278 (p) REVERT: L 20 PHE cc_start: 0.9511 (m-80) cc_final: 0.9200 (m-80) REVERT: L 37 LEU cc_start: 0.9143 (tp) cc_final: 0.8906 (tp) REVERT: L 59 ASP cc_start: 0.8822 (p0) cc_final: 0.8612 (t0) REVERT: L 73 MET cc_start: 0.8222 (mtm) cc_final: 0.7789 (mtm) REVERT: M 102 MET cc_start: 0.9183 (mtm) cc_final: 0.8265 (ttm) REVERT: M 105 ASP cc_start: 0.8480 (t0) cc_final: 0.7760 (p0) REVERT: N 79 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8512 (ptp-170) REVERT: O 110 VAL cc_start: 0.9306 (t) cc_final: 0.9007 (p) REVERT: Q 13 LEU cc_start: 0.9365 (mt) cc_final: 0.9158 (mm) REVERT: Q 35 THR cc_start: 0.9311 (m) cc_final: 0.9043 (p) REVERT: Q 62 PHE cc_start: 0.8577 (t80) cc_final: 0.8315 (t80) REVERT: Q 98 ILE cc_start: 0.9468 (pt) cc_final: 0.9196 (mm) REVERT: R 17 GLN cc_start: 0.9201 (tp40) cc_final: 0.8693 (tp40) REVERT: R 101 PHE cc_start: 0.8688 (m-80) cc_final: 0.8312 (m-80) REVERT: R 109 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9013 (mm-30) REVERT: R 127 HIS cc_start: 0.8917 (t70) cc_final: 0.8712 (t70) REVERT: R 161 MET cc_start: 0.9517 (tmm) cc_final: 0.9232 (tmm) REVERT: R 200 PHE cc_start: 0.9212 (t80) cc_final: 0.8957 (t80) REVERT: R 228 THR cc_start: 0.9347 (m) cc_final: 0.9055 (p) REVERT: R 229 MET cc_start: 0.9306 (tpp) cc_final: 0.9073 (tpt) REVERT: S 78 LEU cc_start: 0.9791 (tp) cc_final: 0.9319 (mt) REVERT: S 79 ASP cc_start: 0.9100 (m-30) cc_final: 0.8521 (t0) REVERT: S 115 MET cc_start: 0.9533 (mtt) cc_final: 0.9208 (ptm) REVERT: S 229 MET cc_start: 0.9433 (mtp) cc_final: 0.9012 (mmm) REVERT: a 397 ILE cc_start: 0.8998 (mm) cc_final: 0.8759 (mm) REVERT: a 540 MET cc_start: 0.8830 (ttm) cc_final: 0.8527 (ptm) REVERT: a 587 LEU cc_start: 0.8596 (tp) cc_final: 0.8362 (tt) REVERT: a 591 ILE cc_start: 0.8528 (mt) cc_final: 0.7637 (mt) REVERT: a 616 MET cc_start: 0.8862 (ttp) cc_final: 0.7960 (tpp) REVERT: a 713 ASP cc_start: 0.7012 (t0) cc_final: 0.6524 (p0) REVERT: a 743 TRP cc_start: 0.8568 (t60) cc_final: 0.8139 (t60) REVERT: a 749 HIS cc_start: 0.7886 (t70) cc_final: 0.7608 (t70) REVERT: b 8 TYR cc_start: 0.7867 (m-80) cc_final: 0.7634 (m-80) REVERT: b 19 MET cc_start: 0.8959 (mtp) cc_final: 0.8428 (mmm) REVERT: b 27 THR cc_start: 0.8562 (m) cc_final: 0.8177 (p) REVERT: b 30 ASP cc_start: 0.8725 (t0) cc_final: 0.8416 (p0) REVERT: b 122 ASP cc_start: 0.7686 (t0) cc_final: 0.7463 (t0) REVERT: b 179 VAL cc_start: 0.9122 (t) cc_final: 0.8908 (t) REVERT: c 420 TRP cc_start: 0.9036 (t-100) cc_final: 0.8750 (t-100) REVERT: c 428 PHE cc_start: 0.8540 (m-80) cc_final: 0.8218 (m-80) REVERT: c 439 MET cc_start: 0.8921 (mmm) cc_final: 0.8633 (mmm) REVERT: d 118 HIS cc_start: 0.9282 (m-70) cc_final: 0.8908 (m170) REVERT: d 190 LEU cc_start: 0.9527 (mt) cc_final: 0.8822 (mt) REVERT: d 320 LYS cc_start: 0.9640 (mmtt) cc_final: 0.9416 (mmmt) REVERT: d 323 GLU cc_start: 0.9119 (tt0) cc_final: 0.8660 (pt0) REVERT: d 348 ILE cc_start: 0.8242 (mm) cc_final: 0.7719 (mt) REVERT: g 14 PHE cc_start: 0.8102 (m-80) cc_final: 0.7860 (m-80) REVERT: g 139 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5704 (mm-30) REVERT: h 78 ASN cc_start: 0.8304 (m-40) cc_final: 0.8026 (p0) REVERT: i 139 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5876 (mm-30) REVERT: j 78 ASN cc_start: 0.8761 (m-40) cc_final: 0.8555 (p0) REVERT: k 115 ASP cc_start: 0.8091 (t70) cc_final: 0.7304 (p0) REVERT: k 137 PHE cc_start: 0.6502 (m-80) cc_final: 0.6023 (m-80) REVERT: l 25 PHE cc_start: 0.8870 (m-80) cc_final: 0.8662 (m-10) REVERT: l 36 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8270 (mttp) REVERT: l 139 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: m 14 PHE cc_start: 0.9139 (m-80) cc_final: 0.8785 (m-80) REVERT: m 32 TYR cc_start: 0.8626 (t80) cc_final: 0.8213 (t80) REVERT: m 37 SER cc_start: 0.8752 (m) cc_final: 0.8524 (p) REVERT: m 67 ILE cc_start: 0.9260 (mt) cc_final: 0.8997 (mt) REVERT: m 71 VAL cc_start: 0.9639 (t) cc_final: 0.9376 (t) REVERT: m 110 ILE cc_start: 0.8589 (mt) cc_final: 0.8122 (tp) REVERT: n 23 MET cc_start: 0.8516 (tpt) cc_final: 0.7630 (tpt) REVERT: n 36 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7477 (ttmm) REVERT: n 53 MET cc_start: 0.7032 (mmp) cc_final: 0.5746 (ttm) REVERT: n 143 LEU cc_start: 0.9403 (tp) cc_final: 0.9045 (tp) REVERT: o 9 GLU cc_start: 0.8484 (mp0) cc_final: 0.8112 (tm-30) REVERT: o 21 SER cc_start: 0.9742 (m) cc_final: 0.9212 (p) REVERT: o 23 MET cc_start: 0.7058 (tpt) cc_final: 0.6720 (mmm) REVERT: o 25 PHE cc_start: 0.8945 (m-80) cc_final: 0.8546 (m-80) REVERT: o 41 ILE cc_start: 0.9431 (mt) cc_final: 0.9219 (mm) REVERT: o 64 ILE cc_start: 0.7792 (mt) cc_final: 0.7396 (mt) REVERT: p 303 TYR cc_start: 0.7507 (t80) cc_final: 0.7250 (t80) REVERT: p 338 ILE cc_start: 0.9172 (pt) cc_final: 0.8371 (pt) outliers start: 37 outliers final: 9 residues processed: 1927 average time/residue: 0.5776 time to fit residues: 1885.8883 Evaluate side-chains 1103 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1091 time to evaluate : 5.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 102 ILE Chi-restraints excluded: chain g residue 139 GLU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain l residue 139 GLU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 140 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 706 optimal weight: 50.0000 chunk 634 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 427 optimal weight: 1.9990 chunk 338 optimal weight: 20.0000 chunk 656 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 398 optimal weight: 40.0000 chunk 488 optimal weight: 4.9990 chunk 760 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 573 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS C 103 GLN C 146 HIS D 181 ASN D 358 ASN D 497 GLN E 456 GLN F 156 GLN F 251 ASN F 497 GLN H 16 GLN H 137 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN L 67 ASN N 80 GLN ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN ** R 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 HIS ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN o 7 ASN o 78 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 63395 Z= 0.270 Angle : 0.726 12.965 85997 Z= 0.371 Chirality : 0.045 0.307 10036 Planarity : 0.006 0.066 11103 Dihedral : 4.931 115.651 9081 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.01 % Favored : 97.98 % Rotamer: Outliers : 2.27 % Allowed : 10.81 % Favored : 86.92 % 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: 1.40 (0.09), residues: 8372 helix: 1.64 (0.07), residues: 4890 sheet: -0.00 (0.19), residues: 748 loop : 0.01 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 808 HIS 0.012 0.001 HIS a 802 PHE 0.050 0.002 PHE o 90 TYR 0.048 0.002 TYR g 144 ARG 0.013 0.001 ARG i 126 *********************** 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 1308 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1170 time to evaluate : 5.318 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: A 65 GLN cc_start: 0.9242 (tp40) cc_final: 0.8315 (tm-30) REVERT: A 116 ILE cc_start: 0.9447 (pt) cc_final: 0.8967 (mm) REVERT: A 139 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.9003 (pttm) REVERT: A 263 LEU cc_start: 0.9731 (tp) cc_final: 0.9289 (pp) REVERT: A 264 SER cc_start: 0.9536 (p) cc_final: 0.9302 (p) REVERT: A 340 MET cc_start: 0.9023 (ttm) cc_final: 0.8779 (ttm) REVERT: A 356 GLU cc_start: 0.9397 (tp30) cc_final: 0.9008 (tp30) REVERT: A 360 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 471 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: A 540 MET cc_start: 0.9370 (mtp) cc_final: 0.9168 (mtp) REVERT: A 567 TRP cc_start: 0.9356 (t-100) cc_final: 0.9105 (t-100) REVERT: A 590 VAL cc_start: 0.8740 (t) cc_final: 0.8488 (p) REVERT: B 39 MET cc_start: 0.8519 (ttm) cc_final: 0.8295 (ttm) REVERT: B 61 MET cc_start: 0.9365 (mtp) cc_final: 0.8981 (mtt) REVERT: B 147 ILE cc_start: 0.9577 (pt) cc_final: 0.9270 (mm) REVERT: B 283 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9350 (mp0) REVERT: B 293 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8859 (mm-30) REVERT: B 306 MET cc_start: 0.8864 (tpp) cc_final: 0.8474 (tpp) REVERT: B 433 TRP cc_start: 0.9283 (m-10) cc_final: 0.8865 (m-10) REVERT: B 458 MET cc_start: 0.8805 (mtp) cc_final: 0.8363 (mmm) REVERT: B 507 ILE cc_start: 0.9527 (mt) cc_final: 0.9326 (mm) REVERT: B 518 ASP cc_start: 0.7475 (t0) cc_final: 0.6834 (t0) REVERT: C 65 GLN cc_start: 0.8536 (tp40) cc_final: 0.8151 (tp-100) REVERT: C 108 ASP cc_start: 0.9450 (m-30) cc_final: 0.9249 (t0) REVERT: C 147 ILE cc_start: 0.9690 (pt) cc_final: 0.9300 (mm) REVERT: C 219 GLU cc_start: 0.8237 (pt0) cc_final: 0.8022 (pm20) REVERT: C 318 MET cc_start: 0.9609 (mmm) cc_final: 0.9047 (mmm) REVERT: C 324 GLU cc_start: 0.9367 (tt0) cc_final: 0.8809 (tp30) REVERT: C 328 TYR cc_start: 0.9247 (m-80) cc_final: 0.8959 (m-10) REVERT: C 340 MET cc_start: 0.8926 (ttm) cc_final: 0.8648 (mtm) REVERT: C 345 SER cc_start: 0.9356 (t) cc_final: 0.9145 (t) REVERT: C 354 TRP cc_start: 0.8433 (t60) cc_final: 0.6859 (t60) REVERT: C 356 GLU cc_start: 0.9404 (tp30) cc_final: 0.9136 (mm-30) REVERT: C 436 ASP cc_start: 0.8579 (t70) cc_final: 0.8246 (t0) REVERT: C 544 MET cc_start: 0.9028 (mtt) cc_final: 0.8594 (mtm) REVERT: C 550 MET cc_start: 0.9469 (mtm) cc_final: 0.9066 (mtp) REVERT: C 610 ASN cc_start: 0.9495 (m-40) cc_final: 0.8855 (p0) REVERT: D 88 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 97 GLN cc_start: 0.9443 (tt0) cc_final: 0.9164 (tm-30) REVERT: D 169 MET cc_start: 0.8873 (tmm) cc_final: 0.8197 (tmm) REVERT: D 234 MET cc_start: 0.8130 (mpp) cc_final: 0.7366 (mtm) REVERT: D 299 ASP cc_start: 0.9037 (m-30) cc_final: 0.8722 (t0) REVERT: D 300 MET cc_start: 0.9000 (mmm) cc_final: 0.8533 (mmm) REVERT: D 302 SER cc_start: 0.9659 (m) cc_final: 0.8654 (t) REVERT: D 354 LEU cc_start: 0.9421 (mm) cc_final: 0.8800 (tt) REVERT: D 358 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7377 (m110) REVERT: D 435 MET cc_start: 0.9387 (tpp) cc_final: 0.9140 (tpp) REVERT: D 491 MET cc_start: 0.8561 (mtp) cc_final: 0.8335 (ptp) REVERT: E 127 MET cc_start: 0.9190 (mtp) cc_final: 0.8692 (mtt) REVERT: E 180 MET cc_start: 0.9089 (mmm) cc_final: 0.8587 (mmm) REVERT: E 254 MET cc_start: 0.8063 (mmm) cc_final: 0.7780 (mmm) REVERT: E 283 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8147 (tm-30) REVERT: E 288 GLN cc_start: 0.8907 (mt0) cc_final: 0.8523 (mp10) REVERT: E 300 MET cc_start: 0.9388 (mmm) cc_final: 0.9041 (mmm) REVERT: E 305 GLU cc_start: 0.9337 (mt-10) cc_final: 0.9109 (tm-30) REVERT: E 356 MET cc_start: 0.8797 (ttp) cc_final: 0.8160 (ttm) REVERT: E 360 ASP cc_start: 0.8595 (t0) cc_final: 0.8119 (t0) REVERT: E 410 MET cc_start: 0.7905 (mmm) cc_final: 0.7597 (mmm) REVERT: E 495 ILE cc_start: 0.9020 (mt) cc_final: 0.8529 (tt) REVERT: F 127 MET cc_start: 0.9028 (mtp) cc_final: 0.8610 (mtp) REVERT: F 254 MET cc_start: 0.8744 (tmm) cc_final: 0.8381 (tpp) REVERT: F 268 THR cc_start: 0.9387 (p) cc_final: 0.9096 (t) REVERT: F 305 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9080 (mt-10) REVERT: F 309 GLU cc_start: 0.9266 (tt0) cc_final: 0.9011 (tt0) REVERT: F 316 GLU cc_start: 0.9232 (tp30) cc_final: 0.8821 (tp30) REVERT: F 328 TYR cc_start: 0.8978 (t80) cc_final: 0.8739 (t80) REVERT: F 402 MET cc_start: 0.9146 (ttm) cc_final: 0.8279 (tmm) REVERT: F 453 GLU cc_start: 0.9311 (tt0) cc_final: 0.8987 (tp30) REVERT: H 11 PRO cc_start: 0.8795 (Cg_exo) cc_final: 0.8101 (Cg_endo) REVERT: H 24 LYS cc_start: 0.9603 (tttt) cc_final: 0.9169 (mttt) REVERT: H 31 ASN cc_start: 0.9543 (m-40) cc_final: 0.9261 (m110) REVERT: H 58 MET cc_start: 0.8254 (tmm) cc_final: 0.7879 (tmm) REVERT: H 81 THR cc_start: 0.9099 (m) cc_final: 0.8886 (p) REVERT: H 109 PHE cc_start: 0.8537 (m-80) cc_final: 0.7563 (m-80) REVERT: H 138 TYR cc_start: 0.9001 (m-80) cc_final: 0.8691 (m-80) REVERT: H 190 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8911 (tm-30) REVERT: I 76 MET cc_start: 0.9209 (mtm) cc_final: 0.8725 (ptm) REVERT: I 94 LEU cc_start: 0.9784 (tp) cc_final: 0.9456 (mt) REVERT: I 128 LEU cc_start: 0.9299 (mt) cc_final: 0.8721 (mt) REVERT: I 129 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8106 (mm-30) REVERT: I 198 SER cc_start: 0.9722 (m) cc_final: 0.9497 (p) REVERT: I 203 ILE cc_start: 0.9724 (mp) cc_final: 0.9475 (tt) REVERT: J 72 MET cc_start: 0.9296 (tmm) cc_final: 0.8849 (tmm) REVERT: J 76 MET cc_start: 0.9254 (mmm) cc_final: 0.8975 (mmp) REVERT: J 97 GLU cc_start: 0.9518 (tp30) cc_final: 0.9060 (tp30) REVERT: J 132 MET cc_start: 0.8659 (mmm) cc_final: 0.8417 (mmm) REVERT: J 203 ILE cc_start: 0.9740 (mt) cc_final: 0.9493 (tp) REVERT: J 207 MET cc_start: 0.9278 (tmm) cc_final: 0.9077 (tpp) REVERT: J 210 GLU cc_start: 0.9077 (mp0) cc_final: 0.8017 (mp0) REVERT: K 76 MET cc_start: 0.9682 (mtm) cc_final: 0.9269 (ptp) REVERT: K 96 ASN cc_start: 0.9726 (m-40) cc_final: 0.9523 (m110) REVERT: K 97 GLU cc_start: 0.9306 (tp30) cc_final: 0.9093 (tm-30) REVERT: K 124 LEU cc_start: 0.9808 (mm) cc_final: 0.9501 (mm) REVERT: K 129 GLU cc_start: 0.8475 (tt0) cc_final: 0.7842 (tm-30) REVERT: K 182 GLU cc_start: 0.8283 (tt0) cc_final: 0.7762 (tt0) REVERT: K 197 GLU cc_start: 0.8976 (mp0) cc_final: 0.8600 (pm20) REVERT: K 207 MET cc_start: 0.9251 (tpp) cc_final: 0.8738 (tpp) REVERT: L 20 PHE cc_start: 0.9477 (m-80) cc_final: 0.9070 (m-80) REVERT: L 73 MET cc_start: 0.8438 (mtm) cc_final: 0.7907 (mtm) REVERT: L 94 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8431 (ttmt) REVERT: M 102 MET cc_start: 0.9322 (mtm) cc_final: 0.8664 (mtp) REVERT: M 105 ASP cc_start: 0.8487 (t0) cc_final: 0.7868 (p0) REVERT: N 84 MET cc_start: 0.8859 (mtp) cc_final: 0.8629 (mmm) REVERT: N 102 MET cc_start: 0.9404 (mtt) cc_final: 0.9096 (mmm) REVERT: O 102 MET cc_start: 0.9472 (mtp) cc_final: 0.9250 (mtp) REVERT: Q 35 THR cc_start: 0.9319 (m) cc_final: 0.9060 (p) REVERT: Q 98 ILE cc_start: 0.9459 (pt) cc_final: 0.9186 (mm) REVERT: Q 161 MET cc_start: 0.9361 (tmm) cc_final: 0.9013 (ppp) REVERT: Q 179 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.9066 (t80) REVERT: R 101 PHE cc_start: 0.8763 (m-80) cc_final: 0.8352 (m-80) REVERT: R 109 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8983 (mm-30) REVERT: R 136 LEU cc_start: 0.9768 (mm) cc_final: 0.9550 (pp) REVERT: R 155 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8736 (mpp) REVERT: R 161 MET cc_start: 0.9525 (tmm) cc_final: 0.9256 (tmm) REVERT: R 200 PHE cc_start: 0.9286 (t80) cc_final: 0.9082 (t80) REVERT: S 33 MET cc_start: 0.8841 (tpt) cc_final: 0.8640 (tmm) REVERT: S 76 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: S 78 LEU cc_start: 0.9764 (tp) cc_final: 0.9299 (mt) REVERT: S 85 SER cc_start: 0.9807 (t) cc_final: 0.9508 (p) REVERT: S 229 MET cc_start: 0.9463 (mtp) cc_final: 0.9077 (mmm) REVERT: a 394 TYR cc_start: 0.7812 (m-80) cc_final: 0.6875 (t80) REVERT: a 616 MET cc_start: 0.8817 (ttp) cc_final: 0.8263 (ttt) REVERT: a 713 ASP cc_start: 0.6832 (t0) cc_final: 0.6413 (p0) REVERT: a 730 LEU cc_start: 0.9354 (mt) cc_final: 0.9093 (pp) REVERT: a 756 LEU cc_start: 0.9330 (mt) cc_final: 0.9124 (pp) REVERT: a 805 ARG cc_start: 0.9532 (mtm110) cc_final: 0.9308 (mtm110) REVERT: b 19 MET cc_start: 0.8970 (mtp) cc_final: 0.8449 (mmm) REVERT: b 137 MET cc_start: 0.8994 (ttm) cc_final: 0.8348 (mmt) REVERT: b 147 SER cc_start: 0.7189 (m) cc_final: 0.6638 (p) REVERT: c 439 MET cc_start: 0.8960 (mmm) cc_final: 0.8714 (mmm) REVERT: c 443 LEU cc_start: 0.8501 (tp) cc_final: 0.8081 (mt) REVERT: d 118 HIS cc_start: 0.9407 (m-70) cc_final: 0.9050 (m170) REVERT: d 293 ARG cc_start: 0.9267 (mmt180) cc_final: 0.9059 (mmm160) REVERT: d 316 TYR cc_start: 0.9139 (t80) cc_final: 0.8285 (t80) REVERT: d 320 LYS cc_start: 0.9669 (mmtt) cc_final: 0.9265 (mmmt) REVERT: d 323 GLU cc_start: 0.9136 (tt0) cc_final: 0.8690 (pt0) REVERT: d 348 ILE cc_start: 0.8219 (mm) cc_final: 0.7855 (mt) REVERT: g 32 TYR cc_start: 0.8880 (t80) cc_final: 0.8092 (t80) REVERT: g 104 LEU cc_start: 0.9032 (mt) cc_final: 0.8451 (mt) REVERT: h 53 MET cc_start: 0.5214 (ppp) cc_final: 0.4942 (ppp) REVERT: h 76 ILE cc_start: 0.7651 (mt) cc_final: 0.7288 (tt) REVERT: h 78 ASN cc_start: 0.8403 (m-40) cc_final: 0.8179 (p0) REVERT: j 47 MET cc_start: 0.8953 (ptm) cc_final: 0.8550 (ppp) REVERT: j 108 PHE cc_start: 0.8461 (m-10) cc_final: 0.8139 (m-80) REVERT: k 17 MET cc_start: 0.8777 (mmp) cc_final: 0.8534 (mmm) REVERT: k 44 MET cc_start: 0.8617 (mmp) cc_final: 0.8406 (mmt) REVERT: k 65 ILE cc_start: 0.7883 (mm) cc_final: 0.7569 (mt) REVERT: k 97 LEU cc_start: 0.9542 (mm) cc_final: 0.9338 (mt) REVERT: l 25 PHE cc_start: 0.8998 (m-80) cc_final: 0.8766 (m-80) REVERT: l 47 MET cc_start: 0.9365 (ttm) cc_final: 0.8510 (ppp) REVERT: l 53 MET cc_start: 0.8588 (mmp) cc_final: 0.8181 (ttt) REVERT: l 61 MET cc_start: 0.6316 (mtt) cc_final: 0.5836 (mtt) REVERT: l 115 ASP cc_start: 0.8238 (t0) cc_final: 0.7847 (m-30) REVERT: m 23 MET cc_start: 0.8197 (tpt) cc_final: 0.7858 (tpt) REVERT: m 67 ILE cc_start: 0.9243 (mt) cc_final: 0.8942 (mt) REVERT: m 71 VAL cc_start: 0.9383 (t) cc_final: 0.9079 (t) REVERT: m 75 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8512 (pp) REVERT: m 131 MET cc_start: 0.9070 (tmm) cc_final: 0.8764 (ppp) REVERT: m 132 ILE cc_start: 0.9418 (mm) cc_final: 0.9126 (mm) REVERT: n 13 PHE cc_start: 0.9038 (t80) cc_final: 0.8587 (t80) REVERT: n 23 MET cc_start: 0.8374 (tpt) cc_final: 0.7425 (tpt) REVERT: n 53 MET cc_start: 0.6977 (mmp) cc_final: 0.5611 (ttm) REVERT: n 88 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.7943 (mmm-85) REVERT: n 143 LEU cc_start: 0.9476 (tp) cc_final: 0.9033 (tp) REVERT: o 9 GLU cc_start: 0.8500 (mp0) cc_final: 0.8046 (tm-30) REVERT: o 25 PHE cc_start: 0.8960 (m-80) cc_final: 0.8718 (m-80) REVERT: o 44 MET cc_start: 0.9047 (ttp) cc_final: 0.8691 (tpp) REVERT: o 47 MET cc_start: 0.8696 (ptm) cc_final: 0.8400 (ppp) REVERT: o 119 ARG cc_start: 0.8721 (mtp85) cc_final: 0.7398 (ttm-80) REVERT: o 143 LEU cc_start: 0.8883 (tp) cc_final: 0.8643 (tp) REVERT: p 303 TYR cc_start: 0.7446 (t80) cc_final: 0.6917 (t80) REVERT: p 328 ILE cc_start: 0.9549 (mm) cc_final: 0.9207 (pt) outliers start: 138 outliers final: 70 residues processed: 1257 average time/residue: 0.5651 time to fit residues: 1207.6629 Evaluate side-chains 1024 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 947 time to evaluate : 5.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 415 PHE Chi-restraints excluded: chain c residue 432 ILE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 139 GLU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 123 GLN Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 9 GLU Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 152 LEU Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 422 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 632 optimal weight: 7.9990 chunk 517 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 761 optimal weight: 0.9980 chunk 822 optimal weight: 0.0270 chunk 678 optimal weight: 8.9990 chunk 755 optimal weight: 0.9980 chunk 259 optimal weight: 0.3980 chunk 610 optimal weight: 20.0000 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 103 GLN B 146 HIS B 314 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN E 181 ASN F 85 GLN F 97 GLN ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** R 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 63395 Z= 0.201 Angle : 0.662 13.734 85997 Z= 0.331 Chirality : 0.044 0.268 10036 Planarity : 0.005 0.056 11103 Dihedral : 4.589 121.573 9066 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.32 % Allowed : 12.29 % Favored : 85.39 % 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: 1.30 (0.09), residues: 8372 helix: 1.59 (0.07), residues: 4910 sheet: 0.16 (0.19), residues: 728 loop : -0.16 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP b 49 HIS 0.006 0.001 HIS D 199 PHE 0.028 0.002 PHE d 221 TYR 0.040 0.002 TYR m 68 ARG 0.014 0.001 ARG B 571 *********************** 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 1201 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1060 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9151 (mtp) cc_final: 0.8741 (tpp) REVERT: A 65 GLN cc_start: 0.9097 (tp40) cc_final: 0.8300 (tm-30) REVERT: A 116 ILE cc_start: 0.9431 (pt) cc_final: 0.8999 (mm) REVERT: A 161 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9456 (tt) REVERT: A 296 MET cc_start: 0.8581 (pmm) cc_final: 0.8149 (pmm) REVERT: A 329 THR cc_start: 0.9559 (m) cc_final: 0.9283 (p) REVERT: A 340 MET cc_start: 0.8749 (ttm) cc_final: 0.8498 (ttm) REVERT: A 346 MET cc_start: 0.8262 (tmm) cc_final: 0.7987 (tmm) REVERT: A 356 GLU cc_start: 0.9326 (tp30) cc_final: 0.8846 (tp30) REVERT: A 360 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 371 ASP cc_start: 0.9225 (t0) cc_final: 0.8924 (t0) REVERT: A 471 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: A 540 MET cc_start: 0.9415 (mtp) cc_final: 0.9169 (mtp) REVERT: A 567 TRP cc_start: 0.9348 (t-100) cc_final: 0.9045 (t-100) REVERT: B 34 MET cc_start: 0.9400 (mmm) cc_final: 0.9183 (mmm) REVERT: B 283 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9350 (mp0) REVERT: B 293 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8827 (mm-30) REVERT: B 296 MET cc_start: 0.7819 (tmm) cc_final: 0.7539 (tmm) REVERT: B 306 MET cc_start: 0.8904 (tpp) cc_final: 0.8525 (tpp) REVERT: B 318 MET cc_start: 0.9599 (mtp) cc_final: 0.8930 (mtp) REVERT: B 340 MET cc_start: 0.8924 (ttm) cc_final: 0.8685 (tpp) REVERT: B 356 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8284 (mp0) REVERT: B 458 MET cc_start: 0.8724 (mtp) cc_final: 0.8365 (mmm) REVERT: B 507 ILE cc_start: 0.9468 (mt) cc_final: 0.9253 (mm) REVERT: B 540 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8328 (ttp) REVERT: B 574 MET cc_start: 0.8727 (mtt) cc_final: 0.8380 (mtt) REVERT: C 65 GLN cc_start: 0.8377 (tp40) cc_final: 0.7995 (tp-100) REVERT: C 147 ILE cc_start: 0.9666 (pt) cc_final: 0.9343 (mm) REVERT: C 318 MET cc_start: 0.9659 (mmm) cc_final: 0.9116 (mmm) REVERT: C 324 GLU cc_start: 0.9366 (tt0) cc_final: 0.8796 (tp30) REVERT: C 354 TRP cc_start: 0.8324 (t60) cc_final: 0.6711 (t60) REVERT: C 436 ASP cc_start: 0.8597 (t70) cc_final: 0.8295 (t0) REVERT: C 544 MET cc_start: 0.9043 (mtt) cc_final: 0.8750 (mtm) REVERT: C 550 MET cc_start: 0.9438 (mtm) cc_final: 0.8892 (mtp) REVERT: C 610 ASN cc_start: 0.9397 (m-40) cc_final: 0.8810 (p0) REVERT: D 88 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 97 GLN cc_start: 0.9431 (tt0) cc_final: 0.9001 (tm-30) REVERT: D 169 MET cc_start: 0.8825 (tmm) cc_final: 0.8228 (tmm) REVERT: D 234 MET cc_start: 0.7991 (mpp) cc_final: 0.7133 (mtm) REVERT: D 249 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9059 (mt-10) REVERT: D 274 THR cc_start: 0.9479 (m) cc_final: 0.9252 (p) REVERT: D 299 ASP cc_start: 0.8966 (m-30) cc_final: 0.8634 (t0) REVERT: D 300 MET cc_start: 0.8979 (mmm) cc_final: 0.7967 (mmm) REVERT: D 302 SER cc_start: 0.9636 (m) cc_final: 0.8572 (t) REVERT: D 309 GLU cc_start: 0.9335 (tp30) cc_final: 0.8971 (tm-30) REVERT: D 327 MET cc_start: 0.9427 (ttp) cc_final: 0.9163 (mtp) REVERT: D 354 LEU cc_start: 0.9493 (mm) cc_final: 0.8895 (tt) REVERT: D 410 MET cc_start: 0.9042 (mtm) cc_final: 0.8024 (ptp) REVERT: E 74 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9358 (pp) REVERT: E 127 MET cc_start: 0.9189 (mtp) cc_final: 0.8709 (mtt) REVERT: E 180 MET cc_start: 0.9051 (mmm) cc_final: 0.8639 (mmm) REVERT: E 254 MET cc_start: 0.8125 (mmm) cc_final: 0.7824 (mmm) REVERT: E 268 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8737 (t) REVERT: E 283 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 288 GLN cc_start: 0.8894 (mt0) cc_final: 0.8541 (mp10) REVERT: E 305 GLU cc_start: 0.9303 (mt-10) cc_final: 0.9047 (tm-30) REVERT: E 356 MET cc_start: 0.8593 (ttp) cc_final: 0.7992 (ttm) REVERT: E 360 ASP cc_start: 0.8608 (t0) cc_final: 0.8071 (t0) REVERT: E 495 ILE cc_start: 0.9102 (mt) cc_final: 0.8728 (tt) REVERT: F 127 MET cc_start: 0.9022 (mtp) cc_final: 0.8566 (mtp) REVERT: F 162 CYS cc_start: 0.9009 (m) cc_final: 0.8777 (p) REVERT: F 180 MET cc_start: 0.8880 (mtp) cc_final: 0.8544 (mtp) REVERT: F 205 GLN cc_start: 0.9515 (tt0) cc_final: 0.9072 (tt0) REVERT: F 268 THR cc_start: 0.9530 (p) cc_final: 0.9158 (t) REVERT: F 300 MET cc_start: 0.9517 (mmm) cc_final: 0.9227 (mmm) REVERT: F 305 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9056 (mt-10) REVERT: F 309 GLU cc_start: 0.9255 (tt0) cc_final: 0.9008 (tt0) REVERT: F 316 GLU cc_start: 0.9293 (tp30) cc_final: 0.8780 (tp30) REVERT: F 330 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8543 (t70) REVERT: F 402 MET cc_start: 0.9058 (ttm) cc_final: 0.8420 (tmm) REVERT: F 453 GLU cc_start: 0.9298 (tt0) cc_final: 0.8972 (tp30) REVERT: H 11 PRO cc_start: 0.8701 (Cg_exo) cc_final: 0.8053 (Cg_endo) REVERT: H 91 GLN cc_start: 0.9493 (tt0) cc_final: 0.9274 (tp40) REVERT: H 109 PHE cc_start: 0.8514 (m-80) cc_final: 0.7494 (m-80) REVERT: H 138 TYR cc_start: 0.9020 (m-80) cc_final: 0.8695 (m-80) REVERT: H 190 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8923 (tm-30) REVERT: I 127 LEU cc_start: 0.9511 (tp) cc_final: 0.9015 (tp) REVERT: I 132 MET cc_start: 0.8865 (mtt) cc_final: 0.8303 (mmt) REVERT: I 194 ASN cc_start: 0.8039 (t0) cc_final: 0.7740 (t0) REVERT: I 198 SER cc_start: 0.9685 (m) cc_final: 0.9440 (p) REVERT: I 203 ILE cc_start: 0.9724 (mp) cc_final: 0.9373 (tt) REVERT: J 72 MET cc_start: 0.9255 (tmm) cc_final: 0.8841 (tmm) REVERT: J 76 MET cc_start: 0.9235 (mmm) cc_final: 0.8910 (mmp) REVERT: J 97 GLU cc_start: 0.9528 (tp30) cc_final: 0.9059 (tp30) REVERT: J 203 ILE cc_start: 0.9706 (mt) cc_final: 0.9415 (tp) REVERT: J 207 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.9000 (tpp) REVERT: J 210 GLU cc_start: 0.9057 (mp0) cc_final: 0.8105 (mp0) REVERT: K 76 MET cc_start: 0.9649 (mtm) cc_final: 0.9410 (ptp) REVERT: K 96 ASN cc_start: 0.9720 (m-40) cc_final: 0.9494 (m110) REVERT: K 97 GLU cc_start: 0.9347 (tp30) cc_final: 0.9023 (tm-30) REVERT: K 182 GLU cc_start: 0.8165 (tt0) cc_final: 0.7706 (tt0) REVERT: K 197 GLU cc_start: 0.8932 (mp0) cc_final: 0.8540 (pm20) REVERT: K 207 MET cc_start: 0.9260 (tpp) cc_final: 0.8728 (tpp) REVERT: K 208 MET cc_start: 0.9236 (mmt) cc_final: 0.8982 (mmm) REVERT: L 14 GLU cc_start: 0.9169 (pm20) cc_final: 0.8784 (tp30) REVERT: L 20 PHE cc_start: 0.9457 (m-80) cc_final: 0.9035 (m-80) REVERT: L 55 PHE cc_start: 0.9045 (m-10) cc_final: 0.8561 (m-10) REVERT: L 73 MET cc_start: 0.8436 (mtm) cc_final: 0.7935 (mtm) REVERT: L 79 ASP cc_start: 0.8825 (m-30) cc_final: 0.8576 (m-30) REVERT: L 94 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8547 (ttmt) REVERT: M 102 MET cc_start: 0.9271 (mtm) cc_final: 0.8671 (mtm) REVERT: M 105 ASP cc_start: 0.8430 (t0) cc_final: 0.7850 (p0) REVERT: N 74 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8716 (tm-30) REVERT: N 102 MET cc_start: 0.9411 (mtt) cc_final: 0.9100 (mmm) REVERT: O 102 MET cc_start: 0.9456 (mtp) cc_final: 0.9192 (mtp) REVERT: Q 35 THR cc_start: 0.9272 (m) cc_final: 0.8993 (p) REVERT: Q 98 ILE cc_start: 0.9443 (pt) cc_final: 0.9150 (mm) REVERT: Q 179 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8999 (t80) REVERT: R 101 PHE cc_start: 0.8770 (m-80) cc_final: 0.8336 (m-80) REVERT: R 109 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8944 (mm-30) REVERT: R 161 MET cc_start: 0.9472 (tmm) cc_final: 0.9196 (tmm) REVERT: R 234 MET cc_start: 0.9067 (ppp) cc_final: 0.8795 (ppp) REVERT: S 33 MET cc_start: 0.8876 (tpt) cc_final: 0.8623 (tmm) REVERT: S 74 CYS cc_start: 0.8865 (m) cc_final: 0.8276 (m) REVERT: S 76 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.7625 (m-40) REVERT: S 133 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9440 (pp) REVERT: S 229 MET cc_start: 0.9442 (mtp) cc_final: 0.9066 (mmm) REVERT: a 397 ILE cc_start: 0.8967 (mm) cc_final: 0.8632 (mp) REVERT: a 538 MET cc_start: 0.6503 (ppp) cc_final: 0.6288 (ppp) REVERT: a 594 LYS cc_start: 0.3000 (OUTLIER) cc_final: 0.2771 (pptt) REVERT: a 616 MET cc_start: 0.8938 (ttp) cc_final: 0.8441 (ttt) REVERT: a 713 ASP cc_start: 0.6760 (t0) cc_final: 0.6309 (p0) REVERT: a 730 LEU cc_start: 0.9367 (mt) cc_final: 0.9080 (pp) REVERT: b 12 PHE cc_start: 0.8615 (m-10) cc_final: 0.8237 (m-80) REVERT: b 19 MET cc_start: 0.8934 (mtp) cc_final: 0.8367 (mmm) REVERT: b 60 LEU cc_start: 0.9065 (tp) cc_final: 0.8474 (tp) REVERT: b 137 MET cc_start: 0.8941 (ttm) cc_final: 0.8631 (tpp) REVERT: b 149 LEU cc_start: 0.9475 (tp) cc_final: 0.9273 (tp) REVERT: b 188 LEU cc_start: 0.9091 (mt) cc_final: 0.8810 (mt) REVERT: c 421 MET cc_start: 0.9204 (mtt) cc_final: 0.8958 (mtt) REVERT: c 443 LEU cc_start: 0.8398 (tp) cc_final: 0.8124 (mt) REVERT: d 118 HIS cc_start: 0.9357 (m-70) cc_final: 0.8897 (m170) REVERT: d 119 GLN cc_start: 0.9266 (tt0) cc_final: 0.8822 (tm-30) REVERT: d 316 TYR cc_start: 0.9126 (t80) cc_final: 0.8474 (t80) REVERT: d 320 LYS cc_start: 0.9664 (mmtt) cc_final: 0.9422 (mmtt) REVERT: d 323 GLU cc_start: 0.9087 (tt0) cc_final: 0.8685 (pt0) REVERT: d 348 ILE cc_start: 0.8175 (mm) cc_final: 0.7776 (mt) REVERT: g 23 MET cc_start: 0.6232 (ttm) cc_final: 0.5218 (ppp) REVERT: g 25 PHE cc_start: 0.8855 (m-80) cc_final: 0.8606 (m-80) REVERT: g 32 TYR cc_start: 0.8720 (t80) cc_final: 0.8223 (t80) REVERT: g 82 ASP cc_start: 0.7537 (t0) cc_final: 0.7173 (m-30) REVERT: g 104 LEU cc_start: 0.9037 (mt) cc_final: 0.8014 (mt) REVERT: h 78 ASN cc_start: 0.8389 (m-40) cc_final: 0.8155 (p0) REVERT: h 104 LEU cc_start: 0.8874 (mt) cc_final: 0.8512 (mt) REVERT: i 53 MET cc_start: 0.8228 (mmt) cc_final: 0.7458 (mtt) REVERT: j 47 MET cc_start: 0.8835 (ptm) cc_final: 0.8425 (ppp) REVERT: j 108 PHE cc_start: 0.8386 (m-10) cc_final: 0.8145 (m-10) REVERT: j 131 MET cc_start: 0.5458 (ppp) cc_final: 0.5165 (ppp) REVERT: k 131 MET cc_start: 0.7542 (tmm) cc_final: 0.6796 (ppp) REVERT: l 25 PHE cc_start: 0.8917 (m-80) cc_final: 0.8641 (m-80) REVERT: l 28 MET cc_start: 0.8795 (mmp) cc_final: 0.8401 (mmm) REVERT: l 47 MET cc_start: 0.9324 (ttm) cc_final: 0.8786 (ppp) REVERT: l 53 MET cc_start: 0.8569 (mmp) cc_final: 0.8022 (ttt) REVERT: l 61 MET cc_start: 0.6110 (mtt) cc_final: 0.5849 (mtt) REVERT: l 115 ASP cc_start: 0.7731 (t0) cc_final: 0.7343 (m-30) REVERT: m 23 MET cc_start: 0.8239 (tpt) cc_final: 0.8023 (tpt) REVERT: m 139 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: n 13 PHE cc_start: 0.9041 (t80) cc_final: 0.8664 (t80) REVERT: n 17 MET cc_start: 0.9438 (ptt) cc_final: 0.9132 (ptt) REVERT: n 23 MET cc_start: 0.8188 (tpt) cc_final: 0.7218 (tpt) REVERT: n 36 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7354 (mtpp) REVERT: n 53 MET cc_start: 0.7037 (mmp) cc_final: 0.5687 (ttm) REVERT: n 104 LEU cc_start: 0.9367 (mt) cc_final: 0.9128 (mt) REVERT: o 9 GLU cc_start: 0.8492 (mp0) cc_final: 0.8035 (tm-30) REVERT: o 25 PHE cc_start: 0.8989 (m-80) cc_final: 0.8738 (m-80) outliers start: 141 outliers final: 67 residues processed: 1146 average time/residue: 0.5396 time to fit residues: 1071.8860 Evaluate side-chains 983 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 903 time to evaluate : 6.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain a residue 417 THR Chi-restraints excluded: chain a residue 594 LYS Chi-restraints excluded: chain a residue 733 ILE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 432 ILE Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 299 VAL Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain h residue 144 TYR Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 9 GLU Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 752 optimal weight: 40.0000 chunk 572 optimal weight: 50.0000 chunk 395 optimal weight: 50.0000 chunk 84 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 chunk 511 optimal weight: 9.9990 chunk 764 optimal weight: 40.0000 chunk 809 optimal weight: 2.9990 chunk 399 optimal weight: 20.0000 chunk 724 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 114 GLN A 468 HIS A 543 ASN B 468 HIS ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS C 225 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 543 ASN E 181 ASN H 16 GLN H 27 GLN H 137 ASN I 66 GLN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN S 50 GLN S 160 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 63395 Z= 0.448 Angle : 0.782 13.675 85997 Z= 0.404 Chirality : 0.045 0.220 10036 Planarity : 0.006 0.055 11103 Dihedral : 4.786 137.485 9063 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.11 % Favored : 96.88 % Rotamer: Outliers : 3.32 % Allowed : 13.09 % Favored : 83.59 % 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: 1.37 (0.07), residues: 4930 sheet: -0.00 (0.19), residues: 746 loop : -0.29 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP b 67 HIS 0.018 0.002 HIS S 184 PHE 0.038 0.003 PHE j 25 TYR 0.064 0.003 TYR m 68 ARG 0.008 0.001 ARG R 153 *********************** 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 1069 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 867 time to evaluate : 5.504 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: A 61 MET cc_start: 0.9231 (mtp) cc_final: 0.8849 (tpp) REVERT: A 65 GLN cc_start: 0.9286 (tp40) cc_final: 0.8274 (tm-30) REVERT: A 100 ASP cc_start: 0.8704 (t0) cc_final: 0.8357 (t0) REVERT: A 296 MET cc_start: 0.8550 (pmm) cc_final: 0.8195 (pmm) REVERT: A 360 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 371 ASP cc_start: 0.9315 (t0) cc_final: 0.9024 (t0) REVERT: A 387 GLU cc_start: 0.9117 (tp30) cc_final: 0.8510 (tp30) REVERT: A 540 MET cc_start: 0.9401 (mtp) cc_final: 0.8719 (mtp) REVERT: A 567 TRP cc_start: 0.9413 (t-100) cc_final: 0.9121 (t-100) REVERT: A 584 MET cc_start: 0.8872 (ptm) cc_final: 0.8409 (ptp) REVERT: B 34 MET cc_start: 0.9532 (mmm) cc_final: 0.9327 (mmm) REVERT: B 61 MET cc_start: 0.9387 (mtt) cc_final: 0.9024 (tpp) REVERT: B 293 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8783 (mp0) REVERT: B 306 MET cc_start: 0.9097 (tpp) cc_final: 0.8806 (tpp) REVERT: B 318 MET cc_start: 0.9422 (mtp) cc_final: 0.8603 (mtp) REVERT: B 356 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: B 458 MET cc_start: 0.8891 (mtp) cc_final: 0.8558 (mmm) REVERT: B 487 GLU cc_start: 0.9319 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 507 ILE cc_start: 0.9577 (mt) cc_final: 0.9372 (mm) REVERT: B 540 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8688 (ttt) REVERT: C 65 GLN cc_start: 0.8509 (tp40) cc_final: 0.8041 (tm-30) REVERT: C 99 PHE cc_start: 0.9240 (m-80) cc_final: 0.9033 (m-80) REVERT: C 201 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: C 318 MET cc_start: 0.9639 (mmm) cc_final: 0.9123 (mmm) REVERT: C 436 ASP cc_start: 0.8692 (t70) cc_final: 0.8436 (t0) REVERT: C 540 MET cc_start: 0.9192 (ptp) cc_final: 0.8869 (ptp) REVERT: C 544 MET cc_start: 0.9202 (mtt) cc_final: 0.8744 (mtm) REVERT: C 550 MET cc_start: 0.9409 (mtm) cc_final: 0.8871 (mtp) REVERT: C 610 ASN cc_start: 0.9524 (m-40) cc_final: 0.8856 (p0) REVERT: D 88 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 97 GLN cc_start: 0.9384 (tt0) cc_final: 0.8917 (tm-30) REVERT: D 119 LEU cc_start: 0.9459 (tt) cc_final: 0.9258 (pp) REVERT: D 234 MET cc_start: 0.8764 (mpp) cc_final: 0.8139 (mpp) REVERT: D 249 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9145 (mt-10) REVERT: D 298 THR cc_start: 0.9415 (m) cc_final: 0.9171 (p) REVERT: D 302 SER cc_start: 0.9709 (m) cc_final: 0.9476 (t) REVERT: D 309 GLU cc_start: 0.9313 (tp30) cc_final: 0.8970 (tm-30) REVERT: D 327 MET cc_start: 0.9468 (ttp) cc_final: 0.9126 (mtp) REVERT: D 356 MET cc_start: 0.8736 (tpp) cc_final: 0.8454 (tpp) REVERT: D 410 MET cc_start: 0.9179 (mtm) cc_final: 0.7996 (ptp) REVERT: E 127 MET cc_start: 0.9154 (mtp) cc_final: 0.8604 (mtt) REVERT: E 180 MET cc_start: 0.9092 (mmm) cc_final: 0.8636 (mmt) REVERT: E 234 MET cc_start: 0.9145 (ptt) cc_final: 0.8831 (ptt) REVERT: E 300 MET cc_start: 0.9341 (mmm) cc_final: 0.9103 (mmm) REVERT: E 305 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9140 (tm-30) REVERT: E 356 MET cc_start: 0.8663 (ttp) cc_final: 0.8375 (ttp) REVERT: E 360 ASP cc_start: 0.8647 (t0) cc_final: 0.8042 (t0) REVERT: E 410 MET cc_start: 0.9087 (mmm) cc_final: 0.8589 (mtp) REVERT: F 87 LEU cc_start: 0.9737 (tp) cc_final: 0.9479 (tt) REVERT: F 127 MET cc_start: 0.9144 (mtp) cc_final: 0.8765 (mtp) REVERT: F 205 GLN cc_start: 0.9567 (tt0) cc_final: 0.9352 (tt0) REVERT: F 254 MET cc_start: 0.8902 (tmm) cc_final: 0.8458 (tmm) REVERT: F 268 THR cc_start: 0.9578 (p) cc_final: 0.9178 (t) REVERT: F 402 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8312 (tmm) REVERT: F 410 MET cc_start: 0.9136 (mtm) cc_final: 0.8727 (ptp) REVERT: F 453 GLU cc_start: 0.9354 (tt0) cc_final: 0.9033 (tp30) REVERT: H 27 GLN cc_start: 0.9439 (pt0) cc_final: 0.9203 (pp30) REVERT: H 31 ASN cc_start: 0.9391 (m-40) cc_final: 0.9153 (p0) REVERT: H 109 PHE cc_start: 0.8603 (m-80) cc_final: 0.7723 (m-80) REVERT: H 190 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8838 (tm-30) REVERT: H 206 GLN cc_start: 0.9523 (mm-40) cc_final: 0.8715 (tp40) REVERT: I 129 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8098 (mm-30) REVERT: I 132 MET cc_start: 0.8819 (mtt) cc_final: 0.8402 (mmt) REVERT: I 198 SER cc_start: 0.9736 (m) cc_final: 0.9495 (p) REVERT: J 72 MET cc_start: 0.9321 (tmm) cc_final: 0.8912 (tmm) REVERT: J 76 MET cc_start: 0.9316 (mmm) cc_final: 0.9040 (mmm) REVERT: J 97 GLU cc_start: 0.9516 (tp30) cc_final: 0.9059 (tp30) REVERT: J 203 ILE cc_start: 0.9758 (mt) cc_final: 0.9546 (tp) REVERT: J 207 MET cc_start: 0.9280 (tmm) cc_final: 0.9035 (tpp) REVERT: J 210 GLU cc_start: 0.9082 (mp0) cc_final: 0.8122 (mp0) REVERT: K 72 MET cc_start: 0.9413 (ppp) cc_final: 0.9148 (ppp) REVERT: K 76 MET cc_start: 0.9635 (mtm) cc_final: 0.9311 (ptp) REVERT: K 115 LEU cc_start: 0.9841 (OUTLIER) cc_final: 0.9598 (pp) REVERT: K 182 GLU cc_start: 0.8204 (tt0) cc_final: 0.7778 (tt0) REVERT: K 197 GLU cc_start: 0.9002 (mp0) cc_final: 0.8649 (pm20) REVERT: K 207 MET cc_start: 0.9411 (tpp) cc_final: 0.9188 (tpp) REVERT: K 208 MET cc_start: 0.9344 (mmt) cc_final: 0.9049 (mmm) REVERT: K 221 ASN cc_start: 0.9401 (m-40) cc_final: 0.9018 (m110) REVERT: L 14 GLU cc_start: 0.9248 (pm20) cc_final: 0.9016 (pm20) REVERT: L 47 GLU cc_start: 0.9513 (mp0) cc_final: 0.9228 (pm20) REVERT: L 53 ARG cc_start: 0.9611 (mtt-85) cc_final: 0.9380 (mmt-90) REVERT: L 73 MET cc_start: 0.8561 (mtm) cc_final: 0.8099 (mtp) REVERT: L 94 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8689 (ttmt) REVERT: M 105 ASP cc_start: 0.8465 (t0) cc_final: 0.8005 (t0) REVERT: N 84 MET cc_start: 0.9081 (mtp) cc_final: 0.8798 (ttm) REVERT: N 102 MET cc_start: 0.9493 (mtt) cc_final: 0.9141 (mmm) REVERT: O 75 GLN cc_start: 0.9430 (mt0) cc_final: 0.9219 (mt0) REVERT: O 96 LEU cc_start: 0.9773 (tp) cc_final: 0.9565 (pp) REVERT: O 102 MET cc_start: 0.9547 (mtp) cc_final: 0.9333 (mtp) REVERT: Q 35 THR cc_start: 0.9358 (m) cc_final: 0.9103 (p) REVERT: Q 98 ILE cc_start: 0.9530 (pt) cc_final: 0.9306 (mm) REVERT: Q 179 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.8993 (t80) REVERT: R 109 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8940 (mm-30) REVERT: R 136 LEU cc_start: 0.9828 (mm) cc_final: 0.9595 (pp) REVERT: R 155 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8901 (mpp) REVERT: S 76 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.7876 (m110) REVERT: S 133 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9561 (pp) REVERT: S 175 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9173 (mm) REVERT: S 229 MET cc_start: 0.9502 (mtp) cc_final: 0.9166 (mmp) REVERT: a 594 LYS cc_start: 0.3464 (OUTLIER) cc_final: 0.3199 (pptt) REVERT: a 616 MET cc_start: 0.9046 (ttp) cc_final: 0.8448 (ttt) REVERT: a 713 ASP cc_start: 0.6995 (t0) cc_final: 0.6426 (p0) REVERT: a 759 MET cc_start: 0.8320 (mmm) cc_final: 0.7989 (tpp) REVERT: b 48 MET cc_start: 0.9308 (mtp) cc_final: 0.9091 (mtp) REVERT: b 137 MET cc_start: 0.8996 (ttm) cc_final: 0.8687 (tpp) REVERT: b 138 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8689 (t80) REVERT: c 421 MET cc_start: 0.9261 (mtt) cc_final: 0.8866 (mmp) REVERT: d 6 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8091 (pp20) REVERT: d 78 MET cc_start: 0.9254 (tmm) cc_final: 0.8838 (tmm) REVERT: d 118 HIS cc_start: 0.9395 (m-70) cc_final: 0.8812 (m170) REVERT: d 119 GLN cc_start: 0.9296 (tt0) cc_final: 0.8909 (tm-30) REVERT: d 138 MET cc_start: 0.7743 (tpp) cc_final: 0.7476 (tpp) REVERT: d 293 ARG cc_start: 0.9234 (mmt180) cc_final: 0.9018 (mmm160) REVERT: d 316 TYR cc_start: 0.9225 (t80) cc_final: 0.8943 (t80) REVERT: d 348 ILE cc_start: 0.8447 (mm) cc_final: 0.8067 (mt) REVERT: e 36 VAL cc_start: 0.8114 (t) cc_final: 0.7759 (p) REVERT: g 82 ASP cc_start: 0.7635 (t0) cc_final: 0.7236 (m-30) REVERT: g 104 LEU cc_start: 0.9139 (mt) cc_final: 0.8071 (mt) REVERT: h 14 PHE cc_start: 0.8563 (m-80) cc_final: 0.8340 (m-80) REVERT: h 78 ASN cc_start: 0.8373 (m-40) cc_final: 0.8061 (p0) REVERT: h 104 LEU cc_start: 0.8970 (mt) cc_final: 0.8531 (mt) REVERT: i 47 MET cc_start: 0.7253 (ppp) cc_final: 0.6947 (ppp) REVERT: i 53 MET cc_start: 0.8396 (mmt) cc_final: 0.7526 (mtp) REVERT: i 65 ILE cc_start: 0.8209 (mm) cc_final: 0.7974 (mt) REVERT: i 119 ARG cc_start: 0.8929 (mtt90) cc_final: 0.7584 (ptm-80) REVERT: j 108 PHE cc_start: 0.8562 (m-10) cc_final: 0.8281 (m-80) REVERT: j 131 MET cc_start: 0.5604 (ppp) cc_final: 0.5383 (ppp) REVERT: k 17 MET cc_start: 0.8907 (mmp) cc_final: 0.8611 (mmm) REVERT: k 131 MET cc_start: 0.7676 (tmm) cc_final: 0.7068 (ppp) REVERT: l 28 MET cc_start: 0.8992 (mmp) cc_final: 0.8753 (mmm) REVERT: l 47 MET cc_start: 0.9356 (ttm) cc_final: 0.8658 (ppp) REVERT: l 53 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8110 (ttt) REVERT: l 115 ASP cc_start: 0.7764 (t0) cc_final: 0.7357 (m-30) REVERT: l 123 GLN cc_start: 0.9058 (mp10) cc_final: 0.8688 (mp10) REVERT: m 53 MET cc_start: 0.8870 (ppp) cc_final: 0.8129 (ppp) REVERT: m 115 ASP cc_start: 0.9112 (t70) cc_final: 0.8875 (m-30) REVERT: m 139 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: n 13 PHE cc_start: 0.9068 (t80) cc_final: 0.8607 (t80) REVERT: n 17 MET cc_start: 0.9428 (ptt) cc_final: 0.9095 (ptt) REVERT: n 36 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7269 (mtpp) REVERT: n 53 MET cc_start: 0.7408 (mmp) cc_final: 0.5811 (ttp) REVERT: o 25 PHE cc_start: 0.8988 (m-80) cc_final: 0.8647 (m-80) REVERT: o 119 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8162 (mtp85) REVERT: o 144 TYR cc_start: 0.8804 (m-10) cc_final: 0.8539 (m-80) REVERT: p 328 ILE cc_start: 0.9618 (mm) cc_final: 0.9415 (pt) outliers start: 202 outliers final: 122 residues processed: 993 average time/residue: 0.5464 time to fit residues: 945.4459 Evaluate side-chains 930 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 793 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 49 THR 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 207 CYS Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 115 MET Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 129 LYS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 175 ILE Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain a residue 417 THR Chi-restraints excluded: chain a residue 594 LYS Chi-restraints excluded: chain a residue 651 MET Chi-restraints excluded: chain a residue 733 ILE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 9 GLU Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 53 MET Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 673 optimal weight: 9.9990 chunk 459 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 602 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 chunk 690 optimal weight: 6.9990 chunk 559 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 6.9990 chunk 726 optimal weight: 30.0000 chunk 204 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN E 433 GLN ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 HIS Q 117 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN a 375 GLN ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 63395 Z= 0.343 Angle : 0.703 12.507 85997 Z= 0.359 Chirality : 0.043 0.390 10036 Planarity : 0.005 0.058 11103 Dihedral : 4.688 137.152 9060 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.11 % Allowed : 14.64 % Favored : 82.25 % 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: 1.01 (0.09), residues: 8372 helix: 1.40 (0.07), residues: 4903 sheet: -0.09 (0.20), residues: 710 loop : -0.35 (0.12), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 49 HIS 0.010 0.001 HIS B 22 PHE 0.035 0.002 PHE j 25 TYR 0.061 0.002 TYR m 68 ARG 0.008 0.001 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 1039 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 850 time to evaluate : 5.355 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: A 61 MET cc_start: 0.9183 (mtp) cc_final: 0.8862 (tpp) REVERT: A 100 ASP cc_start: 0.8679 (t0) cc_final: 0.8338 (t0) REVERT: A 116 ILE cc_start: 0.9534 (pt) cc_final: 0.9129 (mm) REVERT: A 296 MET cc_start: 0.8530 (pmm) cc_final: 0.8158 (pmm) REVERT: A 360 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 361 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9196 (tp) REVERT: A 540 MET cc_start: 0.9349 (mtp) cc_final: 0.8810 (mtp) REVERT: A 567 TRP cc_start: 0.9413 (t-100) cc_final: 0.9111 (t-100) REVERT: A 584 MET cc_start: 0.8908 (ptm) cc_final: 0.8286 (ptp) REVERT: B 39 MET cc_start: 0.9058 (tpp) cc_final: 0.8520 (tpp) REVERT: B 61 MET cc_start: 0.9361 (mtt) cc_final: 0.9088 (mmt) REVERT: B 293 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8795 (mp0) REVERT: B 306 MET cc_start: 0.9147 (tpp) cc_final: 0.8883 (tpp) REVERT: B 318 MET cc_start: 0.9432 (mtp) cc_final: 0.8609 (mtp) REVERT: B 324 GLU cc_start: 0.9345 (tt0) cc_final: 0.9016 (tm-30) REVERT: B 356 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: B 458 MET cc_start: 0.8908 (mtp) cc_final: 0.8635 (mmm) REVERT: B 480 LYS cc_start: 0.9403 (pttt) cc_final: 0.9086 (ptpp) REVERT: B 507 ILE cc_start: 0.9571 (mt) cc_final: 0.9337 (mm) REVERT: B 540 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8451 (mtp) REVERT: C 65 GLN cc_start: 0.8526 (tp40) cc_final: 0.8139 (tm-30) REVERT: C 318 MET cc_start: 0.9629 (mmm) cc_final: 0.9140 (mmm) REVERT: C 436 ASP cc_start: 0.8712 (t70) cc_final: 0.8462 (t0) REVERT: C 550 MET cc_start: 0.9373 (mtm) cc_final: 0.8827 (mtp) REVERT: C 610 ASN cc_start: 0.9556 (m-40) cc_final: 0.8871 (p0) REVERT: D 88 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8068 (tm-30) REVERT: D 97 GLN cc_start: 0.9404 (tt0) cc_final: 0.8688 (tm-30) REVERT: D 231 PHE cc_start: 0.8862 (t80) cc_final: 0.8577 (t80) REVERT: D 234 MET cc_start: 0.8754 (mpp) cc_final: 0.8389 (mtm) REVERT: D 249 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9072 (mt-10) REVERT: D 302 SER cc_start: 0.9700 (m) cc_final: 0.9494 (t) REVERT: D 309 GLU cc_start: 0.9307 (tp30) cc_final: 0.8951 (tm-30) REVERT: D 353 ILE cc_start: 0.9591 (mt) cc_final: 0.9349 (mm) REVERT: E 127 MET cc_start: 0.9162 (mtp) cc_final: 0.8546 (mtt) REVERT: E 180 MET cc_start: 0.8927 (mmm) cc_final: 0.8682 (mmt) REVERT: E 234 MET cc_start: 0.9001 (ptt) cc_final: 0.8697 (ptt) REVERT: E 305 GLU cc_start: 0.9344 (mt-10) cc_final: 0.9132 (tm-30) REVERT: E 356 MET cc_start: 0.8756 (ttp) cc_final: 0.8467 (ttp) REVERT: E 360 ASP cc_start: 0.8722 (t0) cc_final: 0.8104 (t0) REVERT: E 410 MET cc_start: 0.9074 (mmm) cc_final: 0.8438 (mtp) REVERT: F 87 LEU cc_start: 0.9733 (tp) cc_final: 0.9468 (tt) REVERT: F 127 MET cc_start: 0.9114 (mtp) cc_final: 0.8725 (mtp) REVERT: F 205 GLN cc_start: 0.9503 (tt0) cc_final: 0.9088 (tt0) REVERT: F 254 MET cc_start: 0.8936 (mmm) cc_final: 0.8438 (tmm) REVERT: F 268 THR cc_start: 0.9593 (p) cc_final: 0.9201 (t) REVERT: F 327 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8763 (mpp) REVERT: F 402 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8370 (tmm) REVERT: F 410 MET cc_start: 0.9101 (mtm) cc_final: 0.8787 (ptp) REVERT: F 453 GLU cc_start: 0.9332 (tt0) cc_final: 0.9010 (tp30) REVERT: H 24 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9189 (mmtt) REVERT: H 31 ASN cc_start: 0.9389 (m-40) cc_final: 0.9122 (p0) REVERT: H 91 GLN cc_start: 0.9458 (tt0) cc_final: 0.9127 (tp40) REVERT: H 109 PHE cc_start: 0.8667 (m-80) cc_final: 0.7745 (m-80) REVERT: H 190 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8850 (tm-30) REVERT: I 129 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8125 (mm-30) REVERT: I 132 MET cc_start: 0.8787 (mtt) cc_final: 0.8435 (mmt) REVERT: I 198 SER cc_start: 0.9713 (m) cc_final: 0.9437 (p) REVERT: I 203 ILE cc_start: 0.9812 (mp) cc_final: 0.9495 (tt) REVERT: I 207 MET cc_start: 0.8879 (mmt) cc_final: 0.8560 (mmt) REVERT: I 210 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9263 (tp30) REVERT: J 72 MET cc_start: 0.9349 (tmm) cc_final: 0.8943 (tmm) REVERT: J 76 MET cc_start: 0.9354 (mmm) cc_final: 0.9034 (mmm) REVERT: J 97 GLU cc_start: 0.9469 (tp30) cc_final: 0.9021 (tp30) REVERT: J 207 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8800 (tmm) REVERT: J 210 GLU cc_start: 0.9059 (mp0) cc_final: 0.8812 (mp0) REVERT: K 72 MET cc_start: 0.9423 (ppp) cc_final: 0.9198 (ppp) REVERT: K 76 MET cc_start: 0.9648 (mtm) cc_final: 0.9396 (ptp) REVERT: K 115 LEU cc_start: 0.9838 (OUTLIER) cc_final: 0.9579 (pp) REVERT: K 197 GLU cc_start: 0.8974 (mp0) cc_final: 0.8627 (pm20) REVERT: K 207 MET cc_start: 0.9391 (tpp) cc_final: 0.9091 (tpp) REVERT: L 14 GLU cc_start: 0.9227 (pm20) cc_final: 0.8943 (pm20) REVERT: L 47 GLU cc_start: 0.9522 (mp0) cc_final: 0.9223 (pm20) REVERT: L 53 ARG cc_start: 0.9609 (mtt-85) cc_final: 0.9374 (mmt-90) REVERT: L 73 MET cc_start: 0.8556 (mtm) cc_final: 0.8069 (mtp) REVERT: L 94 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8712 (ttmt) REVERT: M 102 MET cc_start: 0.9260 (ttm) cc_final: 0.8973 (ttm) REVERT: M 105 ASP cc_start: 0.8378 (t0) cc_final: 0.7924 (t0) REVERT: N 84 MET cc_start: 0.9063 (mtp) cc_final: 0.8795 (ttm) REVERT: N 102 MET cc_start: 0.9493 (mtt) cc_final: 0.9116 (mmm) REVERT: O 96 LEU cc_start: 0.9769 (tp) cc_final: 0.9547 (pp) REVERT: O 102 MET cc_start: 0.9541 (mtp) cc_final: 0.9245 (mtp) REVERT: Q 35 THR cc_start: 0.9356 (m) cc_final: 0.9093 (p) REVERT: Q 98 ILE cc_start: 0.9532 (pt) cc_final: 0.9320 (mm) REVERT: Q 179 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8945 (t80) REVERT: R 155 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9045 (mpp) REVERT: R 161 MET cc_start: 0.9328 (tmm) cc_final: 0.8996 (ppp) REVERT: R 181 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9107 (pp) REVERT: S 74 CYS cc_start: 0.8867 (m) cc_final: 0.8144 (m) REVERT: S 76 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.7680 (m-40) REVERT: S 133 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9511 (pp) REVERT: S 229 MET cc_start: 0.9463 (mtp) cc_final: 0.9121 (mmm) REVERT: a 538 MET cc_start: 0.5930 (ppp) cc_final: 0.5679 (ppp) REVERT: a 594 LYS cc_start: 0.3480 (OUTLIER) cc_final: 0.3219 (pptt) REVERT: a 616 MET cc_start: 0.9029 (ttp) cc_final: 0.8387 (ttt) REVERT: a 745 LEU cc_start: 0.9395 (mm) cc_final: 0.8796 (mm) REVERT: a 759 MET cc_start: 0.8414 (mmm) cc_final: 0.8092 (tpp) REVERT: b 48 MET cc_start: 0.9388 (mtp) cc_final: 0.8996 (mtp) REVERT: c 451 ASP cc_start: 0.4087 (t0) cc_final: 0.3263 (p0) REVERT: d 78 MET cc_start: 0.9209 (tmm) cc_final: 0.8814 (tmm) REVERT: d 118 HIS cc_start: 0.9386 (m-70) cc_final: 0.8801 (m170) REVERT: d 119 GLN cc_start: 0.9365 (tt0) cc_final: 0.8949 (tm-30) REVERT: d 138 MET cc_start: 0.7998 (tpp) cc_final: 0.7388 (tpp) REVERT: d 293 ARG cc_start: 0.9224 (mmt180) cc_final: 0.8999 (mmm160) REVERT: d 316 TYR cc_start: 0.9198 (t80) cc_final: 0.8993 (t80) REVERT: d 348 ILE cc_start: 0.8482 (mm) cc_final: 0.8072 (mt) REVERT: g 23 MET cc_start: 0.5920 (ttt) cc_final: 0.3892 (tmm) REVERT: g 82 ASP cc_start: 0.7684 (t0) cc_final: 0.7160 (m-30) REVERT: g 101 LEU cc_start: 0.9119 (tp) cc_final: 0.8400 (mt) REVERT: h 14 PHE cc_start: 0.8526 (m-80) cc_final: 0.8304 (m-80) REVERT: h 78 ASN cc_start: 0.8262 (m-40) cc_final: 0.7927 (p0) REVERT: h 104 LEU cc_start: 0.9018 (mt) cc_final: 0.8577 (mt) REVERT: i 47 MET cc_start: 0.7229 (ppp) cc_final: 0.6943 (ppp) REVERT: i 53 MET cc_start: 0.8444 (mmt) cc_final: 0.7484 (mtp) REVERT: i 65 ILE cc_start: 0.8210 (mm) cc_final: 0.7972 (mt) REVERT: j 47 MET cc_start: 0.8907 (ptm) cc_final: 0.7995 (ppp) REVERT: j 131 MET cc_start: 0.5431 (ppp) cc_final: 0.5206 (ppp) REVERT: k 17 MET cc_start: 0.8947 (mmp) cc_final: 0.8706 (mmp) REVERT: k 131 MET cc_start: 0.7635 (tmm) cc_final: 0.7070 (ppp) REVERT: l 28 MET cc_start: 0.8929 (mmp) cc_final: 0.8685 (mmm) REVERT: l 47 MET cc_start: 0.9354 (ttm) cc_final: 0.9121 (ptm) REVERT: l 53 MET cc_start: 0.8683 (mmp) cc_final: 0.8216 (ttt) REVERT: l 115 ASP cc_start: 0.7641 (t0) cc_final: 0.7198 (m-30) REVERT: m 53 MET cc_start: 0.8865 (ppp) cc_final: 0.8185 (ppp) REVERT: m 115 ASP cc_start: 0.8915 (t70) cc_final: 0.8695 (m-30) REVERT: n 13 PHE cc_start: 0.9067 (t80) cc_final: 0.8482 (t80) REVERT: n 17 MET cc_start: 0.9384 (ptt) cc_final: 0.8942 (ptt) REVERT: n 23 MET cc_start: 0.8520 (tpt) cc_final: 0.7526 (tpt) REVERT: n 36 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7262 (mtpp) REVERT: n 53 MET cc_start: 0.7500 (mmp) cc_final: 0.5834 (ttp) REVERT: n 131 MET cc_start: 0.8730 (tmm) cc_final: 0.8439 (ptm) REVERT: o 25 PHE cc_start: 0.8971 (m-80) cc_final: 0.8617 (m-80) REVERT: o 144 TYR cc_start: 0.8850 (m-10) cc_final: 0.8586 (m-80) outliers start: 189 outliers final: 125 residues processed: 972 average time/residue: 0.5423 time to fit residues: 917.3235 Evaluate side-chains 928 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 790 time to evaluate : 5.