Starting phenix.real_space_refine on Mon Mar 25 15:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/03_2024/7uzj_26913_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/03_2024/7uzj_26913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/03_2024/7uzj_26913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/03_2024/7uzj_26913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/03_2024/7uzj_26913_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzj_26913/03_2024/7uzj_26913_updated.pdb" } resolution = 3.3 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= 1.169 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 255 5.16 5 C 31415 2.51 5 N 8533 2.21 5 O 9418 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 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 349": "OD1" <-> "OD2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 130": "OD1" <-> "OD2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 562": "OD1" <-> "OD2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 408": "OE1" <-> "OE2" 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 PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 475": "OE1" <-> "OE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 309": "OE1" <-> "OE2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 408": "OE1" <-> "OE2" 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 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 250": "OD1" <-> "OD2" Residue "G GLU 305": "OE1" <-> "OE2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "G TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 365": "OE1" <-> "OE2" Residue "G TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 162": "OD1" <-> "OD2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 176": "OD1" <-> "OD2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 5": "OD1" <-> "OD2" Residue "J PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 226": "OD1" <-> "OD2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 13": "OD1" <-> "OD2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 103": "OD1" <-> "OD2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 72": "OE1" <-> "OE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P GLU 157": "OE1" <-> "OE2" Residue "P PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 300": "OE1" <-> "OE2" Residue "P TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 327": "OD1" <-> "OD2" Residue "P PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 340": "OE1" <-> "OE2" Residue "P TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 399": "OE1" <-> "OE2" Residue "P ASP 402": "OD1" <-> "OD2" Residue "P GLU 429": "OE1" <-> "OE2" Residue "Q TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 77": "OD1" <-> "OD2" 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 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 209": "OE1" <-> "OE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 63": "OE1" <-> "OE2" Residue "T ASP 118": "OD1" <-> "OD2" Residue "T PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 134": "OD1" <-> "OD2" Residue "T TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49624 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4568 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 558} Chain breaks: 2 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4657 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 570} Chain: "C" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4648 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3603 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3632 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 436} Chain breaks: 1 Chain: "F" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3576 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 429} Chain breaks: 1 Chain: "G" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 9, 'TRANS': 348} Chain breaks: 1 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1689 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 1 Chain: "I" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1774 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "J" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1808 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "K" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1774 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 914 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain: "N" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "O" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "P" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3529 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 8, 'TRANS': 421} Chain breaks: 1 Chain: "Q" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2126 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "S" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2147 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain: "T" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1377 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.88, per 1000 atoms: 0.46 Number of scatterers: 49624 At special positions: 0 Unit cell: (200.34, 186.56, 190.8, 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 255 16.00 P 2 15.00 Mg 1 11.99 O 9418 8.00 N 8533 7.00 C 31415 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: 18.93 Conformation dependent library (CDL) restraints added in 9.5 seconds 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 43 sheets defined 52.2% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.78 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 259 through 265 Processing helix chain 'A' and resid 281 through 293 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 320 through 339 removed outlier: 4.347A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.642A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) 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: 4.034A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.775A pdb=" N GLY A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 458 through 468 removed outlier: 4.460A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 removed outlier: 3.612A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 558 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 586 removed outlier: 4.816A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.835A pdb=" N GLN B 261 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 263 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 265 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 266 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.589A pdb=" N VAL B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 320 through 339 removed outlier: 4.940A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.942A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 437 through 442 removed outlier: 4.083A pdb=" N ARG B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.754A pdb=" N LEU B 461 " --> pdb=" O MET B 458 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP B 462 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU B 463 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP B 466 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 496 removed outlier: 4.044A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.695A 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 582 removed outlier: 6.518A pdb=" N GLU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 594 through 613 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 232 through 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 290 removed outlier: 3.936A pdb=" N VAL C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.692A pdb=" N GLU C 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 328 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 331 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 333 " --> pdb=" O GLY C 330 " (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 388 removed outlier: 4.005A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 427 removed outlier: 3.625A pdb=" N GLY C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.165A pdb=" N ARG C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 removed outlier: 4.884A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 496 removed outlier: 4.090A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 558 Processing helix chain 'C' and resid 567 through 586 removed outlier: 6.749A pdb=" N GLU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 613 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 269 through 287 Proline residue: D 275 - end of helix removed outlier: 3.595A pdb=" N ALA D 278 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 283 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 285 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 287 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.592A pdb=" N THR D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 370 Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.759A pdb=" N ARG D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 removed outlier: 4.210A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 446 through 461 removed outlier: 3.567A pdb=" N GLN D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 removed outlier: 3.506A pdb=" N GLN D 482 " --> pdb=" O ASP D 478 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.500A pdb=" N GLU E 249 " --> pdb=" O LYS E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 256 Processing helix chain 'E' and resid 268 through 287 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 300 through 313 removed outlier: 3.588A pdb=" N ALA E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.645A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 removed outlier: 3.557A pdb=" N TYR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 removed outlier: 3.681A pdb=" N ASN E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 4.071A 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: 3.756A pdb=" N GLN E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.465A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.591A pdb=" N THR F 274 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Proline residue: F 275 - end of helix removed outlier: 3.578A pdb=" N ALA F 278 " --> pdb=" O PRO F 275 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU F 279 " --> pdb=" O ARG F 276 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 314 removed outlier: 3.654A pdb=" N ALA F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) 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: 3.685A 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 removed outlier: 3.512A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 401 through 404 removed outlier: 3.633A pdb=" N SER F 404 " --> pdb=" O LEU F 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 404' Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.906A pdb=" N ASN F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 446 through 461 removed outlier: 3.527A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 456 " --> pdb=" O LEU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 486 removed outlier: 3.909A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 removed outlier: 3.957A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 48 through 80 removed outlier: 3.916A pdb=" N GLY G 53 " --> pdb=" O ASP G 49 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 90 removed outlier: 3.906A pdb=" N ASN G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 118 through 157 removed outlier: 4.039A pdb=" N LEU G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 147 " --> pdb=" O TYR G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 191 through 201 removed outlier: 4.669A pdb=" N ASN G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 removed outlier: 4.015A pdb=" N VAL G 234 " --> pdb=" O LYS G 231 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE G 237 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG G 238 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS G 239 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 241 " --> pdb=" O ARG G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 