Starting phenix.real_space_refine on Sat Mar 16 13:36:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emc_28244/03_2024/8emc_28244.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emc_28244/03_2024/8emc_28244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emc_28244/03_2024/8emc_28244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emc_28244/03_2024/8emc_28244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emc_28244/03_2024/8emc_28244.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emc_28244/03_2024/8emc_28244.pdb" } resolution = 3.6 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= 0.001 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 364 5.16 5 C 46850 2.51 5 N 12409 2.21 5 O 13708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 472": "OD1" <-> "OD2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 485": "OE1" <-> "OE2" Residue "D PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E ASP 119": "OD1" <-> "OD2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 442": "OE1" <-> "OE2" Residue "E TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 474": "OD1" <-> "OD2" Residue "E TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 6": "OD1" <-> "OD2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F ASP 76": "OD1" <-> "OD2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F ASP 274": "OD1" <-> "OD2" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 379": "OD1" <-> "OD2" Residue "F TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 485": "OE1" <-> "OE2" Residue "F GLU 519": "OE1" <-> "OE2" Residue "F TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 119": "OD1" <-> "OD2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 288": "OD1" <-> "OD2" Residue "G GLU 309": "OE1" <-> "OE2" Residue "G PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 379": "OD1" <-> "OD2" Residue "G GLU 387": "OE1" <-> "OE2" Residue "G PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 442": "OE1" <-> "OE2" Residue "G TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "G GLU 485": "OE1" <-> "OE2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H ASP 279": "OD1" <-> "OD2" Residue "H PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 309": "OE1" <-> "OE2" Residue "H GLU 312": "OE1" <-> "OE2" Residue "H GLU 387": "OE1" <-> "OE2" Residue "H PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 453": "OE1" <-> "OE2" Residue "H TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 622": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 290": "OD1" <-> "OD2" Residue "I PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 312": "OE1" <-> "OE2" Residue "I ASP 379": "OD1" <-> "OD2" Residue "I PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 435": "OE1" <-> "OE2" Residue "I TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 453": "OE1" <-> "OE2" Residue "I GLU 462": "OE1" <-> "OE2" Residue "I TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 542": "OE1" <-> "OE2" Residue "I GLU 626": "OE1" <-> "OE2" Residue "I TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 297": "OD1" <-> "OD2" Residue "J PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 342": "OE1" <-> "OE2" Residue "J PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 351": "OD1" <-> "OD2" Residue "J GLU 383": "OE1" <-> "OE2" Residue "J PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 387": "OE1" <-> "OE2" Residue "J GLU 398": "OE1" <-> "OE2" Residue "J TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 477": "OE1" <-> "OE2" Residue "J PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 542": "OE1" <-> "OE2" Residue "J PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 32": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 205": "OD1" <-> "OD2" Residue "K TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 288": "OD1" <-> "OD2" Residue "K GLU 312": "OE1" <-> "OE2" Residue "K GLU 342": "OE1" <-> "OE2" Residue "K TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 462": "OE1" <-> "OE2" Residue "K PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "L TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 150": "OE1" <-> "OE2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "L ASP 205": "OD1" <-> "OD2" Residue "L TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 312": "OE1" <-> "OE2" Residue "L GLU 342": "OE1" <-> "OE2" Residue "L TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 395": "OD1" <-> "OD2" Residue "L GLU 398": "OE1" <-> "OE2" Residue "L TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 129": "OE1" <-> "OE2" Residue "M TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 226": "OE1" <-> "OE2" Residue "M TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 288": "OD1" <-> "OD2" Residue "M PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 328": "OE1" <-> "OE2" Residue "M ASP 346": "OD1" <-> "OD2" Residue "M PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 442": "OE1" <-> "OE2" Residue "M PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 465": "OD1" <-> "OD2" Residue "M ASP 474": "OD1" <-> "OD2" Residue "M TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 648": "OD1" <-> "OD2" Residue "M TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N GLU 129": "OE1" <-> "OE2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "N GLU 150": "OE1" <-> "OE2" Residue "N PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 185": "OD1" <-> "OD2" Residue "N PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 226": "OE1" <-> "OE2" Residue "N PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 290": "OD1" <-> "OD2" Residue "N PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 309": "OE1" <-> "OE2" Residue "N GLU 342": "OE1" <-> "OE2" Residue "N ASP 346": "OD1" <-> "OD2" Residue "N PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 477": "OE1" <-> "OE2" Residue "N TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 519": "OE1" <-> "OE2" Residue "N TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 73331 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5254 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 27, 'TRANS': 640} Chain breaks: 1 Chain: "B" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5269 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 