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 417 THR Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 594 LYS Chi-restraints excluded: chain a residue 651 MET Chi-restraints excluded: chain a residue 733 ILE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain d residue 275 LYS Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 144 TYR Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 78 ASN Chi-restraints excluded: chain l residue 102 SER Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain n residue 148 VAL Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 272 optimal weight: 0.9990 chunk 728 optimal weight: 30.0000 chunk 159 optimal weight: 8.9990 chunk 475 optimal weight: 9.9990 chunk 199 optimal weight: 0.9990 chunk 809 optimal weight: 0.2980 chunk 672 optimal weight: 10.0000 chunk 374 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 425 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 573 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN S 76 ASN S 162 GLN a 375 GLN ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN c 438 HIS d 171 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 ASN l 123 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 63395 Z= 0.201 Angle : 0.668 14.278 85997 Z= 0.330 Chirality : 0.043 0.276 10036 Planarity : 0.004 0.060 11103 Dihedral : 4.553 134.954 9060 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.15 % Allowed : 15.66 % Favored : 82.19 % 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: 1.54 (0.07), residues: 4920 sheet: -0.07 (0.19), residues: 725 loop : -0.30 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 743 HIS 0.006 0.001 HIS c 438 PHE 0.048 0.002 PHE R 200 TYR 0.046 0.001 TYR m 68 ARG 0.009 0.000 ARG h 88 *********************** 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 1015 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 884 time to evaluate : 5.552 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: A 61 MET cc_start: 0.9160 (mtp) cc_final: 0.8851 (tpp) REVERT: A 116 ILE cc_start: 0.9504 (pt) cc_final: 0.9156 (mm) REVERT: A 296 MET cc_start: 0.8519 (pmm) cc_final: 0.8201 (pmm) REVERT: A 340 MET cc_start: 0.8946 (ttm) cc_final: 0.8652 (ttm) REVERT: A 360 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 540 MET cc_start: 0.9298 (mtp) cc_final: 0.8915 (mtp) REVERT: A 584 MET cc_start: 0.8880 (ptm) cc_final: 0.8283 (ptp) REVERT: A 608 MET cc_start: 0.8870 (ppp) cc_final: 0.8530 (ppp) REVERT: B 39 MET cc_start: 0.9194 (tpp) cc_final: 0.8763 (tpp) REVERT: B 95 MET cc_start: 0.8691 (tpp) cc_final: 0.8294 (tmm) REVERT: B 293 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8782 (mp0) REVERT: B 306 MET cc_start: 0.9137 (tpp) cc_final: 0.8729 (tpp) REVERT: B 318 MET cc_start: 0.9494 (mtp) cc_final: 0.8785 (mtp) REVERT: B 324 GLU cc_start: 0.9294 (tt0) cc_final: 0.9000 (tm-30) REVERT: B 346 MET cc_start: 0.9288 (ppp) cc_final: 0.8965 (tmm) REVERT: B 356 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: B 433 TRP cc_start: 0.9252 (m-10) cc_final: 0.9023 (m-10) REVERT: B 480 LYS cc_start: 0.9391 (pttt) cc_final: 0.9115 (pttm) REVERT: B 487 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8688 (tp30) REVERT: B 540 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8438 (mtp) REVERT: C 65 GLN cc_start: 0.8380 (tp40) cc_final: 0.7984 (tp-100) REVERT: C 318 MET cc_start: 0.9645 (mmm) cc_final: 0.9206 (mmm) REVERT: C 388 ARG cc_start: 0.9159 (mtp180) cc_final: 0.8934 (mtp85) REVERT: C 436 ASP cc_start: 0.8684 (t70) cc_final: 0.8443 (t0) REVERT: C 550 MET cc_start: 0.9369 (mtm) cc_final: 0.8837 (mtp) REVERT: C 610 ASN cc_start: 0.9522 (m-40) cc_final: 0.8842 (p0) REVERT: D 97 GLN cc_start: 0.9194 (tt0) cc_final: 0.8638 (tm-30) REVERT: D 254 MET cc_start: 0.8323 (mmm) cc_final: 0.8094 (mmm) REVERT: D 302 SER cc_start: 0.9674 (m) cc_final: 0.9401 (t) REVERT: D 309 GLU cc_start: 0.9256 (tp30) cc_final: 0.8901 (tm-30) REVERT: D 327 MET cc_start: 0.9422 (ttp) cc_final: 0.9132 (mtp) REVERT: D 353 ILE cc_start: 0.9611 (mt) cc_final: 0.9284 (mm) REVERT: D 410 MET cc_start: 0.9212 (mtm) cc_final: 0.8103 (ptp) REVERT: E 74 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9344 (pp) REVERT: E 127 MET cc_start: 0.9143 (mtp) cc_final: 0.8512 (mtt) REVERT: E 234 MET cc_start: 0.8962 (ptt) cc_final: 0.8748 (ptt) REVERT: E 305 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9099 (tm-30) REVERT: E 327 MET cc_start: 0.9246 (ttm) cc_final: 0.8494 (mtm) REVERT: E 356 MET cc_start: 0.8691 (ttp) cc_final: 0.8444 (ttp) REVERT: E 360 ASP cc_start: 0.8692 (t0) cc_final: 0.8128 (t0) REVERT: E 410 MET cc_start: 0.9027 (mmm) cc_final: 0.8494 (mtp) REVERT: F 87 LEU cc_start: 0.9721 (tp) cc_final: 0.9390 (tt) REVERT: F 127 MET cc_start: 0.9056 (mtp) cc_final: 0.8680 (mtp) REVERT: F 205 GLN cc_start: 0.9479 (tt0) cc_final: 0.9043 (tt0) REVERT: F 254 MET cc_start: 0.8841 (mmm) cc_final: 0.8243 (tmm) REVERT: F 268 THR cc_start: 0.9596 (p) cc_final: 0.9216 (t) REVERT: F 305 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8929 (mp0) REVERT: F 330 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8429 (t70) REVERT: F 336 GLU cc_start: 0.9040 (tp30) cc_final: 0.8824 (tp30) REVERT: F 402 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8319 (tmm) REVERT: F 410 MET cc_start: 0.9048 (mtm) cc_final: 0.8740 (ptp) REVERT: H 14 MET cc_start: 0.8734 (tpp) cc_final: 0.8526 (mpp) REVERT: H 24 LYS cc_start: 0.9329 (mmtm) cc_final: 0.9109 (mmtm) REVERT: H 91 GLN cc_start: 0.9490 (tt0) cc_final: 0.9224 (tp-100) REVERT: H 109 PHE cc_start: 0.8513 (m-80) cc_final: 0.7580 (m-80) REVERT: H 190 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8875 (tm-30) REVERT: I 128 LEU cc_start: 0.9469 (mt) cc_final: 0.8890 (mp) REVERT: I 129 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8213 (mm-30) REVERT: I 132 MET cc_start: 0.8750 (mtt) cc_final: 0.8369 (mmt) REVERT: I 198 SER cc_start: 0.9716 (m) cc_final: 0.9449 (p) REVERT: I 207 MET cc_start: 0.8761 (mmt) cc_final: 0.8439 (mmt) REVERT: J 72 MET cc_start: 0.9322 (tmm) cc_final: 0.8850 (tmm) REVERT: J 76 MET cc_start: 0.9332 (mmm) cc_final: 0.8913 (mmm) REVERT: J 97 GLU cc_start: 0.9462 (tp30) cc_final: 0.8978 (tp30) REVERT: J 207 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8943 (tmm) REVERT: K 76 MET cc_start: 0.9643 (mtm) cc_final: 0.9430 (ptp) REVERT: K 97 GLU cc_start: 0.9330 (tp30) cc_final: 0.9052 (tm-30) REVERT: K 207 MET cc_start: 0.9375 (tpp) cc_final: 0.9078 (tpp) REVERT: L 14 GLU cc_start: 0.9195 (pm20) cc_final: 0.8790 (tp30) REVERT: L 20 PHE cc_start: 0.9606 (m-80) cc_final: 0.9316 (m-80) REVERT: L 46 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8827 (p0) REVERT: L 47 GLU cc_start: 0.9514 (mp0) cc_final: 0.9288 (mp0) REVERT: L 73 MET cc_start: 0.8567 (mtm) cc_final: 0.8039 (mtp) REVERT: L 94 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8747 (ttmt) REVERT: M 105 ASP cc_start: 0.8337 (t0) cc_final: 0.7877 (t0) REVERT: N 84 MET cc_start: 0.9007 (mtp) cc_final: 0.8748 (ttm) REVERT: N 102 MET cc_start: 0.9426 (mtt) cc_final: 0.9069 (mmm) REVERT: O 96 LEU cc_start: 0.9766 (tp) cc_final: 0.9489 (pp) REVERT: Q 35 THR cc_start: 0.9356 (m) cc_final: 0.9126 (p) REVERT: Q 98 ILE cc_start: 0.9505 (pt) cc_final: 0.9288 (mm) REVERT: Q 161 MET cc_start: 0.9081 (ppp) cc_final: 0.8745 (ppp) REVERT: Q 179 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8995 (t80) REVERT: Q 194 ASP cc_start: 0.9164 (p0) cc_final: 0.8903 (p0) REVERT: R 155 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.8969 (mpp) REVERT: R 161 MET cc_start: 0.9277 (tmm) cc_final: 0.8979 (ppp) REVERT: S 74 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8416 (m) REVERT: S 76 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.7797 (m-40) REVERT: S 229 MET cc_start: 0.9435 (mtp) cc_final: 0.9131 (mmm) REVERT: a 616 MET cc_start: 0.9037 (ttp) cc_final: 0.8367 (ttt) REVERT: a 645 MET cc_start: 0.7682 (ttt) cc_final: 0.7145 (ptt) REVERT: a 745 LEU cc_start: 0.9420 (mm) cc_final: 0.9175 (tt) REVERT: a 759 MET cc_start: 0.8458 (mmm) cc_final: 0.8018 (tpp) REVERT: b 48 MET cc_start: 0.9316 (mtp) cc_final: 0.8897 (mtp) REVERT: b 137 MET cc_start: 0.8813 (tpp) cc_final: 0.8607 (tpp) REVERT: b 149 LEU cc_start: 0.9517 (tp) cc_final: 0.9296 (tp) REVERT: c 451 ASP cc_start: 0.4241 (t0) cc_final: 0.3558 (p0) REVERT: d 78 MET cc_start: 0.9147 (tmm) cc_final: 0.8752 (tmm) REVERT: d 118 HIS cc_start: 0.9353 (m-70) cc_final: 0.8757 (m170) REVERT: d 119 GLN cc_start: 0.9338 (tt0) cc_final: 0.8942 (tm-30) REVERT: d 293 ARG cc_start: 0.9219 (mmt180) cc_final: 0.8992 (mmm160) REVERT: d 348 ILE cc_start: 0.8429 (mm) cc_final: 0.8022 (mt) REVERT: g 82 ASP cc_start: 0.7736 (t0) cc_final: 0.7208 (m-30) REVERT: g 101 LEU cc_start: 0.9050 (tp) cc_final: 0.8400 (mt) REVERT: h 78 ASN cc_start: 0.8257 (m-40) cc_final: 0.7892 (p0) REVERT: h 104 LEU cc_start: 0.9028 (mt) cc_final: 0.8604 (mt) REVERT: h 131 MET cc_start: 0.8098 (ppp) cc_final: 0.6966 (ppp) REVERT: i 47 MET cc_start: 0.7134 (ppp) cc_final: 0.6897 (ppp) REVERT: i 53 MET cc_start: 0.8387 (mmt) cc_final: 0.7441 (mtp) REVERT: i 65 ILE cc_start: 0.8205 (mm) cc_final: 0.7966 (mt) REVERT: j 34 THR cc_start: 0.8261 (p) cc_final: 0.7965 (p) REVERT: j 47 MET cc_start: 0.8758 (ptm) cc_final: 0.7981 (ppp) REVERT: k 47 MET cc_start: 0.6320 (ptm) cc_final: 0.5256 (pmm) REVERT: k 131 MET cc_start: 0.7558 (tmm) cc_final: 0.7047 (ppp) REVERT: k 144 TYR cc_start: 0.8850 (m-80) cc_final: 0.8470 (m-80) REVERT: l 28 MET cc_start: 0.8909 (mmp) cc_final: 0.8668 (mmm) REVERT: l 47 MET cc_start: 0.9385 (ttm) cc_final: 0.8818 (ppp) REVERT: l 53 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8115 (ttt) REVERT: l 115 ASP cc_start: 0.7611 (t0) cc_final: 0.7147 (m-30) REVERT: l 123 GLN cc_start: 0.8792 (mp-120) cc_final: 0.8549 (mp10) REVERT: m 23 MET cc_start: 0.8378 (tpp) cc_final: 0.7399 (tpt) REVERT: m 53 MET cc_start: 0.8854 (ppp) cc_final: 0.8146 (ppp) REVERT: m 139 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: m 144 TYR cc_start: 0.9304 (m-10) cc_final: 0.8878 (m-80) REVERT: n 13 PHE cc_start: 0.9072 (t80) cc_final: 0.8460 (t80) REVERT: n 17 MET cc_start: 0.9351 (ptt) cc_final: 0.8877 (ptt) REVERT: n 23 MET cc_start: 0.8488 (tpt) cc_final: 0.7512 (tpt) REVERT: n 53 MET cc_start: 0.7452 (mmp) cc_final: 0.5831 (ttp) REVERT: n 131 MET cc_start: 0.8809 (tmm) cc_final: 0.8604 (ptm) REVERT: o 44 MET cc_start: 0.9401 (mmm) cc_final: 0.9083 (mmm) REVERT: o 144 TYR cc_start: 0.8772 (m-10) cc_final: 0.8429 (m-80) REVERT: p 328 ILE cc_start: 0.9583 (mm) cc_final: 0.9306 (pt) outliers start: 131 outliers final: 82 residues processed: 973 average time/residue: 0.5451 time to fit residues: 921.5513 Evaluate side-chains 914 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 819 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 375 GLN Chi-restraints excluded: chain a residue 417 THR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 171 GLN Chi-restraints excluded: chain d residue 275 LYS Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 780 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 461 optimal weight: 30.0000 chunk 591 optimal weight: 0.6980 chunk 458 optimal weight: 10.0000 chunk 681 optimal weight: 0.9990 chunk 452 optimal weight: 50.0000 chunk 806 optimal weight: 9.9990 chunk 504 optimal weight: 5.9990 chunk 491 optimal weight: 3.9990 chunk 372 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN Q 117 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN S 117 GLN ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS d 171 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 63395 Z= 0.204 Angle : 0.675 14.572 85997 Z= 0.330 Chirality : 0.043 0.400 10036 Planarity : 0.004 0.062 11103 Dihedral : 4.481 132.859 9060 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.17 % Allowed : 16.63 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8372 helix: 1.55 (0.07), residues: 4918 sheet: 0.02 (0.19), residues: 711 loop : -0.33 (0.12), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 743 HIS 0.007 0.001 HIS a 802 PHE 0.037 0.002 PHE j 25 TYR 0.048 0.001 TYR n 144 ARG 0.007 0.000 ARG a 805 *********************** 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 994 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 862 time to evaluate : 5.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9155 (mtp) cc_final: 0.8848 (tpp) REVERT: A 116 ILE cc_start: 0.9523 (pt) cc_final: 0.9194 (mm) REVERT: A 296 MET cc_start: 0.8489 (pmm) cc_final: 0.8161 (pmm) REVERT: A 340 MET cc_start: 0.8881 (ttm) cc_final: 0.8533 (ttm) REVERT: A 360 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 608 MET cc_start: 0.8900 (ppp) cc_final: 0.8594 (ppp) REVERT: B 34 MET cc_start: 0.9310 (mmm) cc_final: 0.8903 (mmm) REVERT: B 39 MET cc_start: 0.9235 (tpp) cc_final: 0.8821 (tpp) REVERT: B 95 MET cc_start: 0.8762 (tpp) cc_final: 0.8375 (tmm) REVERT: B 293 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8806 (mp0) REVERT: B 306 MET cc_start: 0.9177 (tpp) cc_final: 0.8764 (tpp) REVERT: B 318 MET cc_start: 0.9498 (mtp) cc_final: 0.8816 (mtp) REVERT: B 346 MET cc_start: 0.9276 (ppp) cc_final: 0.8962 (tmm) REVERT: B 356 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: B 458 MET cc_start: 0.8977 (mtp) cc_final: 0.8580 (mmm) REVERT: B 465 TYR cc_start: 0.9051 (m-80) cc_final: 0.8625 (m-80) REVERT: B 480 LYS cc_start: 0.9411 (pttt) cc_final: 0.9163 (pttm) REVERT: B 540 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8422 (mtp) REVERT: C 61 MET cc_start: 0.8721 (tpp) cc_final: 0.8461 (tpp) REVERT: C 65 GLN cc_start: 0.8295 (tp40) cc_final: 0.7903 (tp-100) REVERT: C 318 MET cc_start: 0.9635 (mmm) cc_final: 0.9220 (mmm) REVERT: C 324 GLU cc_start: 0.9498 (tt0) cc_final: 0.8950 (tm-30) REVERT: C 436 ASP cc_start: 0.8665 (t70) cc_final: 0.8434 (t0) REVERT: C 550 MET cc_start: 0.9336 (mtm) cc_final: 0.8793 (mtp) REVERT: C 610 ASN cc_start: 0.9506 (m-40) cc_final: 0.8827 (p0) REVERT: D 97 GLN cc_start: 0.9190 (tt0) cc_final: 0.8629 (tm-30) REVERT: D 254 MET cc_start: 0.8398 (mmm) cc_final: 0.8104 (mmm) REVERT: D 300 MET cc_start: 0.9547 (tpp) cc_final: 0.9076 (mmp) REVERT: D 302 SER cc_start: 0.9661 (m) cc_final: 0.9393 (t) REVERT: D 309 GLU cc_start: 0.9253 (tp30) cc_final: 0.8890 (tm-30) REVERT: D 327 MET cc_start: 0.9426 (ttp) cc_final: 0.9109 (mtp) REVERT: D 348 ILE cc_start: 0.9541 (mt) cc_final: 0.9329 (mt) REVERT: D 353 ILE cc_start: 0.9568 (mt) cc_final: 0.9289 (mm) REVERT: D 410 MET cc_start: 0.9173 (mtm) cc_final: 0.8110 (ptp) REVERT: E 74 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9323 (pp) REVERT: E 127 MET cc_start: 0.9126 (mtp) cc_final: 0.8505 (mtt) REVERT: E 254 MET cc_start: 0.8667 (mmm) cc_final: 0.8401 (mmm) REVERT: E 305 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9090 (tm-30) REVERT: E 356 MET cc_start: 0.8666 (ttp) cc_final: 0.8045 (ttm) REVERT: E 360 ASP cc_start: 0.8723 (t0) cc_final: 0.8271 (t0) REVERT: E 410 MET cc_start: 0.9031 (mmm) cc_final: 0.8481 (mtp) REVERT: F 87 LEU cc_start: 0.9618 (tp) cc_final: 0.9376 (tt) REVERT: F 127 MET cc_start: 0.9060 (mtp) cc_final: 0.8661 (mtp) REVERT: F 205 GLN cc_start: 0.9483 (tt0) cc_final: 0.9040 (tt0) REVERT: F 254 MET cc_start: 0.8808 (mmm) cc_final: 0.8348 (tpp) REVERT: F 268 THR cc_start: 0.9560 (p) cc_final: 0.9215 (t) REVERT: F 305 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8931 (mp0) REVERT: F 309 GLU cc_start: 0.9334 (tt0) cc_final: 0.9059 (tp30) REVERT: F 330 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8362 (t70) REVERT: F 402 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8368 (tmm) REVERT: F 410 MET cc_start: 0.9075 (mtm) cc_final: 0.8770 (ptp) REVERT: H 91 GLN cc_start: 0.9482 (tt0) cc_final: 0.9238 (tp-100) REVERT: H 109 PHE cc_start: 0.8603 (m-80) cc_final: 0.7636 (m-80) REVERT: H 131 LEU cc_start: 0.9379 (mt) cc_final: 0.9176 (tt) REVERT: H 190 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8894 (tm-30) REVERT: I 128 LEU cc_start: 0.9461 (mt) cc_final: 0.8999 (mt) REVERT: I 129 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8245 (mm-30) REVERT: I 132 MET cc_start: 0.8725 (mtt) cc_final: 0.8426 (mtt) REVERT: I 198 SER cc_start: 0.9707 (m) cc_final: 0.9426 (p) REVERT: J 72 MET cc_start: 0.9328 (tmm) cc_final: 0.8857 (tmm) REVERT: J 76 MET cc_start: 0.9333 (mmm) cc_final: 0.8920 (mmm) REVERT: J 97 GLU cc_start: 0.9457 (tp30) cc_final: 0.8962 (tp30) REVERT: K 72 MET cc_start: 0.9438 (ppp) cc_final: 0.8969 (ppp) REVERT: K 76 MET cc_start: 0.9606 (mtm) cc_final: 0.9035 (ptm) REVERT: K 97 GLU cc_start: 0.9342 (tp30) cc_final: 0.8920 (tm-30) REVERT: K 207 MET cc_start: 0.9348 (tpp) cc_final: 0.9046 (tpp) REVERT: L 14 GLU cc_start: 0.9182 (pm20) cc_final: 0.8782 (tp30) REVERT: L 20 PHE cc_start: 0.9596 (m-80) cc_final: 0.9314 (m-80) REVERT: L 46 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8821 (p0) REVERT: L 73 MET cc_start: 0.8543 (mtm) cc_final: 0.7976 (mtp) REVERT: L 94 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8760 (ttmt) REVERT: M 105 ASP cc_start: 0.8332 (t0) cc_final: 0.7899 (t0) REVERT: N 84 MET cc_start: 0.9017 (mtp) cc_final: 0.8750 (ttm) REVERT: N 102 MET cc_start: 0.9427 (mtt) cc_final: 0.9123 (mmm) REVERT: Q 35 THR cc_start: 0.9341 (m) cc_final: 0.9118 (p) REVERT: Q 62 PHE cc_start: 0.8358 (t80) cc_final: 0.8140 (t80) REVERT: Q 98 ILE cc_start: 0.9506 (pt) cc_final: 0.9280 (mm) REVERT: Q 161 MET cc_start: 0.9091 (ppp) cc_final: 0.8819 (ppp) REVERT: Q 179 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8983 (t80) REVERT: R 136 LEU cc_start: 0.9841 (mm) cc_final: 0.9594 (pp) REVERT: R 155 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.8993 (mpp) REVERT: R 161 MET cc_start: 0.9243 (tmm) cc_final: 0.8978 (ppp) REVERT: S 74 CYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8442 (m) REVERT: S 76 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.7754 (m-40) REVERT: S 229 MET cc_start: 0.9438 (mtp) cc_final: 0.9148 (mmm) REVERT: a 538 MET cc_start: 0.5951 (ppp) cc_final: 0.5508 (ppp) REVERT: a 550 LEU cc_start: 0.9101 (mt) cc_final: 0.8892 (pp) REVERT: a 594 LYS cc_start: 0.3559 (OUTLIER) cc_final: 0.3334 (pptt) REVERT: a 616 MET cc_start: 0.9031 (ttp) cc_final: 0.8713 (ptm) REVERT: a 645 MET cc_start: 0.7632 (ttt) cc_final: 0.6978 (ptt) REVERT: a 745 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9256 (tt) REVERT: a 759 MET cc_start: 0.8440 (mmm) cc_final: 0.8010 (tpp) REVERT: a 805 ARG cc_start: 0.9467 (ttp-110) cc_final: 0.9262 (mtm110) REVERT: b 16 TRP cc_start: 0.9318 (m100) cc_final: 0.9117 (m100) REVERT: b 103 TYR cc_start: 0.7707 (m-10) cc_final: 0.7011 (m-10) REVERT: b 107 MET cc_start: 0.7812 (mtm) cc_final: 0.7366 (mmm) REVERT: c 421 MET cc_start: 0.8900 (mtt) cc_final: 0.8623 (mmt) REVERT: c 429 MET cc_start: 0.9174 (ttt) cc_final: 0.8366 (tmm) REVERT: c 451 ASP cc_start: 0.3920 (t0) cc_final: 0.3208 (p0) REVERT: d 78 MET cc_start: 0.9147 (tmm) cc_final: 0.8750 (tmm) REVERT: d 118 HIS cc_start: 0.9350 (m-70) cc_final: 0.8749 (m170) REVERT: d 119 GLN cc_start: 0.9351 (tt0) cc_final: 0.8944 (tm-30) REVERT: d 293 ARG cc_start: 0.9215 (mmt180) cc_final: 0.8985 (mmm160) REVERT: d 348 ILE cc_start: 0.8437 (mm) cc_final: 0.8018 (mt) REVERT: g 23 MET cc_start: 0.4272 (ttt) cc_final: 0.3050 (tpt) REVERT: g 82 ASP cc_start: 0.7765 (t0) cc_final: 0.7226 (m-30) REVERT: g 101 LEU cc_start: 0.9032 (tp) cc_final: 0.8387 (mt) REVERT: h 78 ASN cc_start: 0.8232 (m-40) cc_final: 0.7887 (p0) REVERT: h 104 LEU cc_start: 0.9037 (mt) cc_final: 0.8597 (mt) REVERT: h 131 MET cc_start: 0.8132 (ppp) cc_final: 0.7110 (ppp) REVERT: i 23 MET cc_start: 0.7171 (tpt) cc_final: 0.6834 (tpt) REVERT: i 53 MET cc_start: 0.8388 (mmt) cc_final: 0.7446 (mtp) REVERT: i 70 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8690 (pp) REVERT: j 34 THR cc_start: 0.8357 (p) cc_final: 0.8082 (p) REVERT: j 47 MET cc_start: 0.8788 (ptm) cc_final: 0.7900 (ppp) REVERT: k 17 MET cc_start: 0.8907 (mmp) cc_final: 0.8484 (mmp) REVERT: k 131 MET cc_start: 0.7567 (tmm) cc_final: 0.7093 (ppp) REVERT: l 23 MET cc_start: 0.8085 (tpp) cc_final: 0.7689 (ttp) REVERT: l 47 MET cc_start: 0.9381 (ttm) cc_final: 0.8857 (ppp) REVERT: l 48 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8437 (ttp-110) REVERT: l 53 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8143 (ttt) REVERT: l 68 TYR cc_start: 0.8890 (m-10) cc_final: 0.8529 (m-80) REVERT: l 115 ASP cc_start: 0.7586 (t0) cc_final: 0.7113 (m-30) REVERT: l 123 GLN cc_start: 0.8758 (mp-120) cc_final: 0.8477 (mp10) REVERT: m 23 MET cc_start: 0.8329 (tpp) cc_final: 0.7428 (tpt) REVERT: m 53 MET cc_start: 0.8854 (ppp) cc_final: 0.8163 (ppp) REVERT: m 139 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: n 13 PHE cc_start: 0.9052 (t80) cc_final: 0.8663 (t80) REVERT: n 17 MET cc_start: 0.9335 (ptt) cc_final: 0.9076 (ptt) REVERT: n 36 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7259 (mmmt) REVERT: n 53 MET cc_start: 0.7373 (mmp) cc_final: 0.5776 (ttp) REVERT: n 131 MET cc_start: 0.8874 (tmm) cc_final: 0.8608 (ptm) REVERT: o 44 MET cc_start: 0.9476 (mmm) cc_final: 0.9222 (mmm) REVERT: o 144 TYR cc_start: 0.8844 (m-10) cc_final: 0.8347 (m-80) REVERT: p 328 ILE cc_start: 0.9551 (mm) cc_final: 0.9202 (pt) outliers start: 132 outliers final: 89 residues processed: 947 average time/residue: 0.5757 time to fit residues: 951.6932 Evaluate side-chains 915 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 810 time to evaluate : 5.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 594 LYS Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 171 GLN Chi-restraints excluded: chain d residue 275 LYS Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 144 TYR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain p residue 325 SER 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: 9.9990 chunk 158 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 512 optimal weight: 0.9990 chunk 549 optimal weight: 6.9990 chunk 398 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 634 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN Q 142 ASN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 171 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 63395 Z= 0.268 Angle : 0.700 14.081 85997 Z= 0.347 Chirality : 0.043 0.329 10036 Planarity : 0.005 0.102 11103 Dihedral : 4.533 133.542 9060 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.35 % Allowed : 16.64 % Favored : 81.00 % 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: 1.12 (0.09), residues: 8372 helix: 1.51 (0.07), residues: 4933 sheet: -0.04 (0.20), residues: 695 loop : -0.35 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 567 HIS 0.008 0.001 HIS a 802 PHE 0.026 0.002 PHE f 70 TYR 0.064 0.002 TYR m 68 ARG 0.022 0.000 ARG h 119 *********************** 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 957 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 814 time to evaluate : 5.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9176 (mtp) cc_final: 0.8875 (tpp) REVERT: A 116 ILE cc_start: 0.9550 (OUTLIER) cc_final: 0.9231 (mm) REVERT: A 205 MET cc_start: 0.8784 (pmm) cc_final: 0.8483 (pmm) REVERT: A 296 MET cc_start: 0.8507 (pmm) cc_final: 0.8215 (pmm) REVERT: A 340 MET cc_start: 0.8916 (ttm) cc_final: 0.8553 (ttm) REVERT: A 360 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 371 ASP cc_start: 0.8957 (t0) cc_final: 0.8730 (t0) REVERT: A 540 MET cc_start: 0.9175 (mtp) cc_final: 0.8886 (ptp) REVERT: A 584 MET cc_start: 0.9063 (ptp) cc_final: 0.8518 (ptp) REVERT: B 34 MET cc_start: 0.9404 (mmm) cc_final: 0.9009 (mmm) REVERT: B 39 MET cc_start: 0.9251 (tpp) cc_final: 0.8800 (tpp) REVERT: B 95 MET cc_start: 0.8878 (tpp) cc_final: 0.8558 (tmm) REVERT: B 306 MET cc_start: 0.9204 (tpp) cc_final: 0.8987 (tpp) REVERT: B 318 MET cc_start: 0.9462 (mtp) cc_final: 0.8803 (mtp) REVERT: B 340 MET cc_start: 0.9419 (tpp) cc_final: 0.9093 (tpp) REVERT: B 346 MET cc_start: 0.9278 (ppp) cc_final: 0.8941 (tmm) REVERT: B 458 MET cc_start: 0.8984 (mtp) cc_final: 0.8644 (mmm) REVERT: B 465 TYR cc_start: 0.9091 (m-80) cc_final: 0.8639 (m-80) REVERT: B 480 LYS cc_start: 0.9420 (pttt) cc_final: 0.9180 (pttm) REVERT: B 487 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8818 (tp30) REVERT: B 540 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8459 (mtp) REVERT: C 61 MET cc_start: 0.8759 (tpp) cc_final: 0.8490 (tpp) REVERT: C 65 GLN cc_start: 0.8338 (tp40) cc_final: 0.7771 (tm-30) REVERT: C 318 MET cc_start: 0.9611 (mmm) cc_final: 0.9195 (mmm) REVERT: C 324 GLU cc_start: 0.9525 (tt0) cc_final: 0.8947 (tm-30) REVERT: C 436 ASP cc_start: 0.8635 (t70) cc_final: 0.8405 (t0) REVERT: C 544 MET cc_start: 0.9114 (mtt) cc_final: 0.8433 (mtm) REVERT: C 550 MET cc_start: 0.9330 (mtm) cc_final: 0.8768 (mtp) REVERT: C 610 ASN cc_start: 0.9532 (m-40) cc_final: 0.8860 (p0) REVERT: D 97 GLN cc_start: 0.9245 (tt0) cc_final: 0.8657 (tm-30) REVERT: D 300 MET cc_start: 0.9543 (tpp) cc_final: 0.8921 (mmp) REVERT: D 302 SER cc_start: 0.9671 (m) cc_final: 0.9435 (t) REVERT: D 309 GLU cc_start: 0.9255 (tp30) cc_final: 0.8913 (tm-30) REVERT: D 314 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8684 (ttm110) REVERT: D 327 MET cc_start: 0.9467 (ttp) cc_final: 0.9147 (mtp) REVERT: D 348 ILE cc_start: 0.9538 (mt) cc_final: 0.9295 (mt) REVERT: D 353 ILE cc_start: 0.9544 (mt) cc_final: 0.9262 (mm) REVERT: D 410 MET cc_start: 0.9213 (mtm) cc_final: 0.8171 (ptp) REVERT: E 74 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9312 (pp) REVERT: E 127 MET cc_start: 0.9122 (mtp) cc_final: 0.8518 (mtt) REVERT: E 254 MET cc_start: 0.8785 (mmm) cc_final: 0.8471 (mmm) REVERT: E 305 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9106 (tm-30) REVERT: E 327 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8458 (mtm) REVERT: E 356 MET cc_start: 0.8583 (ttp) cc_final: 0.8186 (ttm) REVERT: E 360 ASP cc_start: 0.8724 (t0) cc_final: 0.8154 (t0) REVERT: E 410 MET cc_start: 0.9094 (mmm) cc_final: 0.8435 (mtp) REVERT: F 127 MET cc_start: 0.9066 (mtp) cc_final: 0.8744 (mtp) REVERT: F 205 GLN cc_start: 0.9478 (tt0) cc_final: 0.9037 (tt0) REVERT: F 254 MET cc_start: 0.8896 (mmm) cc_final: 0.8315 (tmm) REVERT: F 268 THR cc_start: 0.9558 (p) cc_final: 0.9184 (t) REVERT: F 305 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8966 (mt-10) REVERT: F 309 GLU cc_start: 0.9348 (tt0) cc_final: 0.9071 (tp30) REVERT: F 330 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8455 (t70) REVERT: F 353 ILE cc_start: 0.9525 (mp) cc_final: 0.9303 (mm) REVERT: F 402 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8325 (tmm) REVERT: F 410 MET cc_start: 0.9081 (mtm) cc_final: 0.8836 (ptp) REVERT: H 91 GLN cc_start: 0.9445 (tt0) cc_final: 0.9206 (tp-100) REVERT: H 99 ASP cc_start: 0.9196 (t0) cc_final: 0.8855 (p0) REVERT: H 109 PHE cc_start: 0.8663 (m-80) cc_final: 0.7736 (m-80) REVERT: H 190 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8884 (tm-30) REVERT: H 206 GLN cc_start: 0.9508 (tp40) cc_final: 0.9304 (mm-40) REVERT: I 129 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8216 (mm-30) REVERT: I 132 MET cc_start: 0.8726 (mtt) cc_final: 0.8413 (mtt) REVERT: I 198 SER cc_start: 0.9744 (m) cc_final: 0.9478 (p) REVERT: J 72 MET cc_start: 0.9353 (tmm) cc_final: 0.8882 (tmm) REVERT: J 76 MET cc_start: 0.9354 (mmm) cc_final: 0.8941 (mmm) REVERT: J 97 GLU cc_start: 0.9447 (tp30) cc_final: 0.8948 (tp30) REVERT: J 203 ILE cc_start: 0.9746 (mt) cc_final: 0.9461 (tp) REVERT: J 207 MET cc_start: 0.9149 (tpp) cc_final: 0.8941 (tpp) REVERT: K 72 MET cc_start: 0.9456 (ppp) cc_final: 0.9038 (ppp) REVERT: K 76 MET cc_start: 0.9584 (mtm) cc_final: 0.9369 (mmt) REVERT: K 97 GLU cc_start: 0.9359 (tp30) cc_final: 0.8933 (tm-30) REVERT: K 197 GLU cc_start: 0.8930 (mp0) cc_final: 0.8709 (mp0) REVERT: K 207 MET cc_start: 0.9379 (tpp) cc_final: 0.9076 (tpp) REVERT: K 208 MET cc_start: 0.9273 (mmt) cc_final: 0.8945 (mmm) REVERT: L 46 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8830 (p0) REVERT: L 47 