309 removed outlier: 4.164A pdb=" N LYS G 262 " --> pdb=" O MET G 258 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER G 269 " --> pdb=" O MET G 265 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS G 273 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Proline residue: G 278 - end of helix removed outlier: 3.735A pdb=" N SER G 288 " --> pdb=" O LYS G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 342 removed outlier: 6.075A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 76 removed outlier: 4.670A pdb=" N ARG H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 83 No H-bonds generated for 'chain 'H' and resid 80 through 83' Processing helix chain 'H' and resid 129 through 174 removed outlier: 3.526A pdb=" N LYS H 133 " --> pdb=" O GLN H 130 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 134 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR H 138 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 146 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 148 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA H 149 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR H 153 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 156 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP H 159 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE H 164 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS H 174 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 222 removed outlier: 3.647A pdb=" N ASP H 192 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG H 201 " --> pdb=" O GLU H 197 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 107 removed outlier: 4.375A pdb=" N LYS I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 127 removed outlier: 3.794A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 121 " --> pdb=" O ASP I 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN I 126 " --> pdb=" O GLN I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 159 Proline residue: I 142 - end of helix removed outlier: 3.549A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I 148 " --> pdb=" O LYS I 145 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.615A pdb=" N ILE I 157 " --> pdb=" O MET I 154 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR I 159 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 removed outlier: 3.969A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 216 removed outlier: 3.595A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 107 removed outlier: 3.701A pdb=" N ILE J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN J 66 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN J 71 " --> pdb=" O GLN J 67 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS J 104 " --> pdb=" O GLN J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 127 removed outlier: 3.554A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 159 Proline residue: J 142 - end of helix removed outlier: 3.925A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 148 " --> pdb=" O LYS J 145 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.629A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 removed outlier: 3.604A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 10 through 107 removed outlier: 3.574A pdb=" N PHE K 18 " --> pdb=" O MET K 15 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU K 20 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA K 34 " --> pdb=" O ASP K 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU K 36 " --> pdb=" O LYS K 33 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS K 42 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL K 46 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN K 47 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU K 58 " --> pdb=" O GLU K 55 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU K 61 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN K 66 " --> pdb=" O GLN K 63 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET K 76 " --> pdb=" O SER K 73 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS K 82 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA K 98 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 127 removed outlier: 3.692A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU K 121 " --> pdb=" O ASP K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 159 Proline residue: K 142 - end of helix removed outlier: 4.098A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.717A pdb=" N ILE K 157 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 216 removed outlier: 3.712A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'L' and resid 14 through 18 Processing helix chain 'L' and resid 45 through 57 Processing helix chain 'L' and resid 68 through 71 No H-bonds generated for 'chain 'L' and resid 68 through 71' Processing helix chain 'L' and resid 75 through 79 Processing helix chain 'L' and resid 106 through 108 No H-bonds generated for 'chain 'L' and resid 106 through 108' Processing helix chain 'M' and resid 7 through 89 removed outlier: 3.740A pdb=" N LYS M 27 " --> pdb=" O SER M 23 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS M 29 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASN M 30 " --> pdb=" O ARG M 26 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN M 41 " --> pdb=" O LYS M 37 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 103 removed outlier: 3.567A pdb=" N ALA M 101 " --> pdb=" O ASP M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 89 removed outlier: 3.578A pdb=" N VAL N 22 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 33 " --> pdb=" O ASN N 30 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU N 39 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN N 41 " --> pdb=" O GLU N 38 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE N 44 " --> pdb=" O GLN N 41 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU N 49 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU N 52 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU N 63 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY N 64 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER N 65 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL N 73 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU N 74 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE N 88 " --> pdb=" O GLN N 85 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU N 89 " --> pdb=" O ASN N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 104 removed outlier: 3.612A pdb=" N ALA N 101 " --> pdb=" O ASP N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 104 removed outlier: 4.534A pdb=" N LYS O 34 " --> pdb=" O ASN O 30 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN O 35 " --> pdb=" O ARG O 31 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS O 37 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU O 45 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS O 75 " --> pdb=" O SER O 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU O 76 " --> pdb=" O GLU O 72 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN O 78 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN O 91 " --> pdb=" O TYR O 87 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP O 93 " --> pdb=" O GLU O 89 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU O 94 " --> pdb=" O GLN O 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 28 removed outlier: 3.864A pdb=" N GLU P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 38 Processing helix chain 'P' and resid 44 through 55 Processing helix chain 'P' and resid 59 through 82 removed outlier: 7.548A pdb=" N SER P 71 " --> pdb=" O GLN P 67 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN P 72 " --> pdb=" O THR P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 103 Processing helix chain 'P' and resid 105 through 117 Processing helix chain 'P' and resid 123 through 125 No H-bonds generated for 'chain 'P' and resid 123 through 125' Processing helix chain 'P' and resid 127 through 131 Processing helix chain 'P' and resid 135 through 151 Processing helix chain 'P' and resid 158 through 174 removed outlier: 3.521A pdb=" N SER P 174 " --> pdb=" O THR P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 210 removed outlier: 4.370A pdb=" N CYS P 200 " --> pdb=" O GLN P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 220 removed outlier: 3.736A pdb=" N PHE P 216 " --> pdb=" O ASN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 232 removed outlier: 3.572A pdb=" N MET P 228 " --> pdb=" O ASN P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 252 removed outlier: 3.628A pdb=" N PHE P 252 " --> pdb=" O TRP P 248 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 263 removed outlier: 4.259A pdb=" N ARG P 261 " --> pdb=" O CYS P 257 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG P 262 " --> pdb=" O GLU P 258 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR P 263 " --> pdb=" O HIS P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 275 Processing helix chain 'P' and resid 279 through 295 Processing helix chain 'P' and resid 299 through 311 Processing helix chain 'P' and resid 314 through 323 Processing helix chain 'P' and resid 329 through 349 removed outlier: 4.483A pdb=" N ASP P 334 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER P 345 " --> pdb=" O LYS P 341 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP P 348 " --> pdb=" O GLU P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 360 removed outlier: 3.586A pdb=" N SER P 357 " --> pdb=" O GLU P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 371 No H-bonds generated for 'chain 'P' and resid 368 through 371' Processing helix chain 'P' and resid 373 through 400 removed outlier: 7.664A pdb=" N VAL P 381 " --> pdb=" O ARG P 377 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG P 382 " --> pdb=" O GLU P 378 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU P 383 " --> pdb=" O ASN P 379 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN P 384 " --> pdb=" O ALA P 380 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU P 385 " --> pdb=" O VAL P 381 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS P 386 " --> pdb=" O ARG P 382 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN P 387 " --> pdb=" O LEU P 383 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU P 390 " --> pdb=" O LYS P 386 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU P 391 " --> pdb=" O ASN P 387 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 420 Processing helix chain 'P' and resid 422 through 431 removed outlier: 4.110A pdb=" N ARG P 426 " --> pdb=" O PRO P 422 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 442 removed outlier: 3.589A pdb=" N MET P 441 " --> pdb=" O MET P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 446 through 460 Processing helix chain 'Q' and resid 15 through 36 removed outlier: 3.508A pdb=" N THR Q 35 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 55 removed outlier: 4.293A pdb=" N ASP Q 48 " --> pdb=" O LYS Q 44 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TRP Q 55 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 70 Processing helix chain 'Q' and resid 78 through 97 removed outlier: 3.863A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 117 Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 125 through 139 Processing helix chain 'Q' and resid 147 through 166 Processing helix chain 'Q' and resid 173 through 187 removed outlier: 4.364A pdb=" N LYS Q 180 " --> pdb=" O ASN Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 206 Processing helix chain 'Q' and resid 219 through 233 removed outlier: 3.676A pdb=" N TYR Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 251 removed outlier: 3.814A pdb=" N SER Q 251 " --> pdb=" O SER Q 247 " (cutoff:3.500A) Processing helix chain 'Q' and resid 257 through 272 Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 56 removed outlier: 4.055A pdb=" N ASP R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 70 Processing helix chain 'R' and resid 78 through 97 removed outlier: 3.588A pdb=" N LEU R 94 " --> pdb=" O GLU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 116 Processing helix chain 'R' and resid 