27, 'TRANS': 643} Chain breaks: 1 Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5251 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 27, 'TRANS': 640} Chain breaks: 1 Chain: "D" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5235 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "E" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5239 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "F" Number of atoms: 5237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5237 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "G" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5226 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Chain: "H" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5250 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 27, 'TRANS': 640} Chain breaks: 2 Chain: "I" Number of atoms: 5253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5253 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 27, 'TRANS': 640} Chain breaks: 1 Chain: "J" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5246 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 27, 'TRANS': 639} Chain breaks: 1 Chain: "K" Number of atoms: 5229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5229 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 27, 'TRANS': 637} Chain breaks: 1 Chain: "L" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5211 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 27, 'TRANS': 635} Chain breaks: 1 Chain: "M" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5220 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 27, 'TRANS': 636} Chain breaks: 1 Chain: "N" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5211 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 27, 'TRANS': 635} Chain breaks: 1 Time building chain proxies: 27.88, per 1000 atoms: 0.38 Number of scatterers: 73331 At special positions: 0 Unit cell: (175.16, 177.48, 206.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 364 16.00 O 13708 8.00 N 12409 7.00 C 46850 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: 21.75 Conformation dependent library (CDL) restraints added in 9.9 seconds 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17224 Finding SS restraints... Secondary structure from input PDB file: 473 helices and 117 sheets defined 48.8% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.99 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.527A pdb=" N LEU A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.589A pdb=" N LEU A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 123 through 130 removed outlier: 3.582A pdb=" N VAL A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.920A pdb=" N VAL A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 136' Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.690A pdb=" N LEU A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.751A pdb=" N ILE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.627A pdb=" N TRP A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 289 through 302 removed outlier: 4.597A pdb=" N GLN A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.914A pdb=" N TYR A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 433 through 460 removed outlier: 3.520A pdb=" N VAL A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464 Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 554 through 560 Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 623 through 635 Processing helix chain 'A' and resid 643 through 649 removed outlier: 3.532A pdb=" N ALA A 647 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 25 through 32 removed outlier: 4.083A pdb=" N GLU B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 46 removed outlier: 3.506A pdb=" N LEU B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 89 removed outlier: 3.508A pdb=" N SER B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.607A pdb=" N VAL B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.878A pdb=" N VAL B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 171 through 182 removed outlier: 3.645A pdb=" N LEU B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.738A pdb=" N ILE B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.547A pdb=" N SER B 201 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 219 Proline residue: B 216 - end of helix removed outlier: 3.517A pdb=" N GLU B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 289 through 302 removed outlier: 4.434A pdb=" N GLN B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.556A pdb=" N LYS B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 400' Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 433 through 460 removed outlier: 3.824A pdb=" N VAL B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 537 through 554 Processing helix chain 'B' and resid 554 through 560 Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 585 through 599 Processing helix chain 'B' and resid 623 through 635 Processing helix chain 'B' and resid 642 through 649 removed outlier: 3.658A pdb=" N ALA B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.917A pdb=" N LEU C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.799A pdb=" N LEU C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 68 removed outlier: 4.051A pdb=" N GLU C 58 " --> pdb=" O PRO C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.595A pdb=" N VAL C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 171 through 182 removed outlier: 3.797A pdb=" N LEU C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.734A pdb=" N ILE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.526A pdb=" N SER C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 269 through 272 Processing helix chain 'C' and resid 281 through 284 removed outlier: 3.502A pdb=" N ILE C 284 " --> pdb=" O VAL C 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 289 through 302 removed outlier: 4.496A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 393 through 395 No H-bonds generated for 'chain 'C' and resid 393 through 395' Processing helix chain 'C' and resid 396 through 400 removed outlier: 4.047A pdb=" N TYR C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 400' Processing helix chain 'C' and resid 408 through 427 Processing