GLU cc_start: 0.9547 (mp0) cc_final: 0.9288 (mp0) REVERT: L 73 MET cc_start: 0.8506 (mtm) cc_final: 0.8015 (mtp) REVERT: L 94 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8771 (ttmt) REVERT: L 102 LYS cc_start: 0.8788 (mttt) cc_final: 0.8539 (tptm) REVERT: M 105 ASP cc_start: 0.8372 (t0) cc_final: 0.7990 (t70) REVERT: N 84 MET cc_start: 0.9088 (mtp) cc_final: 0.8788 (ttm) REVERT: N 102 MET cc_start: 0.9473 (mtt) cc_final: 0.9113 (mmm) REVERT: O 73 VAL cc_start: 0.9466 (t) cc_final: 0.9223 (p) REVERT: O 102 MET cc_start: 0.9553 (ttp) cc_final: 0.9040 (ptm) REVERT: Q 35 THR cc_start: 0.9315 (m) cc_final: 0.9096 (p) REVERT: Q 98 ILE cc_start: 0.9536 (pt) cc_final: 0.9313 (mm) REVERT: Q 161 MET cc_start: 0.9140 (ppp) cc_final: 0.8922 (ppp) REVERT: Q 179 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8974 (t80) REVERT: R 155 MET cc_start: 0.9518 (OUTLIER) cc_final: 0.9060 (mpp) REVERT: R 161 MET cc_start: 0.9257 (tmm) cc_final: 0.9008 (ppp) REVERT: R 181 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9108 (pp) REVERT: S 74 CYS cc_start: 0.8722 (m) cc_final: 0.8134 (m) REVERT: S 229 MET cc_start: 0.9439 (mtp) cc_final: 0.9170 (mmm) REVERT: a 538 MET cc_start: 0.5993 (ppp) cc_final: 0.5775 (ppp) REVERT: a 594 LYS cc_start: 0.3592 (OUTLIER) cc_final: 0.3381 (pptt) REVERT: a 641 ILE cc_start: 0.8102 (mm) cc_final: 0.7613 (mp) REVERT: a 645 MET cc_start: 0.7621 (ttt) cc_final: 0.6987 (ptt) REVERT: a 759 MET cc_start: 0.8447 (mmm) cc_final: 0.8029 (tpp) REVERT: b 12 PHE cc_start: 0.8823 (m-10) cc_final: 0.8454 (m-80) REVERT: b 107 MET cc_start: 0.7819 (mtm) cc_final: 0.7440 (mmm) REVERT: c 421 MET cc_start: 0.8964 (mtt) cc_final: 0.8737 (mmt) REVERT: c 429 MET cc_start: 0.9109 (ttt) cc_final: 0.8259 (tmm) REVERT: c 451 ASP cc_start: 0.3466 (t0) cc_final: 0.2822 (p0) REVERT: d 78 MET cc_start: 0.9148 (tmm) cc_final: 0.8733 (tmm) REVERT: d 118 HIS cc_start: 0.9370 (m-70) cc_final: 0.8779 (m170) REVERT: d 119 GLN cc_start: 0.9359 (tt0) cc_final: 0.8942 (tm-30) REVERT: d 293 ARG cc_start: 0.9207 (mmt180) cc_final: 0.8983 (mmm160) REVERT: d 348 ILE cc_start: 0.8494 (mm) cc_final: 0.8262 (mm) REVERT: g 23 MET cc_start: 0.4838 (ttt) cc_final: 0.3972 (ttm) REVERT: g 82 ASP cc_start: 0.7819 (t0) cc_final: 0.7318 (m-30) REVERT: g 101 LEU cc_start: 0.9067 (tp) cc_final: 0.8404 (mt) REVERT: h 78 ASN cc_start: 0.8235 (m-40) cc_final: 0.7856 (p0) REVERT: h 104 LEU cc_start: 0.9058 (mt) cc_final: 0.8593 (mt) REVERT: h 131 MET cc_start: 0.8187 (ppp) cc_final: 0.7217 (ppp) REVERT: i 53 MET cc_start: 0.8404 (mmt) cc_final: 0.7426 (mtp) REVERT: j 34 THR cc_start: 0.8321 (p) cc_final: 0.8017 (p) REVERT: j 47 MET cc_start: 0.8862 (ptm) cc_final: 0.8388 (ppp) REVERT: j 108 PHE cc_start: 0.8311 (m-80) cc_final: 0.7765 (t80) REVERT: k 47 MET cc_start: 0.5956 (ptm) cc_final: 0.5731 (ptm) REVERT: l 23 MET cc_start: 0.7836 (tpp) cc_final: 0.7558 (tpp) REVERT: l 47 MET cc_start: 0.9383 (ttm) cc_final: 0.8839 (ppp) REVERT: l 53 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8133 (ttt) REVERT: l 68 TYR cc_start: 0.8979 (m-10) cc_final: 0.8638 (m-10) REVERT: l 115 ASP cc_start: 0.7649 (t0) cc_final: 0.7146 (m-30) REVERT: m 53 MET cc_start: 0.8869 (ppp) cc_final: 0.8204 (ppp) REVERT: m 139 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: n 13 PHE cc_start: 0.9088 (t80) cc_final: 0.8797 (t80) REVERT: n 14 PHE cc_start: 0.8579 (m-80) cc_final: 0.8042 (m-80) REVERT: n 17 MET cc_start: 0.9349 (ptt) cc_final: 0.9033 (ptt) REVERT: n 23 MET cc_start: 0.8587 (tpt) cc_final: 0.7637 (tpt) REVERT: n 36 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7176 (mtpp) REVERT: n 53 MET cc_start: 0.7439 (mmp) cc_final: 0.5770 (ttp) REVERT: o 44 MET cc_start: 0.9484 (mmm) cc_final: 0.9236 (mmm) REVERT: o 108 PHE cc_start: 0.8743 (m-10) cc_final: 0.8210 (m-10) REVERT: o 144 TYR cc_start: 0.8855 (m-10) cc_final: 0.8452 (m-80) REVERT: p 328 ILE cc_start: 0.9544 (mm) cc_final: 0.9075 (pt) outliers start: 143 outliers final: 107 residues processed: 909 average time/residue: 0.5868 time to fit residues: 929.5279 Evaluate side-chains 900 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 780 time to evaluate : 5.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 417 THR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 594 LYS Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 171 GLN Chi-restraints excluded: chain d residue 275 LYS Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 60 VAL Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 733 optimal weight: 5.9990 chunk 772 optimal weight: 6.9990 chunk 705 optimal weight: 30.0000 chunk 751 optimal weight: 6.9990 chunk 452 optimal weight: 40.0000 chunk 327 optimal weight: 20.0000 chunk 590 optimal weight: 10.0000 chunk 230 optimal weight: 0.2980 chunk 679 optimal weight: 30.0000 chunk 711 optimal weight: 4.9990 chunk 749 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 GLN R 198 HIS ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 HIS ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 63395 Z= 0.311 Angle : 0.739 14.401 85997 Z= 0.367 Chirality : 0.044 0.358 10036 Planarity : 0.005 0.069 11103 Dihedral : 4.613 135.209 9058 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.98 % Favored : 96.01 % Rotamer: Outliers : 2.45 % Allowed : 16.89 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.09), residues: 8372 helix: 1.44 (0.07), residues: 4923 sheet: -0.17 (0.21), residues: 650 loop : -0.39 (0.12), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 567 HIS 0.011 0.001 HIS c 438 PHE 0.041 0.002 PHE c 433 TYR 0.061 0.002 TYR m 68 ARG 0.014 0.001 ARG h 119 *********************** 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 949 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 800 time to evaluate : 5.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9186 (mtp) cc_final: 0.8903 (tpp) REVERT: A 116 ILE cc_start: 0.9556 (OUTLIER) cc_final: 0.9240 (mm) REVERT: A 205 MET cc_start: 0.8745 (pmm) cc_final: 0.8433 (pmm) REVERT: A 296 MET cc_start: 0.8470 (pmm) cc_final: 0.8212 (pmm) REVERT: A 360 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 361 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9190 (tp) REVERT: A 371 ASP cc_start: 0.8986 (t0) cc_final: 0.8779 (t0) REVERT: A 387 GLU cc_start: 0.9025 (tp30) cc_final: 0.8815 (tp30) REVERT: A 584 MET cc_start: 0.9034 (ptp) cc_final: 0.8492 (ptp) REVERT: A 608 MET cc_start: 0.9045 (ppp) cc_final: 0.8815 (ppp) REVERT: B 34 MET cc_start: 0.9469 (mmm) cc_final: 0.9067 (mmm) REVERT: B 39 MET cc_start: 0.9271 (tpp) cc_final: 0.8841 (tpp) REVERT: B 95 MET cc_start: 0.8842 (tpp) cc_final: 0.8499 (tmm) REVERT: B 306 MET cc_start: 0.9247 (tpp) cc_final: 0.8861 (tpp) REVERT: B 318 MET cc_start: 0.9434 (mtp) cc_final: 0.8763 (mtp) REVERT: B 340 MET cc_start: 0.9424 (tpp) cc_final: 0.9076 (tpp) REVERT: B 346 MET cc_start: 0.9304 (ppp) cc_final: 0.8907 (tmm) REVERT: B 347 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8386 (pmm) REVERT: B 458 MET cc_start: 0.9035 (mtp) cc_final: 0.8760 (mmm) REVERT: B 480 LYS cc_start: 0.9429 (pttt) cc_final: 0.9140 (pttm) REVERT: B 487 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8699 (tm-30) REVERT: B 491 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 540 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8412 (mtp) REVERT: C 61 MET cc_start: 0.8771 (tpp) cc_final: 0.8496 (mmm) REVERT: C 65 GLN cc_start: 0.8380 (tp40) cc_final: 0.7781 (tm-30) REVERT: C 318 MET cc_start: 0.9597 (mmm) cc_final: 0.9199 (mmm) REVERT: C 540 MET cc_start: 0.9136 (ptp) cc_final: 0.8506 (ptp) REVERT: C 544 MET cc_start: 0.9120 (mtt) cc_final: 0.8385 (mtm) REVERT: C 550 MET cc_start: 0.9327 (mtm) cc_final: 0.8734 (mtp) REVERT: C 610 ASN cc_start: 0.9579 (m-40) cc_final: 0.8896 (p0) REVERT: D 97 GLN cc_start: 0.9234 (tt0) cc_final: 0.8638 (tm-30) REVERT: D 249 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9084 (mt-10) REVERT: D 300 MET cc_start: 0.9511 (tpp) cc_final: 0.8774 (mmp) REVERT: D 302 SER cc_start: 0.9669 (m) cc_final: 0.9459 (t) REVERT: D 309 GLU cc_start: 0.9249 (tp30) cc_final: 0.8907 (tm-30) REVERT: D 314 ARG cc_start: 0.9104 (ttm110) cc_final: 0.8777 (ttm110) REVERT: D 327 MET cc_start: 0.9463 (ttp) cc_final: 0.9148 (mtp) REVERT: D 353 ILE cc_start: 0.9521 (mt) cc_final: 0.9244 (mm) REVERT: D 410 MET cc_start: 0.9248 (mtm) cc_final: 0.8181 (ptp) REVERT: E 127 MET cc_start: 0.9115 (mtp) cc_final: 0.8459 (mtt) REVERT: E 327 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8516 (mtm) REVERT: E 356 MET cc_start: 0.8666 (ttp) cc_final: 0.8128 (ttm) REVERT: E 360 ASP cc_start: 0.8828 (t0) cc_final: 0.7985 (t0) REVERT: E 410 MET cc_start: 0.9114 (mmm) cc_final: 0.8461 (mtp) REVERT: F 127 MET cc_start: 0.9068 (mtp) cc_final: 0.8753 (mtp) REVERT: F 205 GLN cc_start: 0.9490 (tt0) cc_final: 0.9063 (tt0) REVERT: F 254 MET cc_start: 0.8953 (mmm) cc_final: 0.8385 (tmm) REVERT: F 268 THR cc_start: 0.9568 (p) cc_final: 0.9164 (t) REVERT: F 305 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8964 (mt-10) REVERT: F 330 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8422 (t70) REVERT: F 353 ILE cc_start: 0.9544 (mp) cc_final: 0.9323 (mm) REVERT: F 402 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8493 (tmm) REVERT: F 410 MET cc_start: 0.9107 (mtm) cc_final: 0.8865 (ptp) REVERT: H 91 GLN cc_start: 0.9427 (tt0) cc_final: 0.9173 (tp-100) REVERT: H 99 ASP cc_start: 0.9254 (t0) cc_final: 0.8965 (p0) REVERT: H 109 PHE cc_start: 0.8643 (m-80) cc_final: 0.7680 (m-80) REVERT: H 190 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8836 (tm-30) REVERT: H 206 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.9219 (mm-40) REVERT: I 132 MET cc_start: 0.8698 (mtt) cc_final: 0.8341 (mtt) REVERT: I 198 SER cc_start: 0.9747 (m) cc_final: 0.9483 (p) REVERT: J 72 MET cc_start: 0.9359 (tmm) cc_final: 0.8884 (tmm) REVERT: J 76 MET cc_start: 0.9380 (mmm) cc_final: 0.8958 (mmm) REVERT: J 97 GLU cc_start: 0.9445 (tp30) cc_final: 0.8959 (tp30) REVERT: J 207 MET cc_start: 0.9144 (tpp) cc_final: 0.8913 (tpp) REVERT: K 72 MET cc_start: 0.9477 (ppp) cc_final: 0.9101 (ppp) REVERT: K 97 GLU cc_start: 0.9355 (tp30) cc_final: 0.9061 (tm-30) REVERT: K 115 LEU cc_start: 0.9832 (OUTLIER) cc_final: 0.9579 (pp) REVERT: K 197 GLU cc_start: 0.8908 (mp0) cc_final: 0.8696 (mp0) REVERT: K 208 MET cc_start: 0.9305 (mmt) cc_final: 0.8984 (mmm) REVERT: L 14 GLU cc_start: 0.9255 (pm20) cc_final: 0.8797 (tp30) REVERT: L 46 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.8874 (p0) REVERT: L 47 GLU cc_start: 0.9533 (mp0) cc_final: 0.9268 (mp0) REVERT: L 73 MET cc_start: 0.8539 (mtm) cc_final: 0.8068 (mtp) REVERT: L 94 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8757 (ttmt) REVERT: M 105 ASP cc_start: 0.8344 (t0) cc_final: 0.7986 (t70) REVERT: N 84 MET cc_start: 0.9162 (mtp) cc_final: 0.8843 (ttm) REVERT: N 102 MET cc_start: 0.9492 (mtt) cc_final: 0.9162 (mmm) REVERT: O 96 LEU cc_start: 0.9780 (tp) cc_final: 0.9494 (pp) REVERT: Q 35 THR cc_start: 0.9335 (m) cc_final: 0.9111 (p) REVERT: Q 98 ILE cc_start: 0.9549 (pt) cc_final: 0.9331 (mm) REVERT: Q 161 MET cc_start: 0.9148 (ppp) cc_final: 0.8938 (ppp) REVERT: Q 194 ASP cc_start: 0.9201 (p0) cc_final: 0.8925 (p0) REVERT: R 155 MET cc_start: 0.9501 (OUTLIER) cc_final: 0.8882 (mpp) REVERT: R 161 MET cc_start: 0.9283 (tmm) cc_final: 0.9071 (ppp) REVERT: R 181 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9097 (pp) REVERT: S 229 MET cc_start: 0.9438 (mtp) cc_final: 0.9170 (mmm) REVERT: a 594 LYS cc_start: 0.3772 (OUTLIER) cc_final: 0.3561 (pptt) REVERT: a 616 MET cc_start: 0.9082 (ttp) cc_final: 0.8700 (ptp) REVERT: a 645 MET cc_start: 0.7541 (ttt) cc_final: 0.6921 (ptt) REVERT: a 651 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6916 (mtt) REVERT: a 759 MET cc_start: 0.8392 (mmm) cc_final: 0.7990 (tpp) REVERT: b 107 MET cc_start: 0.7801 (mtm) cc_final: 0.7450 (mmm) REVERT: c 429 MET cc_start: 0.9151 (ttt) cc_final: 0.8322 (tmm) REVERT: d 78 MET cc_start: 0.9197 (tmm) cc_final: 0.8801 (tmm) REVERT: d 118 HIS cc_start: 0.9379 (m-70) cc_final: 0.8785 (m170) REVERT: d 119 GLN cc_start: 0.9371 (tt0) cc_final: 0.8928 (tm-30) REVERT: d 293 ARG cc_start: 0.9203 (mmt180) cc_final: 0.8968 (mmm160) REVERT: d 348 ILE cc_start: 0.8578 (mm) cc_final: 0.8343 (mm) REVERT: e 37 ILE cc_start: 0.6741 (mt) cc_final: 0.6412 (tt) REVERT: g 23 MET cc_start: 0.5027 (ttt) cc_final: 0.3965 (ttm) REVERT: g 44 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6624 (tmm) REVERT: g 101 LEU cc_start: 0.9020 (tp) cc_final: 0.8330 (mt) REVERT: h 78 ASN cc_start: 0.8264 (m-40) cc_final: 0.7811 (p0) REVERT: h 104 LEU cc_start: 0.9030 (mt) cc_final: 0.8594 (mt) REVERT: h 131 MET cc_start: 0.8342 (ppp) cc_final: 0.7344 (ppp) REVERT: j 34 THR cc_start: 0.8377 (p) cc_final: 0.8070 (p) REVERT: j 47 MET cc_start: 0.8874 (ptm) cc_final: 0.7954 (ppp) REVERT: k 47 MET cc_start: 0.6111 (ptm) cc_final: 0.5862 (ptm) REVERT: k 131 MET cc_start: 0.7565 (tmm) cc_final: 0.6986 (ppp) REVERT: l 47 MET cc_start: 0.9402 (ttm) cc_final: 0.8874 (ppp) REVERT: l 53 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8202 (ttt) REVERT: l 68 TYR cc_start: 0.8984 (m-10) cc_final: 0.8668 (m-10) REVERT: l 115 ASP cc_start: 0.7649 (t0) cc_final: 0.7131 (m-30) REVERT: m 23 MET cc_start: 0.8394 (tpp) cc_final: 0.8049 (tpp) REVERT: m 53 MET cc_start: 0.8906 (ppp) cc_final: 0.8284 (ppp) REVERT: m 139 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: n 13 PHE cc_start: 0.9089 (t80) cc_final: 0.8591 (t80) REVERT: n 14 PHE cc_start: 0.8656 (m-80) cc_final: 0.8140 (m-80) REVERT: n 17 MET cc_start: 0.9364 (ptt) cc_final: 0.8889 (ptt) REVERT: n 47 MET cc_start: 0.9336 (pmm) cc_final: 0.8927 (pmm) REVERT: n 104 LEU cc_start: 0.9506 (pp) cc_final: 0.9099 (mt) REVERT: n 123 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7732 (mt0) REVERT: n 131 MET cc_start: 0.8816 (tmm) cc_final: 0.8518 (ptm) REVERT: o 44 MET cc_start: 0.9534 (mmm) cc_final: 0.9315 (mmm) REVERT: o 110 ILE cc_start: 0.8858 (mm) cc_final: 0.8607 (pt) REVERT: o 144 TYR cc_start: 0.8876 (m-10) cc_final: 0.8398 (m-80) REVERT: p 328 ILE cc_start: 0.9554 (mm) cc_final: 0.9354 (tp) outliers start: 149 outliers final: 112 residues processed: 895 average time/residue: 0.5372 time to fit residues: 836.0329 Evaluate side-chains 897 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 768 time to evaluate : 5.