121 through 123 No H-bonds generated for 'chain 'R' and resid 121 through 123' Processing helix chain 'R' and resid 125 through 141 removed outlier: 3.959A pdb=" N TYR R 139 " --> pdb=" O GLN R 135 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.548A 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 236 Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 240 through 251 removed outlier: 4.122A pdb=" N LEU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 273 Processing helix chain 'S' and resid 15 through 36 Processing helix chain 'S' and resid 43 through 48 Processing helix chain 'S' and resid 50 through 53 No H-bonds generated for 'chain 'S' and resid 50 through 53' Processing helix chain 'S' and resid 62 through 70 Processing helix chain 'S' and resid 78 through 97 removed outlier: 3.544A pdb=" N LEU S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU S 94 " --> pdb=" O GLU S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 116 Processing helix chain 'S' and resid 125 through 140 removed outlier: 3.739A pdb=" N TYR S 139 " --> pdb=" O GLN S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 Processing helix chain 'S' and resid 173 through 187 Processing helix chain 'S' and resid 193 through 206 Processing helix chain 'S' and resid 219 through 234 removed outlier: 3.712A pdb=" N TYR S 232 " --> pdb=" O THR S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 240 through 251 removed outlier: 3.520A pdb=" N SER S 251 " --> pdb=" O SER S 247 " (cutoff:3.500A) Processing helix chain 'S' and resid 257 through 273 Processing helix chain 'T' and resid 64 through 71 removed outlier: 3.617A pdb=" N GLN T 69 " --> pdb=" O MET T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 103 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.527A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.685A 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 98 through 100 removed outlier: 9.028A pdb=" N PHE A 99 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 311 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN A 314 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 276 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER A 403 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N MET A 346 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER A 405 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA A 348 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 407 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 183 through 186 removed outlier: 6.918A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.033A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 219 through 221 removed outlier: 4.343A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 295 through 297 Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.625A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 186 removed outlier: 5.631A pdb=" N GLU B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.579A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.089A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 406 through 410 removed outlier: 3.568A pdb=" N ILE B 248 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 431 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N TRP B 433 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= O, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.643A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'C' and resid 98 through 100 removed outlier: 8.860A pdb=" N PHE C 99 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU C 311 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASN C 314 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY C 276 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 271 " --> pdb=" O HIS C 343 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER C 403 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET C 346 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER C 405 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ALA C 348 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 407 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 183 through 186 removed outlier: 5.392A pdb=" N GLU C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.330A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 219 through 221 removed outlier: 4.322A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (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: 6.520A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.644A 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: 8.436A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE D 351 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 376 through 378 Processing sheet with id= Z, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.801A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.578A 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 130 through 133 removed outlier: 3.900A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N HIS E 292 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE E 351 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 376 through 378 Processing sheet with id= AD, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.789A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AF, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.869A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE F 351 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 376 through 378 Processing sheet with id= AH, first strand: chain 'G' and resid 370 through 375 removed outlier: 3.613A pdb=" N VAL G 370 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU G 3 " --> pdb=" O PRO G 323 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 182 through 190 removed outlier: 6.478A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 92 through 101 Processing sheet with id= AK, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= AL, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AM, first strand: chain 'K' and resid 164 through 167 Processing sheet with id= AN, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.713A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA L 9 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE L 64 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE L 11 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE L 66 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA L 87 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE L 66 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU L 89 " --> pdb=" O ILE L 66 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'T' and resid 151 through 155 removed outlier: 4.405A pdb=" N ILE T 121 " --> pdb=" O PHE T 147 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR T 219 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU T 85 " --> pdb=" O THR T 219 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'T' and resid 164 through 166 Processing sheet with id= AQ, first strand: chain 'T' and resid 190 through 192 2476 hydrogen bonds defined for protein. 6441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.83 Time building geometry restraints manager: 20.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10159 1.32 - 1.45: 10808 1.45 - 1.57: 29071 1.57 - 1.70: 1 1.70 - 1.83: 447 Bond restraints: 50486 Sorted by residual: bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C5 ADP C 701 " pdb=" C6 ADP C 701 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" CZ ARG B 338 " pdb=" NH2 ARG B 338 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.28e+01 bond pdb=" CZ ARG A 338 " pdb=" NH2 ARG A 338 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" CA PRO B 169 " pdb=" C PRO B 169 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.25e+01 ... (remaining 50481 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.63: 750 104.63 - 112.35: 22256 112.35 - 120.08: 24525 120.08 - 127.80: 20293 127.80 - 135.53: 285 Bond angle restraints: 68109 Sorted by residual: angle pdb=" CA ASP L 60 " pdb=" CB ASP L 60 " pdb=" CG ASP L 60 " ideal model delta sigma weight residual 112.60 120.02 -7.42 1.00e+00 1.00e+00 5.51e+01 angle pdb=" CA ASN L 67 " pdb=" CB ASN L 67 " pdb=" CG ASN L 67 " ideal model delta sigma weight residual 112.60 119.18 -6.58 1.00e+00 1.00e+00 4.33e+01 angle pdb=" CA ASP B 466 " pdb=" CB ASP B 466 " pdb=" CG ASP B 466 " ideal model delta sigma weight residual 112.60 119.10 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA ASP C 186 " pdb=" CB ASP C 186 " pdb=" CG ASP C 186 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CA ASP E 359 " pdb=" CB ASP E 359 " pdb=" CG ASP E 359 " ideal model delta sigma weight residual 112.60 118.74 -6.14 1.00e+00 1.00e+00 3.77e+01 ... (remaining 68104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 30567 35.99 - 71.97: 439 71.97 - 107.96: 70 107.96 - 143.94: 1 143.94 - 179.93: 1 Dihedral angle restraints: 31078 sinusoidal: 12891 harmonic: 18187 Sorted by residual: dihedral pdb=" O1B ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PB ADP C 701 " pdb=" PA ADP C 701 " ideal model delta sinusoidal sigma weight residual 300.00 120.07 179.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA LEU H 202 " pdb=" C LEU H 202 " pdb=" N LYS H 203 " pdb=" CA LYS H 203 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLU G 12 " pdb=" C GLU G 12 " pdb=" N LYS G 13 " pdb=" CA LYS G 13 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 31075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5929 0.103 - 0.206: 1499 0.206 - 0.309: 150 0.309 - 0.412: 27 0.412 - 0.515: 4 Chirality restraints: 7609 Sorted by residual: chirality pdb=" CA ASP F 299 " pdb=" N ASP F 299 " pdb=" C ASP F 299 " pdb=" CB ASP F 299 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA ASP E 299 " pdb=" N ASP E 299 " pdb=" C ASP E 299 " pdb=" CB ASP E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA TYR A 40 " pdb=" N TYR A 40 " pdb=" C TYR A 40 " pdb=" CB TYR A 40 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 7606 not shown) Planarity restraints: 8813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP T 218 " 0.171 2.00e-02 2.50e+03 9.39e-02 2.21e+02 pdb=" CG TRP T 218 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP T 218 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP T 218 " -0.104 2.00e-02 2.50e+03 pdb=" NE1 TRP T 218 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TRP T 218 " -0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP T 218 " -0.126 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 218 " 0.091 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 218 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP T 218 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 122 " -0.138 2.00e-02 2.50e+03 7.88e-02 1.55e+02 pdb=" CG TRP R 122 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP R 122 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP R 122 " 0.065 2.00e-02 2.50e+03 pdb=" NE1 TRP R 122 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 TRP R 122 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP R 122 " 0.114 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 122 " -0.093 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 122 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP R 122 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 114 " 0.158 2.00e-02 2.50e+03 8.78e-02 1.54e+02 pdb=" CG TYR O 114 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR O 114 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR O 114 " -0.073 2.00e-02 2.50e+03 pdb=" CE1 TYR O 114 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR O 114 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR O 114 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR O 114 " 0.138 2.00e-02 2.50e+03 ... (remaining 8810 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 18496 2.91 - 3.41: 49610 3.41 - 3.91: 83636 3.91 - 4.40: 93479 4.40 - 4.90: 160533 Nonbonded interactions: 405754 Sorted by model distance: nonbonded pdb=" OG1 THR C 257 " pdb="MG MG C 702 " model vdw 2.417 2.170 nonbonded pdb=" O2B ADP C 701 " pdb="MG MG C 702 " model vdw 2.442 2.170 nonbonded pdb=" OH TYR F 303 " pdb=" OD1 ASP F 330 " model vdw 2.500 2.440 nonbonded pdb=" OH