helix chain 'C' and resid 433 through 460 removed outlier: 3.784A pdb=" N VAL C 451 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 464 Processing helix chain 'C' and resid 537 through 554 Processing helix chain 'C' and resid 554 through 560 Processing helix chain 'C' and resid 563 through 565 No H-bonds generated for 'chain 'C' and resid 563 through 565' Processing helix chain 'C' and resid 585 through 599 Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 643 through 649 removed outlier: 3.621A pdb=" N ALA C 647 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 667 through 677 removed outlier: 3.598A pdb=" N GLY C 677 " --> pdb=" O PHE C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 17 Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.515A pdb=" N ILE D 30 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.513A pdb=" N LEU D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 70 Processing helix chain 'D' and resid 78 through 88 Processing helix chain 'D' and resid 123 through 130 removed outlier: 3.519A pdb=" N VAL D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.623A pdb=" N LEU D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.710A pdb=" N ILE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.505A pdb=" N SER D 201 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 269 through 272 Processing helix chain 'D' and resid 281 through 284 Processing helix chain 'D' and resid 289 through 302 removed outlier: 4.431A pdb=" N GLN D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 395 through 400 removed outlier: 3.513A pdb=" N LYS D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 400 " --> pdb=" O SER D 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 395 through 400' Processing helix chain 'D' and resid 408 through 427 Processing helix chain 'D' and resid 433 through 460 removed outlier: 3.530A pdb=" N VAL D 437 " --> pdb=" O ASN D 433 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 451 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 464 Processing helix chain 'D' and resid 537 through 554 Processing helix chain 'D' and resid 554 through 560 Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 586 through 599 Processing helix chain 'D' and resid 623 through 635 Processing helix chain 'D' and resid 642 through 649 removed outlier: 3.685A pdb=" N ALA D 647 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 658 Processing helix chain 'D' and resid 667 through 677 Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 25 through 31 removed outlier: 3.636A pdb=" N LEU E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 49 removed outlier: 3.563A pdb=" N LEU E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.556A pdb=" N ALA E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN E 71 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 123 through 130 removed outlier: 3.562A pdb=" N VAL E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 171 through 181 removed outlier: 3.530A pdb=" N LEU E 175 " --> pdb=" O ASN E 171 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.762A pdb=" N ILE E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 216 through 218 No H-bonds generated for 'chain 'E' and resid 216 through 218' Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 269 through 272 Processing helix chain 'E' and resid 281 through 284 Processing helix chain 'E' and resid 289 through 302 removed outlier: 4.686A pdb=" N GLN E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 341 through 345 removed outlier: 3.509A pdb=" N ILE E 345 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 377 through 389 Processing helix chain 'E' and resid 395 through 400 removed outlier: 3.667A pdb=" N LYS E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR E 400 " --> pdb=" O SER E 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 395 through 400' Processing helix chain 'E' and resid 408 through 427 Processing helix chain 'E' and resid 433 through 460 removed outlier: 3.603A pdb=" N VAL E 437 " --> pdb=" O ASN E 433 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 451 " --> pdb=" O VAL E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 464 Processing helix chain 'E' and resid 537 through 554 Processing helix chain 'E' and resid 554 through 560 Processing helix chain 'E' and resid 563 through 565 No H-bonds generated for 'chain 'E' and resid 563 through 565' Processing helix chain 'E' and resid 585 through 599 Processing helix chain 'E' and resid 623 through 635 Processing helix chain 'E' and resid 642 through 652 removed outlier: 3.614A pdb=" N ALA E 647 " --> pdb=" O SER E 644 " (cutoff:3.500A) Proline residue: E 650 - end of helix Processing helix chain 'E' and resid 653 through 658 Processing helix chain 'E' and resid 667 through 677 removed outlier: 3.535A pdb=" N GLY E 677 " --> pdb=" O PHE E 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 17 removed outlier: 3.630A pdb=" N GLU F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 32 removed outlier: 4.111A pdb=" N GLU F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 49 removed outlier: 3.678A pdb=" N LEU F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 69 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 77 through 89 Processing helix chain 'F' and resid 123 through 130 removed outlier: 3.618A pdb=" N VAL F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.852A pdb=" N VAL F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY F 136 " --> pdb=" O LYS F 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 131 through 136' Processing helix chain 'F' and resid 171 through 181 removed outlier: 3.565A pdb=" N LEU F 175 " --> pdb=" O ASN F 171 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 203 through 215 Processing helix chain 'F' and resid 216 through 218 No H-bonds generated for 'chain 'F' and resid 216 through 218' Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 269 through 272 Processing helix chain 'F' and resid 281 through 284 Processing helix chain 'F' and resid 289 through 302 removed outlier: 4.608A pdb=" N GLN F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 334 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 377 through 389 Processing helix chain 'F' and resid 395 through 400 removed