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 417 THR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 594 LYS Chi-restraints excluded: chain a residue 651 MET Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 751 GLN Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain c residue 428 PHE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain d residue 275 LYS Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 60 VAL Chi-restraints excluded: chain l residue 123 GLN Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 493 optimal weight: 0.8980 chunk 794 optimal weight: 0.8980 chunk 485 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 552 optimal weight: 0.9980 chunk 833 optimal weight: 40.0000 chunk 767 optimal weight: 30.0000 chunk 664 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 512 optimal weight: 2.9990 chunk 407 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 225 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 171 GLN d 243 HIS i 123 GLN l 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 63395 Z= 0.195 Angle : 0.739 15.560 85997 Z= 0.356 Chirality : 0.045 0.454 10036 Planarity : 0.004 0.063 11103 Dihedral : 4.541 130.956 9058 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.38 % Favored : 96.61 % Rotamer: Outliers : 1.69 % Allowed : 17.91 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 8372 helix: 1.46 (0.07), residues: 4958 sheet: 0.08 (0.21), residues: 650 loop : -0.39 (0.12), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 567 HIS 0.006 0.001 HIS Q 118 PHE 0.053 0.002 PHE b 138 TYR 0.054 0.001 TYR m 68 ARG 0.014 0.000 ARG h 119 ********************** 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 948 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 845 time to evaluate : 5.396 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: A 61 MET cc_start: 0.9174 (mtp) cc_final: 0.8914 (tpp) REVERT: A 99 PHE cc_start: 0.8873 (m-80) cc_final: 0.8489 (m-10) REVERT: A 116 ILE cc_start: 0.9502 (pt) cc_final: 0.9221 (mm) REVERT: A 205 MET cc_start: 0.8708 (pmm) cc_final: 0.8397 (pmm) REVERT: A 263 LEU cc_start: 0.9709 (tp) cc_final: 0.9395 (pp) REVERT: A 347 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8007 (mtp) REVERT: A 371 ASP cc_start: 0.8998 (t0) cc_final: 0.8751 (t0) REVERT: A 540 MET cc_start: 0.9428 (ptm) cc_final: 0.9181 (ptp) REVERT: A 574 MET cc_start: 0.8885 (ptp) cc_final: 0.8055 (mtt) REVERT: A 584 MET cc_start: 0.8949 (ptp) cc_final: 0.8522 (ptp) REVERT: A 608 MET cc_start: 0.9052 (ppp) cc_final: 0.8810 (ppp) REVERT: B 34 MET cc_start: 0.9450 (mmm) cc_final: 0.9040 (mmm) REVERT: B 39 MET cc_start: 0.9292 (tpp) cc_final: 0.8991 (tpp) REVERT: B 95 MET cc_start: 0.8869 (tpp) cc_final: 0.8567 (tmm) REVERT: B 306 MET cc_start: 0.9268 (tpp) cc_final: 0.8913 (tpp) REVERT: B 318 MET cc_start: 0.9456 (mtp) cc_final: 0.8885 (mtp) REVERT: B 340 MET cc_start: 0.9376 (tpp) cc_final: 0.9122 (tpp) REVERT: B 346 MET cc_start: 0.9236 (ppp) cc_final: 0.8786 (tmm) REVERT: B 356 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: B 387 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 458 MET cc_start: 0.8947 (mtp) cc_final: 0.8613 (mmm) REVERT: B 465 TYR cc_start: 0.9095 (m-80) cc_final: 0.8732 (m-80) REVERT: B 480 LYS cc_start: 0.9401 (pttt) cc_final: 0.9090 (pttm) REVERT: B 540 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8437 (mtp) REVERT: C 61 MET cc_start: 0.8794 (tpp) cc_final: 0.8517 (mmm) REVERT: C 65 GLN cc_start: 0.8271 (tp40) cc_final: 0.7861 (tp-100) REVERT: C 318 MET cc_start: 0.9631 (mmm) cc_final: 0.9297 (mmm) REVERT: C 324 GLU cc_start: 0.9507 (tt0) cc_final: 0.8955 (tm-30) REVERT: C 436 ASP cc_start: 0.8610 (t70) cc_final: 0.8394 (t0) REVERT: C 540 MET cc_start: 0.9120 (ptp) cc_final: 0.8498 (ptp) REVERT: C 544 MET cc_start: 0.9079 (mtt) cc_final: 0.8443 (mtm) REVERT: C 550 MET cc_start: 0.9326 (mtm) cc_final: 0.8784 (mtp) REVERT: C 610 ASN cc_start: 0.9558 (m-40) cc_final: 0.8885 (p0) REVERT: D 97 GLN cc_start: 0.9234 (tt0) cc_final: 0.8678 (tm-30) REVERT: D 123 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8607 (p) REVERT: D 300 MET cc_start: 0.9513 (tpp) cc_final: 0.8982 (mmp) REVERT: D 302 SER cc_start: 0.9649 (m) cc_final: 0.9370 (t) REVERT: D 309 GLU cc_start: 0.9223 (tp30) cc_final: 0.8849 (tm-30) REVERT: D 314 ARG cc_start: 0.9059 (ttm110) cc_final: 0.8576 (ttm110) REVERT: D 327 MET cc_start: 0.9430 (ttp) cc_final: 0.9108 (mtp) REVERT: D 353 ILE cc_start: 0.9553 (mt) cc_final: 0.9297 (mm) REVERT: D 410 MET cc_start: 0.9079 (mtm) cc_final: 0.8127 (ptp) REVERT: E 74 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9308 (pp) REVERT: E 127 MET cc_start: 0.9098 (mtp) cc_final: 0.8536 (mtp) REVERT: E 180 MET cc_start: 0.8623 (tpt) cc_final: 0.8217 (tpp) REVERT: E 327 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8413 (mtm) REVERT: E 356 MET cc_start: 0.8620 (ttp) cc_final: 0.8338 (ttm) REVERT: E 360 ASP cc_start: 0.8868 (t0) cc_final: 0.8351 (t0) REVERT: E 410 MET cc_start: 0.9062 (mmm) cc_final: 0.8448 (mtp) REVERT: F 87 LEU cc_start: 0.9600 (tp) cc_final: 0.9338 (tt) REVERT: F 127 MET cc_start: 0.9031 (mtp) cc_final: 0.8701 (mtp) REVERT: F 205 GLN cc_start: 0.9451 (tt0) cc_final: 0.9005 (tt0) REVERT: F 254 MET cc_start: 0.8825 (mmm) cc_final: 0.8166 (tmm) REVERT: F 268 THR cc_start: 0.9543 (p) cc_final: 0.9256 (t) REVERT: F 305 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8926 (mt-10) REVERT: F 402 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8431 (tmm) REVERT: F 410 MET cc_start: 0.9004 (mtm) cc_final: 0.8732 (ptm) REVERT: F 430 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9110 (mmmm) REVERT: H 91 GLN cc_start: 0.9487 (tt0) cc_final: 0.9242 (tp-100) REVERT: H 99 ASP cc_start: 0.9281 (t0) cc_final: 0.8949 (p0) REVERT: H 109 PHE cc_start: 0.8512 (m-80) cc_final: 0.7617 (m-80) REVERT: H 190 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8853 (tm-30) REVERT: I 129 GLU cc_start: 0.8331 (tt0) cc_final: 0.7651 (tt0) REVERT: I 198 SER cc_start: 0.9734 (m) cc_final: 0.9458 (p) REVERT: J 72 MET cc_start: 0.9331 (tmm) cc_final: 0.8826 (tmm) REVERT: J 76 MET cc_start: 0.9361 (mmm) cc_final: 0.8931 (mmm) REVERT: J 97 GLU cc_start: 0.9419 (tp30) cc_final: 0.8927 (tp30) REVERT: J 207 MET cc_start: 0.9126 (tpp) cc_final: 0.8890 (tpp) REVERT: K 72 MET cc_start: 0.9469 (ppp) cc_final: 0.9213 (ppp) REVERT: K 97 GLU cc_start: 0.9348 (tp30) cc_final: 0.8884 (tm-30) REVERT: K 115 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9557 (pp) REVERT: K 197 GLU cc_start: 0.8846 (mp0) cc_final: 0.8621 (mp0) REVERT: K 208 MET cc_start: 0.9236 (mmt) cc_final: 0.8989 (mmm) REVERT: L 14 GLU cc_start: 0.9212 (pm20) cc_final: 0.8764 (tp30) REVERT: L 46 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.8925 (p0) REVERT: L 47 GLU cc_start: 0.9541 (mp0) cc_final: 0.9322 (pm20) REVERT: L 73 MET cc_start: 0.8564 (mtm) cc_final: 0.7986 (mtp) REVERT: L 94 LYS cc_start: 0.9037 (ttpt) cc_final: 0.8740 (ttmt) REVERT: M 105 ASP cc_start: 0.8320 (t0) cc_final: 0.7947 (t70) REVERT: N 79 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8800 (ttp-110) REVERT: N 84 MET cc_start: 0.9104 (mtp) cc_final: 0.8810 (ttm) REVERT: N 102 MET cc_start: 0.9451 (mtt) cc_final: 0.9124 (mmm) REVERT: O 84 MET cc_start: 0.9284 (mpp) cc_final: 0.9002 (pmm) REVERT: Q 10 MET cc_start: 0.7196 (mmm) cc_final: 0.6766 (mmm) REVERT: Q 35 THR cc_start: 0.9289 (m) cc_final: 0.9063 (p) REVERT: Q 179 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8971 (t80) REVERT: R 155 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.8882 (mpp) REVERT: R 181 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9070 (pp) REVERT: S 229 MET cc_start: 0.9388 (mtp) cc_final: 0.9154 (mmm) REVERT: a 616 MET cc_start: 0.9032 (ttp) cc_final: 0.8671 (ptp) REVERT: a 641 ILE cc_start: 0.7878 (mm) cc_final: 0.7174 (mp) REVERT: a 645 MET cc_start: 0.7459 (ttt) cc_final: 0.6862 (ptt) REVERT: a 651 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6496 (mtt) REVERT: a 759 MET cc_start: 0.8407 (mmm) cc_final: 0.7996 (tpp) REVERT: b 107 MET cc_start: 0.7865 (mtm) cc_final: 0.7565 (mmm) REVERT: c 429 MET cc_start: 0.9064 (ttt) cc_final: 0.8228 (tmm) REVERT: c 451 ASP cc_start: 0.3488 (t0) cc_final: 0.2812 (p0) REVERT: d 78 MET cc_start: 0.9119 (tmm) cc_final: 0.8678 (tmm) REVERT: d 118 HIS cc_start: 0.9339 (m-70) cc_final: 0.8742 (m170) REVERT: d 119 GLN cc_start: 0.9365 (tt0) cc_final: 0.8925 (tm-30) REVERT: d 138 MET cc_start: 0.8000 (tpt) cc_final: 0.7698 (tpt) REVERT: d 243 HIS cc_start: 0.9334 (m-70) cc_final: 0.9067 (m-70) REVERT: d 264 VAL cc_start: 0.9485 (t) cc_final: 0.9283 (p) REVERT: d 293 ARG cc_start: 0.9198 (mmt180) cc_final: 0.8969 (mmm160) REVERT: d 348 ILE cc_start: 0.8493 (mm) cc_final: 0.8258 (mm) REVERT: e 37 ILE cc_start: 0.6721 (mt) cc_final: 0.6384 (tt) REVERT: g 23 MET cc_start: 0.5213 (ttt) cc_final: 0.4608 (ttm) REVERT: g 82 ASP cc_start: 0.7739 (t0) cc_final: 0.7333 (m-30) REVERT: h 78 ASN cc_start: 0.8207 (m-40) cc_final: 0.7765 (p0) REVERT: h 104 LEU cc_start: 0.9057 (mt) cc_final: 0.8609 (mt) REVERT: h 131 MET cc_start: 0.8272 (ppp) cc_final: 0.7439 (ppp) REVERT: i 53 MET cc_start: 0.8292 (mmt) cc_final: 0.7343 (mtt) REVERT: i 119 ARG cc_start: 0.8873 (mtt90) cc_final: 0.8644 (mpt90) REVERT: i 123 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: j 34 THR cc_start: 0.8323 (p) cc_final: 0.8042 (p) REVERT: j 47 MET cc_start: 0.8771 (ptm) cc_final: 0.8333 (ppp) REVERT: j 108 PHE cc_start: 0.8235 (m-80) cc_final: 0.7857 (t80) REVERT: k 47 MET cc_start: 0.6001 (ptm) cc_final: 0.5752 (ptm) REVERT: k 144 TYR cc_start: 0.8607 (m-80) cc_final: 0.8274 (m-80) REVERT: l 47 MET cc_start: 0.9423 (ttm) cc_final: 0.8885 (ppp) REVERT: l 53 MET cc_start: 0.8656 (mmp) cc_final: 0.8242 (ttt) REVERT: l 68 TYR cc_start: 0.9006 (m-10) cc_final: 0.8700 (m-10) REVERT: l 115 ASP cc_start: 0.7520 (t0) cc_final: 0.6955 (m-30) REVERT: m 37 SER cc_start: 0.8518 (m) cc_final: 0.8185 (p) REVERT: m 53 MET cc_start: 0.8873 (ppp) cc_final: 0.8236 (ppp) REVERT: m 115 ASP cc_start: 0.8732 (m-30) cc_final: 0.8412 (m-30) REVERT: m 131 MET cc_start: 0.9211 (tmm) cc_final: 0.8846 (ppp) REVERT: m 139 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: n 13 PHE cc_start: 0.9073 (t80) cc_final: 0.8564 (t80) REVERT: n 14 PHE cc_start: 0.8649 (m-80) cc_final: 0.8130 (m-80) REVERT: n 17 MET cc_start: 0.9332 (ptt) cc_final: 0.8893 (ptt) REVERT: n 47 MET cc_start: 0.9334 (pmm) cc_final: 0.8904 (pmm) REVERT: n 53 MET cc_start: 0.7438 (mmp) cc_final: 0.5788 (ttp) REVERT: n 123 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7314 (mt0) REVERT: n 139 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9131 (mm-30) REVERT: o 44 MET cc_start: 0.9548 (mmm) cc_final: 0.9280 (mmm) REVERT: o 110 ILE cc_start: 0.8808 (mm) cc_final: 0.8602 (pt) REVERT: o 144 TYR cc_start: 0.8836 (m-10) cc_final: 0.8371 (m-80) outliers start: 103 outliers final: 74 residues processed: 909 average time/residue: 0.5413 time to fit residues: 856.7554 Evaluate side-chains 890 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 801 time to evaluate : 5.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 417 THR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 651 MET Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 275 LYS Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 123 GLN Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 527 optimal weight: 9.9990 chunk 707 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 612 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 184 optimal weight: 0.5980 chunk 665 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 682 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 573 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.094039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.078002 restraints weight = 422049.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079311 restraints weight = 185821.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.080027 restraints weight = 101216.135| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.363 63395 Z= 0.384 Angle : 0.810 59.200 85997 Z= 0.408 Chirality : 0.049 1.079 10036 Planarity : 0.005 0.067 11103 Dihedral : 4.506 130.818 9058 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.37 % Favored : 96.62 % Rotamer: Outliers : 1.64 % Allowed : 18.31 % Favored : 80.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 8372 helix: 1.44 (0.07), residues: 4959 sheet: -0.00 (0.20), residues: 681 loop : -0.38 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.003 TRP A 567 HIS 0.039 0.001 HIS A 468 PHE 0.098 0.002 PHE b 138 TYR 0.064 0.002 TYR o 32 ARG 0.009 0.000 ARG j 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15747.54 seconds wall clock time: 275 minutes 40.04 seconds (16540.04 seconds total)