TYR D 303 " pdb=" OD1 ASP D 330 " model vdw 2.513 2.440 nonbonded pdb=" OH TYR E 303 " pdb=" OD1 ASP E 330 " model vdw 2.541 2.440 ... (remaining 405749 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 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) selection = (chain 'C' and (resid 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) } ncs_group { reference = (chain 'D' and (resid 38 through 213 or resid 226 through 506)) selection = (chain 'E' and (resid 38 through 213 or resid 226 through 506)) selection = chain 'F' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 9 through 226) selection = chain 'K' } ncs_group { reference = chain 'M' selection = (chain 'N' and resid 6 through 116) selection = (chain 'O' and resid 6 through 116) } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 13 through 274) selection = (chain 'S' and resid 13 through 274) } 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 individual isotropic 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 12.150 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 127.190 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.142 50486 Z= 0.782 Angle : 1.742 13.209 68109 Z= 1.182 Chirality : 0.088 0.515 7609 Planarity : 0.015 0.189 8813 Dihedral : 13.567 179.929 19334 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.11 % Favored : 96.66 % Rotamer: Outliers : 0.68 % Allowed : 2.98 % Favored : 96.34 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.86 % 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: -0.72 (0.10), residues: 6176 helix: -0.46 (0.08), residues: 3234 sheet: 0.09 (0.19), residues: 660 loop : -0.39 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.171 0.028 TRP T 218 HIS 0.018 0.003 HIS L 33 PHE 0.111 0.012 PHE P 49 TYR 0.158 0.021 TYR O 114 ARG 0.015 0.001 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1396 time to evaluate : 5.498 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: A 219 GLU cc_start: 0.7730 (tt0) cc_final: 0.7517 (tt0) REVERT: A 359 ARG cc_start: 0.9120 (ttp-170) cc_final: 0.8460 (ttp-170) REVERT: A 384 SER cc_start: 0.8954 (t) cc_final: 0.8662 (p) REVERT: A 467 LYS cc_start: 0.8138 (tttt) cc_final: 0.7840 (tppp) REVERT: B 167 MET cc_start: 0.9319 (mtm) cc_final: 0.9111 (mtp) REVERT: B 197 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8112 (tm-30) REVERT: B 443 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8551 (mmtm) REVERT: B 550 MET cc_start: 0.7769 (mmm) cc_final: 0.7175 (mtt) REVERT: B 574 MET cc_start: 0.7816 (mtp) cc_final: 0.7609 (mtt) REVERT: B 604 LEU cc_start: 0.8078 (mp) cc_final: 0.7838 (mp) REVERT: B 605 LEU cc_start: 0.8467 (tp) cc_final: 0.7837 (tp) REVERT: B 609 GLN cc_start: 0.8582 (mt0) cc_final: 0.8016 (mt0) REVERT: C 61 MET cc_start: 0.8676 (mtt) cc_final: 0.8274 (mtm) REVERT: C 95 MET cc_start: 0.9489 (mmp) cc_final: 0.9207 (mmp) REVERT: C 468 HIS cc_start: 0.8833 (m-70) cc_final: 0.8386 (m170) REVERT: C 471 GLU cc_start: 0.7805 (pm20) cc_final: 0.7536 (pm20) REVERT: C 485 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7300 (mt-10) REVERT: C 550 MET cc_start: 0.7319 (mmm) cc_final: 0.6908 (mtt) REVERT: C 584 MET cc_start: 0.8920 (mtm) cc_final: 0.8539 (mtp) REVERT: C 598 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7282 (mtmm) REVERT: C 607 ASP cc_start: 0.6734 (m-30) cc_final: 0.6327 (m-30) REVERT: D 106 ASP cc_start: 0.8861 (p0) cc_final: 0.8600 (p0) REVERT: D 251 ASN cc_start: 0.7699 (t0) cc_final: 0.7221 (t0) REVERT: D 345 ASN cc_start: 0.8364 (t0) cc_final: 0.7944 (t0) REVERT: E 127 MET cc_start: 0.8978 (mtp) cc_final: 0.8700 (mtt) REVERT: E 410 MET cc_start: 0.9268 (mtm) cc_final: 0.9058 (mtm) REVERT: F 249 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7731 (mt-10) REVERT: F 365 ILE cc_start: 0.9341 (mt) cc_final: 0.9016 (mt) REVERT: F 369 THR cc_start: 0.9515 (m) cc_final: 0.9215 (m) REVERT: F 387 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8298 (mp10) REVERT: F 485 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7747 (mtt90) REVERT: F 491 MET cc_start: 0.8699 (mtp) cc_final: 0.8467 (mtp) REVERT: H 27 GLN cc_start: 0.7660 (mt0) cc_final: 0.6865 (mt0) REVERT: I 89 ASP cc_start: 0.7531 (m-30) cc_final: 0.7307 (m-30) REVERT: I 93 ASP cc_start: 0.7924 (m-30) cc_final: 0.7695 (m-30) REVERT: I 108 ASP cc_start: 0.7821 (t0) cc_final: 0.7293 (t0) REVERT: I 125 TYR cc_start: 0.9339 (m-10) cc_final: 0.9086 (m-10) REVERT: I 132 MET cc_start: 0.8893 (mtm) cc_final: 0.8535 (mtm) REVERT: I 154 MET cc_start: 0.8775 (mtm) cc_final: 0.8545 (mtm) REVERT: J 19 ILE cc_start: 0.9548 (mt) cc_final: 0.9044 (mm) REVERT: J 24 ASN cc_start: 0.9592 (m-40) cc_final: 0.8657 (m110) REVERT: J 25 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8499 (tm-30) REVERT: J 29 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7761 (mm-30) REVERT: J 54 MET cc_start: 0.8662 (ttm) cc_final: 0.8336 (ttp) REVERT: J 57 TYR cc_start: 0.8146 (m-80) cc_final: 0.7742 (m-80) REVERT: J 97 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7696 (mm-30) REVERT: J 141 PHE cc_start: 0.8657 (t80) cc_final: 0.8307 (t80) REVERT: K 18 PHE cc_start: 0.9315 (t80) cc_final: 0.8872 (t80) REVERT: K 58 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8230 (mt-10) REVERT: K 69 LYS cc_start: 0.7370 (mttt) cc_final: 0.7084 (mtmt) REVERT: L 112 MET cc_start: 0.6076 (ttm) cc_final: 0.5489 (mpp) REVERT: O 98 ASN cc_start: 0.8313 (m-40) cc_final: 0.8036 (m-40) REVERT: O 102 PHE cc_start: 0.7952 (m-80) cc_final: 0.7282 (m-10) REVERT: O 104 CYS cc_start: 0.8507 (m) cc_final: 0.8097 (m) REVERT: O 105 ASP cc_start: 0.8078 (t0) cc_final: 0.7840 (t70) REVERT: P 156 MET cc_start: 0.0091 (mtp) cc_final: -0.2121 (mmt) REVERT: P 391 LEU cc_start: 0.9341 (mt) cc_final: 0.9041 (mt) REVERT: P 434 LYS cc_start: 0.9352 (pttp) cc_final: 0.9075 (mtpt) REVERT: P 451 ASN cc_start: 0.9181 (m-40) cc_final: 0.8590 (t0) REVERT: Q 98 ILE cc_start: 0.7977 (mt) cc_final: 0.7763 (mt) REVERT: Q 101 PHE cc_start: 0.8670 (m-80) cc_final: 0.8445 (m-10) REVERT: Q 103 MET cc_start: 0.7713 (mtp) cc_final: 0.7471 (ttm) REVERT: Q 107 LEU cc_start: 0.8720 (mt) cc_final: 0.8290 (mt) REVERT: Q 188 MET cc_start: 0.7145 (ttm) cc_final: 0.6802 (ttm) REVERT: Q 229 MET cc_start: 0.8946 (tpp) cc_final: 0.7983 (mmt) REVERT: R 96 SER cc_start: 0.9039 (m) cc_final: 0.8774 (p) REVERT: R 125 ASP cc_start: 0.8290 (m-30) cc_final: 0.8074 (t70) REVERT: R 168 ILE cc_start: 0.8752 (mm) cc_final: 0.8534 (pt) REVERT: R 205 LYS cc_start: 0.8469 (tptt) cc_final: 0.7918 (mmmt) REVERT: R 213 PHE cc_start: 0.8533 (m-80) cc_final: 0.8235 (m-10) REVERT: R 234 MET cc_start: 0.8486 (ttm) cc_final: 0.7942 (mmm) REVERT: S 60 TYR cc_start: 0.4011 (p90) cc_final: 0.3667 (p90) REVERT: S 129 LYS cc_start: 0.8676 (mttp) cc_final: 0.8427 (ttmm) REVERT: S 188 MET cc_start: 0.7253 (tpp) cc_final: 0.6818 (ttm) REVERT: S 197 TYR cc_start: 0.7098 (m-80) cc_final: 0.6892 (t80) REVERT: S 229 MET cc_start: 0.8143 (tpp) cc_final: 0.7736 (mmm) REVERT: S 255 LEU cc_start: 0.8418 (tp) cc_final: 0.8149 (tp) REVERT: T 90 LEU cc_start: 0.9013 (tp) cc_final: 0.8604 (mt) REVERT: T 117 MET cc_start: 0.8710 (mmt) cc_final: 0.8297 (mmt) REVERT: T 118 ASP cc_start: 0.8274 (m-30) cc_final: 0.8016 (m-30) outliers start: 37 outliers final: 8 residues processed: 1417 average time/residue: 0.6767 time to fit residues: 1506.2442 Evaluate side-chains 898 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 889 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain P residue 447 GLN Chi-restraints excluded: chain T residue 77 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 3.9990 chunk 466 optimal weight: 2.9990 chunk 259 optimal weight: 0.0570 chunk 159 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 482 optimal weight: 50.0000 chunk 186 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 chunk 359 optimal weight: 6.9990 chunk 559 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 468 HIS ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN B 213 GLN B 610 ASN C 430 GLN C 468 HIS D 38 ASN D 482 GLN F 54 ASN G 286 ASN I 139 GLN J 96 ASN K 49 GLN L 96 HIS N 66 HIS N 85 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN P 457 GLN Q 198 HIS ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 274 ASN S 117 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 50486 Z= 0.202 Angle : 0.631 10.502 68109 Z= 0.336 Chirality : 0.043 0.181 7609 Planarity : 0.005 0.189 8813 Dihedral : 6.210 169.234 6820 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.32 % Favored : 97.67 % Rotamer: Outliers : 2.03 % Allowed : 8.32 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.10), residues: 6176 helix: 0.87 (0.09), residues: 3232 sheet: 0.11 (0.18), residues: 729 loop : 0.01 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 567 HIS 0.014 0.001 HIS A 573 PHE 0.027 0.002 PHE P 49 TYR 0.029 0.002 TYR G 253 ARG 0.008 0.001 ARG R 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 929 time to evaluate : 6.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9247 (p) cc_final: 0.9047 (m) REVERT: A 268 ASN cc_start: 0.7384 (m-40) cc_final: 0.7176 (m-40) REVERT: A 384 SER cc_start: 0.8884 (t) cc_final: 0.8569 (p) REVERT: A 501 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8032 (tt) REVERT: A 530 ARG cc_start: 0.6347 (ttm-80) cc_final: 0.6073 (ttm-80) REVERT: A 578 LEU cc_start: 0.8319 (mt) cc_final: 0.7797 (pp) REVERT: B 201 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6416 (mp0) REVERT: B 213 GLN cc_start: 0.8498 (mt0) cc_final: 0.8283 (mt0) REVERT: B 443 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8668 (mmmm) REVERT: B 471 GLU cc_start: 0.7826 (pm20) cc_final: 0.7539 (pm20) REVERT: B 550 MET cc_start: 0.7721 (mmm) cc_final: 0.7422 (mtt) REVERT: B 603 GLN cc_start: 0.7976 (tp40) cc_final: 0.7729 (tp40) REVERT: C 61 MET cc_start: 0.8609 (mtt) cc_final: 0.8315 (mtm) REVERT: C 95 MET cc_start: 0.9475 (mmp) cc_final: 0.9241 (mmp) REVERT: C 364 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8431 (mmt180) REVERT: C 438 LYS cc_start: 0.8396 (mttt) cc_final: 0.8119 (mmtp) REVERT: C 485 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7284 (mt-10) REVERT: C 550 MET cc_start: 0.7057 (mmm) cc_final: 0.6659 (mtt) REVERT: C 584 MET cc_start: 0.8816 (mtm) cc_final: 0.8331 (mtp) REVERT: C 607 ASP cc_start: 0.6269 (m-30) cc_final: 0.6051 (m-30) REVERT: C 610 ASN cc_start: 0.7210 (m-40) cc_final: 0.6820 (m-40) REVERT: D 251 ASN cc_start: 0.7610 (t0) cc_final: 0.7126 (t0) REVERT: D 345 ASN cc_start: 0.8417 (t0) cc_final: 0.7920 (t0) REVERT: F 369 THR cc_start: 0.9495 (m) cc_final: 0.9207 (m) REVERT: G 377 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7642 (t0) REVERT: I 70 ILE cc_start: 0.7920 (mp) cc_final: 0.7676 (mp) REVERT: I 76 MET cc_start: 0.8285 (mmm) cc_final: 0.8048 (mmm) REVERT: J 24 ASN cc_start: 0.9242 (m-40) cc_final: 0.8802 (m110) REVERT: J 57 TYR cc_start: 0.7997 (m-80) cc_final: 0.7526 (m-80) REVERT: J 72 MET cc_start: 0.7955 (mmp) cc_final: 0.7592 (tpp) REVERT: J 75 LEU cc_start: 0.8555 (mm) cc_final: 0.7888 (pp) REVERT: J 141 PHE cc_start: 0.8734 (t80) cc_final: 0.8464 (t80) REVERT: J 172 TYR cc_start: 0.8772 (m-80) cc_final: 0.8286 (m-80) REVERT: K 15 MET cc_start: 0.8180 (mtt) cc_final: 0.7771 (mmm) REVERT: K 18 PHE cc_start: 0.9329 (t80) cc_final: 0.8920 (t80) REVERT: K 52 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8814 (ptpp) REVERT: K 58 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8340 (mt-10) REVERT: L 112 MET cc_start: 0.5961 (ttm) cc_final: 0.5495 (pmm) REVERT: N 75 LYS cc_start: 0.8833 (tmmt) cc_final: 0.8441 (tmmt) REVERT: O 98 ASN cc_start: 0.7985 (m-40) cc_final: 0.7775 (m-40) REVERT: O 102 PHE cc_start: 0.7666 (m-80) cc_final: 0.6953 (m-10) REVERT: O 104 CYS cc_start: 0.8229 (m) cc_final: 0.7893 (m) REVERT: P 156 MET cc_start: -0.0602 (mtp) cc_final: -0.2189 (mmt) REVERT: P 309 MET cc_start: 0.7579 (mtm) cc_final: 0.6582 (mpp) REVERT: P 391 LEU cc_start: 0.9300 (mt) cc_final: 0.8911 (mt) REVERT: P 451 ASN cc_start: 0.9232 (m-40) cc_final: 0.8839 (t0) REVERT: Q 34 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8199 (tm-30) REVERT: Q 107 LEU cc_start: 0.8711 (mt) cc_final: 0.8469 (mt) REVERT: Q 181 LEU cc_start: 0.8478 (mm) cc_final: 0.8128 (tp) REVERT: Q 186 LEU cc_start: 0.8149 (tt) cc_final: 0.7925 (tt) REVERT: Q 188 MET cc_start: 0.7093 (ttm) cc_final: 0.6526 (ttm) REVERT: R 96 SER cc_start: 0.8930 (m) cc_final: 0.8695 (p) REVERT: R 109 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7613 (tm-30) REVERT: R 205 LYS cc_start: 0.8435 (tptt) cc_final: 0.7922 (mmmt) REVERT: R 256 THR cc_start: 0.8696 (p) cc_final: 0.8407 (t) REVERT: S 51 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7079 (p0) REVERT: S 103 MET cc_start: 0.6686 (mtp) cc_final: 0.6430 (ttm) REVERT: S 188 MET cc_start: 0.7198 (tpp) cc_final: 0.6691 (ttm) REVERT: S 232 TYR cc_start: 0.7489 (t80) cc_final: 0.6407 (t80) outliers start: 110 outliers final: 55 residues processed: 985 average time/residue: 0.6364 time to fit residues: 1011.4365 Evaluate side-chains 853 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 795 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 560 optimal weight: 0.8980 chunk 605 optimal weight: 0.9990 chunk 499 optimal weight: 7.9990 chunk 555 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 449 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 468 HIS ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS B 610 ASN C 397 ASN F 226 ASN F 256 ASN F 345 ASN F 358 ASN J 96 ASN L 67 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 GLN S 59 ASN T 135 HIS T 213 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 50486 Z= 0.367 Angle : 0.634 10.318 68109 Z= 0.331 Chirality : 0.045 0.327 7609 Planarity : 0.005 0.055 8813 Dihedral : 5.660 148.230 6803 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.10 % Allowed : 10.03 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.54 (0.11), residues: 6176 helix: 1.00 (0.09), residues: 3238 sheet: 0.00 (0.20), residues: 676 loop : -0.34 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 197 HIS 0.021 0.001 HIS Q 198 PHE 0.026 0.002 PHE B 612 TYR 0.031 0.002 TYR G 75 ARG 0.007 0.001 ARG C 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 814 time to evaluate : 5.854 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: A 234 LEU cc_start: 0.8762 (mp) cc_final: 0.8521 (mt) REVERT: A 384 SER cc_start: 0.9053 (t) cc_final: 0.8704 (p) REVERT: A 501 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8119 (tt) REVERT: A 523 ASN cc_start: 0.7096 (t0) cc_final: 0.6720 (t0) REVERT: A 530 ARG cc_start: 0.6576 (ttm-80) cc_final: 0.6273 (ttm-80) REVERT: B 197 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 443 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8875 (mmmm) REVERT: B 471 GLU cc_start: 0.7810 (pm20) cc_final: 0.7395 (pm20) REVERT: B 486 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 530 ARG cc_start: 0.7885 (ptp90) cc_final: 0.7664 (ptm-80) REVERT: B 550 MET cc_start: 0.7678 (mmm) cc_final: 0.7242 (mtt) REVERT: B 552 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7697 (ttt90) REVERT: B 604 LEU cc_start: 0.7798 (tp) cc_final: 0.7234 (tt) REVERT: B 609 GLN cc_start: 0.8989 (mt0) cc_final: 0.8764 (mm-40) REVERT: C 39 MET cc_start: 0.9505 (mmm) cc_final: 0.9172 (mmm) REVERT: C 61 MET cc_start: 0.8696 (mtt) cc_final: 0.8388 (mtm) REVERT: C 103 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8872 (tt0) REVERT: C 364 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8709 (mmt-90) REVERT: C 485 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7375 (mt-10) REVERT: C 550 MET cc_start: 0.7015 (mmm) cc_final: 0.6743 (mtt) REVERT: C 607 ASP cc_start: 0.6424 (m-30) cc_final: 0.6054 (m-30) REVERT: D 251 ASN cc_start: 0.7716 (t0) cc_final: 0.7370 (t0) REVERT: D 345 ASN cc_start: 0.8364 (t0) cc_final: 0.7867 (t0) REVERT: D 386 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7601 (mtp85) REVERT: D 410 MET cc_start: 0.7690 (mmm) cc_final: 0.7277 (mpp) REVERT: E 54 ASN cc_start: 0.8881 (t0) cc_final: 0.8556 (t0) REVERT: F 315 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8006 (mm-30) REVERT: G 180 GLU cc_start: 0.8508 (pm20) cc_final: 0.8194 (pm20) REVERT: I 70 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7636 (mp) REVERT: I 72 MET cc_start: 0.8089 (tpp) cc_final: 0.7873 (mmt) REVERT: I 76 MET cc_start: 0.8346 (mmm) cc_final: 0.8127 (mmm) REVERT: I 226 ASP cc_start: 0.7814 (t0) cc_final: 0.7543 (m-30) REVERT: J 24 ASN cc_start: 0.9196 (m-40) cc_final: 0.8836 (m110) REVERT: J 52 LYS cc_start: 0.8939 (tppp) cc_final: 0.8603 (tppp) REVERT: J 141 PHE cc_start: 0.8809 (t80) cc_final: 0.8468 (t80) REVERT: J 172 TYR cc_start: 0.8839 (m-80) cc_final: 0.8441 (m-80) REVERT: K 15 MET cc_start: 0.8413 (mtt) cc_final: 0.8105 (mmm) REVERT: K 18 PHE cc_start: 0.9364 (t80) cc_final: 0.9101 (t80) REVERT: K 58 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8392 (mt-10) REVERT: L 112 MET cc_start: 0.5692 (ttm) cc_final: 0.5224 (ptm) REVERT: N 30 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (p0) REVERT: N 31 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8379 (mtm-85) REVERT: O 104 CYS cc_start: 0.8339 (m) cc_final: 0.7946 (m) REVERT: P 100 MET cc_start: 0.0180 (ppp) cc_final: -0.0205 (ppp) REVERT: P 156 MET cc_start: -0.1049 (mtp) cc_final: -0.2577 (mmt) REVERT: P 208 MET cc_start: 0.5218 (mmm) cc_final: 0.4974 (mmm) REVERT: P 309 MET cc_start: 0.7649 (mtm) cc_final: 0.6704 (mpp) REVERT: P 391 LEU cc_start: 0.9318 (mt) cc_final: 0.9092 (mt) REVERT: Q 161 MET cc_start: 0.8840 (tmm) cc_final: 0.8598 (tmm) REVERT: Q 178 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8126 (tt) REVERT: Q 181 LEU cc_start: 0.8704 (mm) cc_final: 0.8126 (tp) REVERT: Q 188 MET cc_start: 0.7351 (ttm) cc_final: 0.6843 (ttm) REVERT: R 109 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7495 (tm-30) REVERT: R 146 THR cc_start: 0.8233 (t) cc_final: 0.8002 (t) REVERT: R 161 MET cc_start: 0.8635 (tmm) cc_final: 0.8431 (tpp) REVERT: R 205 LYS cc_start: 0.8593 (tptt) cc_final: 0.8123 (mmmt) REVERT: S 51 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7301 (p0) REVERT: S 103 MET cc_start: 0.6863 (mtp) cc_final: 0.6479 (ttm) REVERT: S 161 MET cc_start: 0.8555 (tpp) cc_final: 0.8072 (mmm) REVERT: S 170 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7425 (mp0) REVERT: S 188 MET cc_start: 0.7266 (tpp) cc_final: 0.6760 (ttm) REVERT: S 197 TYR cc_start: 0.7271 (t80) cc_final: 0.6762 (t80) outliers start: 114 outliers final: 78 residues processed: 878 average time/residue: 0.6392 time to fit residues: 907.1759 Evaluate side-chains 829 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 744 time to evaluate : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 214 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 7.9990 chunk 421 optimal weight: 0.8980 chunk 290 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 376 optimal weight: 7.9990 chunk 562 optimal weight: 2.9990 chunk 595 optimal weight: 20.0000 chunk 293 optimal weight: 2.9990 chunk 533 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 468 HIS ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN F 226 ASN F 358 ASN J 96 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 HIS ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 50486 Z= 0.254 Angle : 0.563 13.318 68109 Z= 0.292 Chirality : 0.042 0.202 7609 Planarity : 0.004 0.048 8813 Dihedral : 5.293 132.518 6801 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 11.21 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.72 (0.11), residues: 6176 helix: 1.21 (0.09), residues: 3235 sheet: 0.04 (0.19), residues: 706 loop : -0.33 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 567 HIS 0.009 0.001 HIS A 444 PHE 0.031 0.001 PHE B 612 TYR 0.031 0.002 TYR M 47 ARG 0.007 0.000 ARG B 553 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 799 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 LEU cc_start: 0.8724 (mp) cc_final: 0.8474 (mt) REVERT: A 384 SER cc_start: 0.9035 (t) cc_final: 0.8681 (p) REVERT: A 523 ASN cc_start: 0.7072 (t0) cc_final: 0.6730 (t0) REVERT: A 530 ARG cc_start: 0.6578 (ttm-80) cc_final: 0.6306 (ttm-80) REVERT: A 578 LEU cc_start: 0.8360 (mt) cc_final: 0.7826 (pp) REVERT: B 197 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 291 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: B 443 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8932 (mmmm) REVERT: B 471 GLU cc_start: 0.7875 (pm20) cc_final: 0.7395 (pm20) REVERT: B 486 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8295 (tt0) REVERT: B 550 MET cc_start: 0.7593 (mmm) cc_final: 0.7386 (mtt) REVERT: B 604 LEU cc_start: 0.7817 (tp) cc_final: 0.7292 (tt) REVERT: C 39 MET cc_start: 0.9495 (mmm) cc_final: 0.9132 (mmm) REVERT: C 61 MET cc_start: 0.8650 (mtt) cc_final: 0.8439 (mtm) REVERT: C 484 GLN cc_start: 0.8341 (tp40) cc_final: 0.7846 (tt0) REVERT: C 550 MET cc_start: 0.7046 (mmm) cc_final: 0.6805 (mtt) REVERT: C 607 ASP cc_start: 0.6460 (m-30) cc_final: 0.6250 (m-30) REVERT: D 251 ASN cc_start: 0.7575 (t0) cc_final: 0.7282 (t0) REVERT: D 345 ASN cc_start: 0.8350 (t0) cc_final: 0.7735 (t0) REVERT: D 410 MET cc_start: 0.7724 (mmm) cc_final: 0.6553 (mpp) REVERT: E 54 ASN cc_start: 0.8818 (t0) cc_final: 0.8482 (t0) REVERT: E 475 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: F 315 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8058 (mm-30) REVERT: F 369 THR cc_start: 0.9564 (m) cc_final: 0.9322 (m) REVERT: F 408 GLU cc_start: 0.8880 (tp30) cc_final: 0.8625 (tp30) REVERT: I 72 MET cc_start: 0.7995 (tpp) cc_final: 0.7790 (mmm) REVERT: I 76 MET cc_start: 0.8320 (mmm) cc_final: 0.8039 (mmm) REVERT: I 78 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: I 183 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8987 (mm) REVERT: I 226 ASP cc_start: 0.7764 (t0) cc_final: 0.7518 (m-30) REVERT: J 24 ASN cc_start: 0.9188 (m-40) cc_final: 0.8831 (m-40) REVERT: J 52 LYS cc_start: 0.8944 (tppp) cc_final: 0.8639 (tppp) REVERT: J 141 PHE cc_start: 0.8838 (t80) cc_final: 0.8549 (t80) REVERT: J 172 TYR cc_start: 0.8840 (m-80) cc_final: 0.8458 (m-80) REVERT: K 18 PHE cc_start: 0.9379 (t80) cc_final: 0.9025 (t80) REVERT: K 58 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8371 (mt-10) REVERT: O 81 MET cc_start: 0.8008 (mtp) cc_final: 0.7806 (mtm) REVERT: O 104 CYS cc_start: 0.8343 (m) cc_final: 0.8004 (m) REVERT: P 156 MET cc_start: -0.0991 (mtp) cc_final: -0.2480 (mmt) REVERT: P 309 MET cc_start: 0.7754 (mtm) cc_final: 0.6801 (mpp) REVERT: P 357 SER cc_start: 0.8648 (m) cc_final: 0.8158 (p) REVERT: Q 42 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7406 (pp) REVERT: Q 161 MET cc_start: 0.8823 (tmm) cc_final: 0.8192 (tmm) REVERT: Q 181 LEU cc_start: 0.8685 (mm) cc_final: 0.8057 (tp) REVERT: Q 188 MET cc_start: 0.7368 (ttm) cc_final: 0.6810 (ttm) REVERT: R 109 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7412 (tm-30) REVERT: R 146 THR cc_start: 0.8274 (t) cc_final: 0.8035 (t) REVERT: R 161 MET cc_start: 0.8579 (tmm) cc_final: 0.8364 (tpp) REVERT: R 199 LEU cc_start: 0.8868 (tp) cc_final: 0.8667 (tt) REVERT: R 205 LYS cc_start: 0.8565 (tptt) cc_final: 0.8082 (mmmt) REVERT: S 51 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7315 (p0) REVERT: S 93 ARG cc_start: 0.8790 (ttp80) cc_final: 0.8526 (ttp80) REVERT: S 103 MET cc_start: 0.6913 (mtp) cc_final: 0.6618 (ttm) REVERT: S 161 MET cc_start: 0.8564 (tpp) cc_final: 0.7915 (mmm) REVERT: S 188 MET cc_start: 0.7318 (tpp) cc_final: 0.6841 (ttm) REVERT: S 193 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7505 (mp) REVERT: T 90 LEU cc_start: 0.9118 (mt) cc_final: 0.8644 (mt) outliers start: 116 outliers final: 70 residues processed: 868 average time/residue: 0.6442 time to fit residues: 912.2620 Evaluate side-chains 821 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 744 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain P residue 351 SER Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 193 ILE Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 187 ASP Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 214 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 40.0000 chunk 337 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 443 optimal weight: 50.0000 chunk 245 optimal weight: 0.8980 chunk 508 optimal weight: 50.0000 chunk 411 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 534 optimal weight: 0.0270 chunk 150 optimal weight: 2.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 444 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 164 HIS ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN F 358 ASN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 GLN J 96 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 347 GLN Q 19 HIS ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 50486 Z= 0.340 Angle : 0.588 9.715 68109 Z= 0.304 Chirality : 0.043 0.342 7609 Planarity : 0.004 0.062 8813 Dihedral : 5.217 122.444 6801 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.39 % Allowed : 11.89 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.11), residues: 6176 helix: 1.25 (0.09), residues: 3227 sheet: -0.02 (0.20), residues: 690 loop : -0.43 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 197 HIS 0.009 0.001 HIS K 14 PHE 0.029 0.002 PHE B 612 TYR 0.021 0.002 TYR P 92 ARG 0.014 0.001 ARG N 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 769 time to evaluate : 5.581 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: A 33 ASP cc_start: 0.7980 (m-30) cc_final: 0.7746 (t0) REVERT: A 234 LEU cc_start: 0.8744 (mp) cc_final: 0.8406 (mt) REVERT: A 384 SER cc_start: 0.9077 (t) cc_final: 0.8732 (p) REVERT: A 523 ASN cc_start: 0.7111 (t0) cc_final: 0.6850 (t0) REVERT: A 530 ARG cc_start: 0.6665 (ttm-80) cc_final: 0.6396 (ttm-80) REVERT: B 291 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: B 443 LYS cc_start: 0.9250 (mmtm) cc_final: 0.8994 (mmmm) REVERT: B 486 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8221 (tt0) REVERT: B 604 LEU cc_start: 0.7795 (tp) cc_final: 0.7369 (tt) REVERT: C 39 MET cc_start: 0.9481 (mmm) cc_final: 0.9086 (mmm) REVERT: C 103 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8934 (tt0) REVERT: C 308 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8485 (ptt-90) REVERT: C 484 GLN cc_start: 0.8334 (tp40) cc_final: 0.7850 (tt0) REVERT: C 569 ILE cc_start: 0.9482 (mm) cc_final: 0.9269 (tt) REVERT: C 571 ARG cc_start: 0.8589 (ptm-80) cc_final: 0.8360 (ptm-80) REVERT: C 607 ASP cc_start: 0.6454 (m-30) cc_final: 0.6236 (m-30) REVERT: D 251 ASN cc_start: 0.7600 (t0) cc_final: 0.7320 (t0) REVERT: D 345 ASN cc_start: 0.8332 (t0) cc_final: 0.7766 (t0) REVERT: D 410 MET cc_start: 0.7773 (mmm) cc_final: 0.7563 (mpp) REVERT: E 54 ASN cc_start: 0.8943 (t0) cc_final: 0.8615 (t0) REVERT: E 358 ASN cc_start: 0.8773 (t0) cc_final: 0.8467 (t0) REVERT: E 475 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: F 369 THR cc_start: 0.9560 (m) cc_final: 0.9327 (m) REVERT: F 408 GLU cc_start: 0.8923 (tp30) cc_final: 0.8563 (tp30) REVERT: I 72 MET cc_start: 0.8036 (tpp) cc_final: 0.7710 (mmm) REVERT: I 76 MET cc_start: 0.8347 (mmm) cc_final: 0.8066 (mmm) REVERT: I 78 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: I 117 ASP cc_start: 0.7615 (m-30) cc_final: 0.7335 (m-30) REVERT: I 183 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8982 (mm) REVERT: J 18 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: J 24 ASN cc_start: 0.9151 (m-40) cc_final: 0.8779 (m-40) REVERT: J 52 LYS cc_start: 0.8943 (tppp) cc_final: 0.8660 (tppp) REVERT: J 94 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8505 (tt) REVERT: J 141 PHE cc_start: 0.8860 (t80) cc_final: 0.8551 (t80) REVERT: J 172 TYR cc_start: 0.8857 (m-80) cc_final: 0.8403 (m-80) REVERT: K 18 PHE cc_start: 0.9312 (t80) cc_final: 0.8966 (t80) REVERT: K 52 LYS cc_start: 0.8913 (ptpp) cc_final: 0.8679 (ptpp) REVERT: K 58 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8389 (mt-10) REVERT: K 62 LYS cc_start: 0.9060 (tppp) cc_final: 0.8633 (tppp) REVERT: O 102 PHE cc_start: 0.7433 (m-80) cc_final: 0.7174 (t80) REVERT: O 104 CYS cc_start: 0.8400 (m) cc_final: 0.8043 (m) REVERT: P 156 MET cc_start: -0.1034 (mtp) cc_final: -0.2416 (mmt) REVERT: P 309 MET cc_start: 0.7797 (mtm) cc_final: 0.6794 (mpp) REVERT: P 357 SER cc_start: 0.8928 (m) cc_final: 0.8463 (p) REVERT: P 426 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.8312 (ptm-80) REVERT: P 451 ASN cc_start: 0.9097 (m-40) cc_final: 0.8889 (m-40) REVERT: Q 42 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7406 (pp) REVERT: Q 161 MET cc_start: 0.8817 (tmm) cc_final: 0.8123 (tmm) REVERT: Q 181 LEU cc_start: 0.8705 (mm) cc_final: 0.8145 (tp) REVERT: Q 188 MET cc_start: 0.7517 (ttm) cc_final: 0.6869 (ttm) REVERT: R 109 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7381 (tm-30) REVERT: R 146 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7867 (t) REVERT: R 161 MET cc_start: 0.8608 (tmm) cc_final: 0.7924 (tmm) REVERT: R 205 LYS cc_start: 0.8566 (tptt) cc_final: 0.8179 (mmtt) REVERT: R 256 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8704 (t) REVERT: S 103 MET cc_start: 0.6855 (mtp) cc_final: 0.6608 (ttm) REVERT: S 161 MET cc_start: 0.8553 (tpp) cc_final: 0.7951 (mmm) REVERT: S 188 MET cc_start: 0.7320 (tpp) cc_final: 0.6868 (ttm) REVERT: T 90 LEU cc_start: 0.9175 (mt) cc_final: 0.8732 (mt) outliers start: 130 outliers final: 92 residues processed: 853 average time/residue: 0.6298 time to fit residues: 872.9168 Evaluate side-chains 823 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 720 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 351 SER Chi-restraints excluded: chain P residue 364 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 256 THR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 187 ASP Chi-restraints excluded: chain T residue 209 ASP Chi-restraints excluded: chain T residue 214 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 0.4980 chunk 536 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 349 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 596 optimal weight: 8.9990 chunk 494 optimal weight: 9.9990 chunk 275 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 468 HIS B 609 GLN C 140 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN J 122 GLN J 194 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 ASN S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 50486 Z= 0.302 Angle : 0.567 11.724 68109 Z= 0.293 Chirality : 0.042 0.325 7609 Planarity : 0.004 0.048 8813 Dihedral : 5.120 121.725 6801 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.45 % Allowed : 12.59 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.73 (0.11), residues: 6176 helix: 1.32 (0.09), residues: 3229 sheet: -0.02 (0.20), residues: 690 loop : -0.47 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 197 HIS 0.008 0.001 HIS A 444 PHE 0.030 0.001 PHE B 612 TYR 0.023 0.002 TYR G 75 ARG 0.011 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 751 time to evaluate : 6.698 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: A 384 SER cc_start: 0.9072 (t) cc_final: 0.8722 (p) REVERT: A 523 ASN cc_start: 0.7159 (t0) cc_final: 0.6837 (t0) REVERT: A 530 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.6403 (ttm-80) REVERT: A 584 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.6120 (mtm) REVERT: B 291 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: B 443 LYS cc_start: 0.9265 (mmtm) cc_final: 0.9011 (mmmm) REVERT: B 523 ASN cc_start: 0.8290 (t0) cc_final: 0.8077 (t0) REVERT: B 604 LEU cc_start: 0.7902 (tp) cc_final: 0.7559 (tt) REVERT: B 609 GLN cc_start: 0.9058 (mt0) cc_final: 0.8679 (mm-40) REVERT: C 39 MET cc_start: 0.9490 (mmm) cc_final: 0.9064 (mmm) REVERT: C 103 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8961 (tt0) REVERT: C 484 GLN cc_start: 0.8197 (tp40) cc_final: 0.7970 (tt0) REVERT: C 571 ARG cc_start: 0.8592 (ptm-80) cc_final: 0.8352 (ptm-80) REVERT: C 607 ASP cc_start: 0.6507 (m-30) cc_final: 0.6281 (m-30) REVERT: D 238 MET cc_start: 0.9027 (tpp) cc_final: 0.8798 (tpp) REVERT: D 251 ASN cc_start: 0.7538 (t0) cc_final: 0.7240 (t0) REVERT: D 345 ASN cc_start: 0.8321 (t0) cc_final: 0.7759 (t0) REVERT: D 387 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8386 (mm-40) REVERT: E 54 ASN cc_start: 0.8896 (t0) cc_final: 0.8470 (t0) REVERT: E 358 ASN cc_start: 0.8716 (t0) cc_final: 0.8276 (t0) REVERT: E 475 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: F 369 THR cc_start: 0.9547 (m) cc_final: 0.9317 (m) REVERT: F 408 GLU cc_start: 0.8944 (tp30) cc_final: 0.8557 (tp30) REVERT: I 72 MET cc_start: 0.8103 (tpp) cc_final: 0.7619 (mmm) REVERT: I 76 MET cc_start: 0.8380 (mmm) cc_final: 0.7939 (mmm) REVERT: I 78 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: I 117 ASP cc_start: 0.7572 (m-30) cc_final: 0.7273 (m-30) REVERT: I 183 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9006 (mm) REVERT: J 24 ASN cc_start: 0.9164 (m-40) cc_final: 0.8835 (m110) REVERT: J 94 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8543 (tt) REVERT: J 116 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8200 (mt) REVERT: J 141 PHE cc_start: 0.8871 (t80) cc_final: 0.8511 (t80) REVERT: J 172 TYR cc_start: 0.8932 (m-80) cc_final: 0.8547 (m-10) REVERT: K 52 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8594 (pttm) REVERT: K 58 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8582 (mt-10) REVERT: N 31 ARG cc_start: 0.8530 (mmp80) cc_final: 0.8321 (mmp80) REVERT: O 102 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7166 (t80) REVERT: O 104 CYS cc_start: 0.8434 (m) cc_final: 0.8102 (m) REVERT: P 156 MET cc_start: -0.0842 (mtp) cc_final: -0.2252 (mmt) REVERT: P 309 MET cc_start: 0.7846 (mtm) cc_final: 0.6889 (mpp) REVERT: P 357 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8518 (p) REVERT: P 451 ASN cc_start: 0.9093 (m-40) cc_final: 0.8884 (m-40) REVERT: Q 42 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7460 (pp) REVERT: Q 115 MET cc_start: 0.7331 (mmt) cc_final: 0.6973 (mmt) REVERT: Q 161 MET cc_start: 0.8737 (tmm) cc_final: 0.8051 (tmm) REVERT: Q 188 MET cc_start: 0.7494 (ttm) cc_final: 0.6954 (ttm) REVERT: R 103 MET cc_start: 0.8464 (mtp) cc_final: 0.7328 (mmt) REVERT: R 109 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7399 (tm-30) REVERT: R 146 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7892 (t) REVERT: R 205 LYS cc_start: 0.8558 (tptt) cc_final: 0.8264 (mmtt) REVERT: R 256 THR cc_start: 0.9041 (p) cc_final: 0.8682 (t) REVERT: S 10 MET cc_start: 0.7112 (mtm) cc_final: 0.6885 (mtt) REVERT: S 103 MET cc_start: 0.6973 (mtp) cc_final: 0.6696 (ttm) REVERT: S 161 MET cc_start: 0.8530 (tpp) cc_final: 0.7954 (mmm) REVERT: S 188 MET cc_start: 0.7369 (tpp) cc_final: 0.6973 (ttm) REVERT: T 90 LEU cc_start: 0.9175 (mt) cc_final: 0.8867 (mt) outliers start: 133 outliers final: 89 residues processed: 835 average time/residue: 0.6531 time to fit residues: 889.7869 Evaluate side-chains 820 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 719 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 102 PHE Chi-restraints excluded: chain P residue 351 SER Chi-restraints excluded: chain P residue 357 SER Chi-restraints excluded: chain P residue 364 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 172 ASN Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 187 ASP Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 339 optimal weight: 0.0030 chunk 435 optimal weight: 40.0000 chunk 337 optimal weight: 8.9990 chunk 501 optimal weight: 20.0000 chunk 332 optimal weight: 3.9990 chunk 593 optimal weight: 0.9980 chunk 371 optimal weight: 40.0000 chunk 361 optimal weight: 8.9990 chunk 274 optimal weight: 2.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS C 140 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN F 226 ASN I 66 GLN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 50486 Z= 0.389 Angle : 0.606 10.430 68109 Z= 0.313 Chirality : 0.044 0.306 7609 Planarity : 0.005 0.048 8813 Dihedral : 5.181 118.565 6801 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.69 % Allowed : 12.89 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 6176 helix: 1.28 (0.09), residues: 3219 sheet: -0.15 (0.20), residues: 690 loop : -0.57 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 197 HIS 0.008 0.001 HIS A 444 PHE 0.033 0.002 PHE S 151 TYR 0.022 0.002 TYR R 232 ARG 0.010 0.001 ARG B 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 740 time to evaluate : 5.981 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: A 297 GLU cc_start: 0.7653 (tt0) cc_final: 0.7233 (tt0) REVERT: A 384 SER cc_start: 0.9106 (t) cc_final: 0.8762 (p) REVERT: A 517 ASP cc_start: 0.7781 (m-30) cc_final: 0.7470 (m-30) REVERT: A 523 ASN cc_start: 0.7348 (t0) cc_final: 0.7139 (t0) REVERT: A 530 ARG cc_start: 0.6742 (ttm-80) cc_final: 0.6453 (ttm-80) REVERT: A 584 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6253 (mtm) REVERT: B 291 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: B 443 LYS cc_start: 0.9308 (mmtm) cc_final: 0.9048 (mmmm) REVERT: B 486 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8220 (tt0) REVERT: B 523 ASN cc_start: 0.8325 (t0) cc_final: 0.8114 (t0) REVERT: B 609 GLN cc_start: 0.9057 (mt0) cc_final: 0.8664 (mm-40) REVERT: C 39 MET cc_start: 0.9487 (mmm) cc_final: 0.9044 (mmm) REVERT: C 103 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8968 (tt0) REVERT: C 484 GLN cc_start: 0.8242 (tp40) cc_final: 0.7972 (tt0) REVERT: C 571 ARG cc_start: 0.8617 (ptm-80) cc_final: 0.8354 (ptm-80) REVERT: C 584 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8620 (ttm) REVERT: C 607 ASP cc_start: 0.6626 (m-30) cc_final: 0.6380 (m-30) REVERT: D 251 ASN cc_start: 0.7590 (t0) cc_final: 0.7275 (t0) REVERT: D 345 ASN cc_start: 0.8329 (t0) cc_final: 0.7691 (t0) REVERT: D 387 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8488 (mm-40) REVERT: E 54 ASN cc_start: 0.8962 (t0) cc_final: 0.8497 (t0) REVERT: E 358 ASN cc_start: 0.8756 (t0) cc_final: 0.8314 (t0) REVERT: E 475 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: F 315 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8111 (mm-30) REVERT: F 408 GLU cc_start: 0.8946 (tp30) cc_final: 0.8561 (tp30) REVERT: H 14 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7653 (ptm) REVERT: I 15 MET cc_start: 0.1038 (OUTLIER) cc_final: 0.0515 (ppp) REVERT: I 72 MET cc_start: 0.8066 (tpp) cc_final: 0.7565 (mmm) REVERT: I 76 MET cc_start: 0.8365 (mmm) cc_final: 0.8012 (mmm) REVERT: I 78 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: I 117 ASP cc_start: 0.7582 (m-30) cc_final: 0.7279 (m-30) REVERT: I 154 MET cc_start: 0.8992 (mtm) cc_final: 0.8790 (mtm) REVERT: I 183 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9026 (mm) REVERT: I 226 ASP cc_start: 0.7725 (m-30) cc_final: 0.7488 (m-30) REVERT: J 24 ASN cc_start: 0.9142 (m-40) cc_final: 0.8754 (m-40) REVERT: J 94 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8541 (tt) REVERT: J 116 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8189 (mt) REVERT: J 141 PHE cc_start: 0.8923 (t80) cc_final: 0.8521 (t80) REVERT: J 172 TYR cc_start: 0.8959 (m-80) cc_final: 0.8546 (m-10) REVERT: K 62 LYS cc_start: 0.9105 (tppp) cc_final: 0.8739 (tppp) REVERT: O 102 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7205 (t80) REVERT: O 105 ASP cc_start: 0.8402 (t70) cc_final: 0.7326 (t70) REVERT: O 107 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7567 (mtm110) REVERT: P 156 MET cc_start: -0.0878 (mtp) cc_final: -0.2221 (mmt) REVERT: P 309 MET cc_start: 0.7889 (mtm) cc_final: 0.6943 (mpp) REVERT: P 357 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8509 (p) REVERT: P 451 ASN cc_start: 0.9101 (m-40) cc_final: 0.8894 (m-40) REVERT: Q 115 MET cc_start: 0.7369 (mmt) cc_final: 0.7066 (mmt) REVERT: Q 140 LEU cc_start: 0.9298 (pp) cc_final: 0.8962 (mt) REVERT: Q 161 MET cc_start: 0.8721 (tmm) cc_final: 0.8020 (tmm) REVERT: Q 188 MET cc_start: 0.7471 (ttm) cc_final: 0.7028 (ttm) REVERT: R 109 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7393 (tm-30) REVERT: R 112 TYR cc_start: 0.8323 (t80) cc_final: 0.8068 (t80) REVERT: R 146 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.8022 (t) REVERT: R 161 MET cc_start: 0.8546 (tmm) cc_final: 0.8099 (tmm) REVERT: R 205 LYS cc_start: 0.8576 (tptt) cc_final: 0.8256 (mmtt) REVERT: R 207 GLN cc_start: 0.7155 (tp40) cc_final: 0.6787 (tp-100) REVERT: R 256 THR cc_start: 0.9046 (p) cc_final: 0.8544 (t) REVERT: S 139 TYR cc_start: 0.8530 (t80) cc_final: 0.8318 (t80) REVERT: S 161 MET cc_start: 0.8551 (tpp) cc_final: 0.8038 (mmm) REVERT: S 188 MET cc_start: 0.7370 (tpp) cc_final: 0.6863 (ttm) REVERT: T 90 LEU cc_start: 0.9205 (mt) cc_final: 0.8747 (mt) outliers start: 146 outliers final: 103 residues processed: 828 average time/residue: 0.6293 time to fit residues: 849.8327 Evaluate side-chains 841 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 724 time to evaluate : 5.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 102 PHE Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 351 SER Chi-restraints excluded: chain P residue 357 SER Chi-restraints excluded: chain P residue 364 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain P residue 457 GLN Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 172 ASN Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 354 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 377 optimal weight: 2.9990 chunk 404 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 466 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 468 HIS C 140 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 50486 Z= 0.312 Angle : 0.578 12.037 68109 Z= 0.298 Chirality : 0.043 0.287 7609 Planarity : 0.004 0.049 8813 Dihedral : 5.088 119.094 6801 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.56 % Allowed : 13.44 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.11), residues: 6176 helix: 1.37 (0.09), residues: 3208 sheet: -0.19 (0.19), residues: 703 loop : -0.54 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 433 HIS 0.008 0.001 HIS A 444 PHE 0.031 0.002 PHE S 151 TYR 0.016 0.001 TYR G 75 ARG 0.010 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 745 time to evaluate : 6.423 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: A 297 GLU cc_start: 0.7648 (tt0) cc_final: 0.7218 (tt0) REVERT: A 384 SER cc_start: 0.9092 (t) cc_final: 0.8738 (p) REVERT: A 523 ASN cc_start: 0.7243 (t0) cc_final: 0.6990 (t0) REVERT: A 530 ARG cc_start: 0.6696 (ttm-80) cc_final: 0.6422 (ttm-80) REVERT: A 584 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.6172 (mtm) REVERT: B 291 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: B 443 LYS cc_start: 0.9322 (mmtm) cc_final: 0.9066 (mmmm) REVERT: B 486 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8226 (tt0) REVERT: B 552 ARG cc_start: 0.7985 (ttt-90) cc_final: 0.7630 (ttt90) REVERT: C 39 MET cc_start: 0.9483 (mmm) cc_final: 0.9015 (mmm) REVERT: C 103 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8975 (tt0) REVERT: C 194 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8234 (pp) REVERT: C 308 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8349 (ptt-90) REVERT: C 571 ARG cc_start: 0.8599 (ptm-80) cc_final: 0.8368 (tmm-80) REVERT: C 584 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8545 (ttm) REVERT: C 603 GLN cc_start: 0.7458 (tp40) cc_final: 0.6561 (tp40) REVERT: C 607 ASP cc_start: 0.6600 (m-30) cc_final: 0.6121 (m-30) REVERT: D 238 MET cc_start: 0.9002 (tpp) cc_final: 0.8742 (tpp) REVERT: D 251 ASN cc_start: 0.7577 (t0) cc_final: 0.7287 (t0) REVERT: D 345 ASN cc_start: 0.8321 (t0) cc_final: 0.7692 (t0) REVERT: D 387 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8503 (mm-40) REVERT: E 54 ASN cc_start: 0.8965 (t0) cc_final: 0.8571 (t0) REVERT: E 358 ASN cc_start: 0.8724 (t0) cc_final: 0.8347 (t0) REVERT: E 475 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: F 315 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8130 (mm-30) REVERT: F 369 THR cc_start: 0.9558 (m) cc_final: 0.9337 (m) REVERT: F 408 GLU cc_start: 0.8927 (tp30) cc_final: 0.8549 (tp30) REVERT: G 204 LEU cc_start: 0.8569 (pt) cc_final: 0.8287 (pp) REVERT: I 15 MET cc_start: 0.1070 (OUTLIER) cc_final: 0.0574 (ppp) REVERT: I 54 MET cc_start: 0.8849 (mmt) cc_final: 0.8534 (mpp) REVERT: I 70 ILE cc_start: 0.7798 (mp) cc_final: 0.7534 (mp) REVERT: I 72 MET cc_start: 0.8089 (tpp) cc_final: 0.7658 (mmm) REVERT: I 76 MET cc_start: 0.8380 (mmm) cc_final: 0.8116 (mmm) REVERT: I 78 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: I 117 ASP cc_start: 0.7573 (m-30) cc_final: 0.7263 (m-30) REVERT: I 154 MET cc_start: 0.8965 (mtm) cc_final: 0.8753 (mtm) REVERT: I 183 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9042 (mm) REVERT: I 226 ASP cc_start: 0.7691 (m-30) cc_final: 0.7454 (m-30) REVERT: J 16 MET cc_start: 0.8792 (ppp) cc_final: 0.8519 (ppp) REVERT: J 24 ASN cc_start: 0.9110 (m-40) cc_final: 0.8738 (m-40) REVERT: J 56 TYR cc_start: 0.8645 (t80) cc_final: 0.8271 (t80) REVERT: J 94 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8627 (tt) REVERT: J 116 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8177 (mt) REVERT: J 133 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9022 (mp) REVERT: J 141 PHE cc_start: 0.8932 (t80) cc_final: 0.8541 (t80) REVERT: J 172 TYR cc_start: 0.8942 (m-80) cc_final: 0.8536 (m-10) REVERT: K 52 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8512 (ptpp) REVERT: O 16 LYS cc_start: 0.9551 (ptpp) cc_final: 0.9326 (ptpp) REVERT: O 75 LYS cc_start: 0.9004 (mttp) cc_final: 0.8712 (ptpp) REVERT: O 102 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7194 (t80) REVERT: O 105 ASP cc_start: 0.8369 (t70) cc_final: 0.7848 (t70) REVERT: P 156 MET cc_start: -0.0800 (mtp) cc_final: -0.2107 (mmt) REVERT: P 309 MET cc_start: 0.7923 (mtm) cc_final: 0.6988 (mpp) REVERT: P 357 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8462 (p) REVERT: P 451 ASN cc_start: 0.9062 (m-40) cc_final: 0.8859 (m-40) REVERT: Q 139 TYR cc_start: 0.8733 (t80) cc_final: 0.8509 (t80) REVERT: Q 161 MET cc_start: 0.8714 (tmm) cc_final: 0.8007 (tmm) REVERT: Q 188 MET cc_start: 0.7417 (ttm) cc_final: 0.6950 (ttm) REVERT: R 103 MET cc_start: 0.8505 (mtp) cc_final: 0.7358 (mmt) REVERT: R 146 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7936 (t) REVERT: R 161 MET cc_start: 0.8475 (tmm) cc_final: 0.8063 (tmm) REVERT: R 205 LYS cc_start: 0.8543 (tptt) cc_final: 0.8230 (mmtt) REVERT: R 256 THR cc_start: 0.9048 (p) cc_final: 0.8697 (t) REVERT: S 139 TYR cc_start: 0.8530 (t80) cc_final: 0.8294 (t80) REVERT: S 155 MET cc_start: 0.8469 (mtp) cc_final: 0.8011 (tpp) REVERT: S 161 MET cc_start: 0.8558 (tpp) cc_final: 0.8068 (mmm) REVERT: S 188 MET cc_start: 0.7395 (tpp) cc_final: 0.6983 (ttm) REVERT: T 90 LEU cc_start: 0.9180 (mt) cc_final: 0.8725 (mt) outliers start: 139 outliers final: 103 residues processed: 828 average time/residue: 0.6591 time to fit residues: 895.3332 Evaluate side-chains 836 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 717 time to evaluate : 5.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 102 PHE Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 357 SER Chi-restraints excluded: chain P residue 364 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain P residue 457 GLN Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 172 ASN Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 2.9990 chunk 568 optimal weight: 10.0000 chunk 518 optimal weight: 8.9990 chunk 553 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 434 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 499 optimal weight: 20.0000 chunk 523 optimal weight: 4.9990 chunk 551 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 573 HIS C 140 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 50486 Z= 0.499 Angle : 0.665 12.478 68109 Z= 0.343 Chirality : 0.046 0.274 7609 Planarity : 0.005 0.051 8813 Dihedral : 5.294 114.884 6801 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.45 % Allowed : 14.18 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.43 (0.11), residues: 6176 helix: 1.22 (0.09), residues: 3206 sheet: -0.43 (0.19), residues: 711 loop : -0.75 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 197 HIS 0.010 0.001 HIS T 58 PHE 0.036 0.002 PHE K 18 TYR 0.028 0.002 TYR G 75 ARG 0.014 0.001 ARG P 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 736 time to evaluate : 5.874 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: A 294 LEU cc_start: 0.8872 (mp) cc_final: 0.8589 (mt) REVERT: A 297 GLU cc_start: 0.7684 (tt0) cc_final: 0.7246 (tt0) REVERT: A 384 SER cc_start: 0.9132 (t) cc_final: 0.8807 (p) REVERT: A 517 ASP cc_start: 0.7576 (m-30) cc_final: 0.7136 (m-30) REVERT: A 523 ASN cc_start: 0.7463 (t0) cc_final: 0.7234 (t0) REVERT: A 530 ARG cc_start: 0.6746 (ttm-80) cc_final: 0.6438 (ttm-80) REVERT: A 584 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6280 (mtm) REVERT: B 291 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: B 443 LYS cc_start: 0.9327 (mmtm) cc_final: 0.8954 (mmmm) REVERT: B 486 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8149 (tt0) REVERT: B 552 ARG cc_start: 0.7995 (ttt-90) cc_final: 0.7641 (ttt90) REVERT: B 609 GLN cc_start: 0.9052 (mt0) cc_final: 0.8742 (mm-40) REVERT: B 612 PHE cc_start: 0.6909 (m-10) cc_final: 0.6691 (m-10) REVERT: C 39 MET cc_start: 0.9480 (mmm) cc_final: 0.8993 (mmm) REVERT: C 103 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.9005 (tt0) REVERT: C 584 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8665 (ttm) REVERT: C 607 ASP cc_start: 0.6654 (m-30) cc_final: 0.6401 (m-30) REVERT: D 251 ASN cc_start: 0.7633 (t0) cc_final: 0.7353 (t0) REVERT: D 345 ASN cc_start: 0.8317 (t0) cc_final: 0.7650 (t0) REVERT: D 387 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8568 (mm-40) REVERT: E 54 ASN cc_start: 0.9067 (t0) cc_final: 0.8589 (t0) REVERT: E 472 THR cc_start: 0.9231 (p) cc_final: 0.8374 (p) REVERT: E 475 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: F 256 ASN cc_start: 0.8173 (m-40) cc_final: 0.7839 (p0) REVERT: F 315 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8193 (mm-30) REVERT: F 408 GLU cc_start: 0.8930 (tp30) cc_final: 0.8513 (tp30) REVERT: G 204 LEU cc_start: 0.8609 (pt) cc_final: 0.8359 (pp) REVERT: I 15 MET cc_start: 0.1025 (OUTLIER) cc_final: 0.0501 (ppp) REVERT: I 70 ILE cc_start: 0.7896 (mp) cc_final: 0.7678 (mp) REVERT: I 72 MET cc_start: 0.8081 (tpp) cc_final: 0.7760 (mmm) REVERT: I 78 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: I 117 ASP cc_start: 0.7605 (m-30) cc_final: 0.7302 (m-30) REVERT: I 154 MET cc_start: 0.9022 (mtm) cc_final: 0.8786 (mtm) REVERT: I 183 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9069 (mm) REVERT: I 226 ASP cc_start: 0.7685 (m-30) cc_final: 0.7437 (m-30) REVERT: J 24 ASN cc_start: 0.9103 (m-40) cc_final: 0.8733 (m110) REVERT: J 56 TYR cc_start: 0.8658 (t80) cc_final: 0.8339 (t80) REVERT: J 94 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8545 (tt) REVERT: J 116 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8121 (mt) REVERT: J 133 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9034 (mp) REVERT: J 141 PHE cc_start: 0.8966 (t80) cc_final: 0.8552 (t80) REVERT: J 172 TYR cc_start: 0.8958 (m-80) cc_final: 0.8462 (m-10) REVERT: K 18 PHE cc_start: 0.9249 (t80) cc_final: 0.9018 (t80) REVERT: N 97 ASP cc_start: 0.7735 (m-30) cc_final: 0.7413 (m-30) REVERT: O 75 LYS cc_start: 0.8982 (mttp) cc_final: 0.8761 (ptpp) REVERT: O 102 PHE cc_start: 0.7463 (m-80) cc_final: 0.7227 (t80) REVERT: O 105 ASP cc_start: 0.8387 (t70) cc_final: 0.7868 (t70) REVERT: P 156 MET cc_start: -0.0661 (mtp) cc_final: -0.2015 (mmt) REVERT: P 309 MET cc_start: 0.7994 (mtm) cc_final: 0.7087 (mpp) REVERT: P 357 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8668 (p) REVERT: P 451 ASN cc_start: 0.9118 (m-40) cc_final: 0.8887 (m-40) REVERT: Q 161 MET cc_start: 0.8755 (tmm) cc_final: 0.7994 (tmm) REVERT: Q 188 MET cc_start: 0.7410 (ttm) cc_final: 0.6908 (ttm) REVERT: Q 242 LEU cc_start: 0.8871 (mt) cc_final: 0.8354 (mt) REVERT: R 60 TYR cc_start: 0.7761 (m-80) cc_final: 0.7462 (m-80) REVERT: R 103 MET cc_start: 0.8525 (mtp) cc_final: 0.7385 (mmt) REVERT: R 161 MET cc_start: 0.8531 (tmm) cc_final: 0.8094 (tmm) REVERT: R 205 LYS cc_start: 0.8543 (tptt) cc_final: 0.8260 (mmtt) REVERT: R 256 THR cc_start: 0.9051 (p) cc_final: 0.8709 (t) REVERT: S 51 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7427 (p0) REVERT: S 161 MET cc_start: 0.8564 (tpp) cc_final: 0.8134 (mmm) REVERT: S 188 MET cc_start: 0.7415 (tpp) cc_final: 0.6990 (ttm) REVERT: T 90 LEU cc_start: 0.9215 (mt) cc_final: 0.8761 (mt) outliers start: 133 outliers final: 104 residues processed: 818 average time/residue: 0.6404 time to fit residues: 852.6972 Evaluate side-chains 839 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 722 time to evaluate : 5.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 357 SER Chi-restraints excluded: chain P residue 364 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain P residue 457 GLN Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 172 ASN Chi-restraints excluded: chain S residue 184 HIS Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 20.0000 chunk 585 optimal weight: 2.9990 chunk 357 optimal weight: 50.0000 chunk 277 optimal weight: 0.5980 chunk 406 optimal weight: 0.0970 chunk 613 optimal weight: 0.5980 chunk 564 optimal weight: 2.9990 chunk 488 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 377 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS C 140 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 50486 Z= 0.176 Angle : 0.563 12.907 68109 Z= 0.289 Chirality : 0.041 0.261 7609 Planarity : 0.004 0.048 8813 Dihedral : 4.921 120.633 6801 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.60 % Allowed : 15.10 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.80 (0.11), residues: 6176 helix: 1.46 (0.09), residues: 3214 sheet: -0.22 (0.19), residues: 708 loop : -0.50 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 197 HIS 0.008 0.001 HIS A 444 PHE 0.031 0.001 PHE S 200 TYR 0.027 0.001 TYR G 75 ARG 0.013 0.000 ARG C 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12352 Ramachandran restraints generated. 6176 Oldfield, 0 Emsley, 6176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 778 time to evaluate : 6.449 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: A 294 LEU cc_start: 0.8872 (mp) cc_final: 0.8583 (mt) REVERT: A 297 GLU cc_start: 0.7647 (tt0) cc_final: 0.7208 (tt0) REVERT: A 306 MET cc_start: 0.9020 (tpt) cc_final: 0.8785 (tpt) REVERT: A 384 SER cc_start: 0.9050 (t) cc_final: 0.8690 (p) REVERT: A 523 ASN cc_start: 0.7323 (t0) cc_final: 0.7098 (t0) REVERT: A 530 ARG cc_start: 0.6665 (ttm-80) cc_final: 0.6392 (ttm-80) REVERT: A 584 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.6157 (mtm) REVERT: B 197 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 291 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: B 296 MET cc_start: 0.8466 (ptt) cc_final: 0.8225 (ptt) REVERT: B 443 LYS cc_start: 0.9315 (mmtm) cc_final: 0.8956 (mmmm) REVERT: B 486 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8135 (tt0) REVERT: B 552 ARG cc_start: 0.7950 (ttt-90) cc_final: 0.7590 (ttt90) REVERT: B 553 ARG cc_start: 0.6744 (ttp80) cc_final: 0.6481 (ttp80) REVERT: B 604 LEU cc_start: 0.8035 (tp) cc_final: 0.7796 (tt) REVERT: B 609 GLN cc_start: 0.8982 (mt0) cc_final: 0.8637 (mm-40) REVERT: B 612 PHE cc_start: 0.6769 (m-10) cc_final: 0.6515 (m-10) REVERT: C 39 MET cc_start: 0.9469 (mmm) cc_final: 0.8957 (mmm) REVERT: C 194 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8186 (pp) REVERT: C 571 ARG cc_start: 0.8767 (ptm-80) cc_final: 0.8544 (tmm-80) REVERT: C 603 GLN cc_start: 0.7419 (tp40) cc_final: 0.6750 (tp40) REVERT: C 607 ASP cc_start: 0.6548 (m-30) cc_final: 0.6231 (m-30) REVERT: D 238 MET cc_start: 0.8955 (tpp) cc_final: 0.8639 (tpt) REVERT: D 345 ASN cc_start: 0.8306 (t0) cc_final: 0.7677 (t0) REVERT: D 387 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8481 (mm-40) REVERT: E 54 ASN cc_start: 0.8840 (t0) cc_final: 0.8456 (t0) REVERT: E 475 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: F 315 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8198 (mm-30) REVERT: F 369 THR cc_start: 0.9519 (m) cc_final: 0.9312 (m) REVERT: F 408 GLU cc_start: 0.8909 (tp30) cc_final: 0.8601 (tp30) REVERT: G 204 LEU cc_start: 0.8503 (pt) cc_final: 0.8241 (pp) REVERT: I 15 MET cc_start: 0.0925 (OUTLIER) cc_final: 0.0367 (ppp) REVERT: I 70 ILE cc_start: 0.7863 (mp) cc_final: 0.7656 (mp) REVERT: I 72 MET cc_start: 0.7921 (tpp) cc_final: 0.7680 (mmm) REVERT: I 78 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: I 95 LEU cc_start: 0.8514 (mp) cc_final: 0.8302 (mm) REVERT: I 117 ASP cc_start: 0.7530 (m-30) cc_final: 0.7194 (m-30) REVERT: I 183 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9074 (mm) REVERT: I 194 ASN cc_start: 0.9236 (t0) cc_final: 0.8980 (m-40) REVERT: I 226 ASP cc_start: 0.7740 (m-30) cc_final: 0.7363 (m-30) REVERT: J 24 ASN cc_start: 0.9090 (m-40) cc_final: 0.8732 (m-40) REVERT: J 56 TYR cc_start: 0.8680 (t80) cc_final: 0.8369 (t80) REVERT: J 94 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8720 (tt) REVERT: J 116 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8180 (mt) REVERT: J 133 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9007 (mp) REVERT: J 141 PHE cc_start: 0.8936 (t80) cc_final: 0.8520 (t80) REVERT: J 172 TYR cc_start: 0.8933 (m-80) cc_final: 0.8473 (m-10) REVERT: K 18 PHE cc_start: 0.9270 (t80) cc_final: 0.9024 (t80) REVERT: K 65 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7972 (mm-30) REVERT: N 31 ARG cc_start: 0.8544 (mmp80) cc_final: 0.8342 (mmp80) REVERT: O 75 LYS cc_start: 0.8962 (mttp) cc_final: 0.8746 (ptpp) REVERT: O 102 PHE cc_start: 0.7379 (m-80) cc_final: 0.7159 (t80) REVERT: O 116 ILE cc_start: 0.6912 (tp) cc_final: 0.6593 (pt) REVERT: P 156 MET cc_start: -0.1054 (mtp) cc_final: -0.2240 (mmt) REVERT: P 309 MET cc_start: 0.7970 (mtm) cc_final: 0.7084 (mpp) REVERT: P 357 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8453 (p) REVERT: P 451 ASN cc_start: 0.9128 (m-40) cc_final: 0.8894 (m-40) REVERT: Q 115 MET cc_start: 0.7260 (mmt) cc_final: 0.6941 (mmp) REVERT: Q 161 MET cc_start: 0.8809 (tmm) cc_final: 0.8047 (tmm) REVERT: Q 188 MET cc_start: 0.7479 (ttm) cc_final: 0.6977 (ttm) REVERT: R 15 SER cc_start: 0.7251 (m) cc_final: 0.7031 (t) REVERT: R 103 MET cc_start: 0.8502 (mtp) cc_final: 0.7352 (mmt) REVERT: R 161 MET cc_start: 0.8467 (tmm) cc_final: 0.8038 (tmm) REVERT: R 205 LYS cc_start: 0.8489 (tptt) cc_final: 0.8208 (mmtt) REVERT: R 207 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6753 (tp-100) REVERT: R 256 THR cc_start: 0.9032 (p) cc_final: 0.8689 (t) REVERT: S 51 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7445 (p0) REVERT: S 161 MET cc_start: 0.8595 (tpp) cc_final: 0.8218 (mmm) REVERT: S 171 ASP cc_start: 0.8518 (p0) cc_final: 0.7983 (p0) REVERT: S 188 MET cc_start: 0.7343 (tpp) cc_final: 0.6916 (ttm) REVERT: S 197 TYR cc_start: 0.6964 (t80) cc_final: 0.6626 (t80) REVERT: T 90 LEU cc_start: 0.9134 (mt) cc_final: 0.8750 (mt) outliers start: 87 outliers final: 63 residues processed: 834 average time/residue: 0.6253 time to fit residues: 849.4672 Evaluate side-chains 817 residues out of total 5432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 742 time to evaluate : 5.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 475 GLU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 357 SER Chi-restraints excluded: chain P residue 364 LEU Chi-restraints excluded: chain P residue 412 HIS Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 163 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 51 ASP Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 172 ASN Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 266 ILE Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 209 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 2.9990 chunk 520 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 450 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 489 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 502 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140487 restraints weight = 66338.119| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.12 r_work: 0.3113 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 50486 Z= 0.495 Angle : 0.673 12.192 68109 Z= 0.346 Chirality : 0.046 0.245 7609 Planarity : 0.005 0.102 8813 Dihedral : 5.192 114.303 6801 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.75 % Allowed : 15.39 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.50 (0.11), residues: 6176 helix: 1.25 (0.09), residues: 3211 sheet: -0.38 (0.19), residues: 704 loop : -0.69 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 294 HIS 0.010 0.001 HIS T 58 PHE 0.039 0.002 PHE A 18 TYR 0.046 0.002 TYR Q 197 ARG 0.015 0.001 ARG A 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15056.32 seconds wall clock time: 269 minutes 7.87 seconds (16147.87 seconds total)