outlier: 3.548A pdb=" N LYS F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR F 400 " --> pdb=" O SER F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 400' Processing helix chain 'F' and resid 408 through 427 Processing helix chain 'F' and resid 433 through 460 removed outlier: 3.561A pdb=" N VAL F 437 " --> pdb=" O ASN F 433 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 451 " --> pdb=" O VAL F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 464 Processing helix chain 'F' and resid 537 through 554 Processing helix chain 'F' and resid 554 through 560 Processing helix chain 'F' and resid 563 through 565 No H-bonds generated for 'chain 'F' and resid 563 through 565' Processing helix chain 'F' and resid 585 through 599 Processing helix chain 'F' and resid 623 through 635 Processing helix chain 'F' and resid 642 through 649 removed outlier: 3.948A pdb=" N ALA F 647 " --> pdb=" O SER F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 658 Processing helix chain 'F' and resid 667 through 677 removed outlier: 3.547A pdb=" N GLY F 677 " --> pdb=" O PHE F 673 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 17 Processing helix chain 'G' and resid 25 through 32 removed outlier: 4.295A pdb=" N LEU G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 46 Processing helix chain 'G' and resid 53 through 71 removed outlier: 3.701A pdb=" N ASN G 71 " --> pdb=" O VAL G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.579A pdb=" N ARG G 86 " --> pdb=" O LYS G 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 128 removed outlier: 3.861A pdb=" N VAL G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 135 removed outlier: 6.486A pdb=" N LYS G 132 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 180 Processing helix chain 'G' and resid 183 through 195 Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.504A pdb=" N SER G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 219 Proline residue: G 216 - end of helix Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 269 through 272 Processing helix chain 'G' and resid 281 through 284 removed outlier: 3.543A pdb=" N ILE G 284 " --> pdb=" O VAL G 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 281 through 284' Processing helix chain 'G' and resid 289 through 302 removed outlier: 4.668A pdb=" N GLN G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 334 Processing helix chain 'G' and resid 341 through 345 removed outlier: 3.517A pdb=" N ILE G 345 " --> pdb=" O GLU G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 351 Processing helix chain 'G' and resid 360 through 362 No H-bonds generated for 'chain 'G' and resid 360 through 362' Processing helix chain 'G' and resid 366 through 370 Processing helix chain 'G' and resid 377 through 389 Processing helix chain 'G' and resid 395 through 400 removed outlier: 3.539A pdb=" N LYS G 399 " --> pdb=" O ASP G 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR G 400 " --> pdb=" O SER G 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 395 through 400' Processing helix chain 'G' and resid 408 through 427 Processing helix chain 'G' and resid 433 through 460 removed outlier: 3.559A pdb=" N VAL G 437 " --> pdb=" O ASN G 433 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL G 451 " --> pdb=" O VAL G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 464 Processing helix chain 'G' and resid 537 through 554 Processing helix chain 'G' and resid 554 through 560 Processing helix chain 'G' and resid 563 through 565 No H-bonds generated for 'chain 'G' and resid 563 through 565' Processing helix chain 'G' and resid 585 through 599 Processing helix chain 'G' and resid 623 through 635 Processing helix chain 'G' and resid 643 through 649 Processing helix chain 'G' and resid 653 through 658 Processing helix chain 'G' and resid 667 through 677 removed outlier: 3.550A pdb=" N GLY G 677 " --> pdb=" O PHE G 673 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 24 through 31 removed outlier: 3.659A pdb=" N LYS H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.659A pdb=" N LEU H 41 " --> pdb=" O PRO H 37 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET H 47 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 69 Processing helix chain 'H' and resid 78 through 89 removed outlier: 3.719A pdb=" N LYS H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 130 Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 175 through 181 Processing helix chain 'H' and resid 183 through 195 removed outlier: 3.729A pdb=" N ARG H 188 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE H 195 " --> pdb=" O LEU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 removed outlier: 3.658A pdb=" N LYS H 203 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing helix chain 'H' and resid 215 through 218 Processing helix chain 'H' and resid 235 through 241 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 280 through 284 Processing helix chain 'H' and resid 290 through 302 Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 341 through 345 Processing helix chain 'H' and resid 346 through 352 removed outlier: 3.729A pdb=" N ARG H 352 " --> pdb=" O ALA H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 376 No H-bonds generated for 'chain 'H' and resid 376 through 376' Processing helix chain 'H' and resid 379 through 389 Processing helix chain 'H' and resid 395 through 400 removed outlier: 3.831A pdb=" N LYS H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR H 400 " --> pdb=" O SER H 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 395 through 400' Processing helix chain 'H' and resid 408 through 427 Processing helix chain 'H' and resid 433 through 459 removed outlier: 3.774A pdb=" N VAL H 437 " --> pdb=" O ASN H 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 537 through 554 Processing helix chain 'H' and resid 554 through 560 Processing helix chain 'H' and resid 563 through 565 No H-bonds generated for 'chain 'H' and resid 563 through 565' Processing helix chain 'H' and resid 585 through 599 Processing helix chain 'H' and resid 623 through 634 Processing helix chain 'H' and resid 642 through 649 removed outlier: 4.363A pdb=" N ALA H 647 " --> pdb=" O SER H 644 " (cutoff:3.500A) Processing helix chain 'H' and resid 653 through 658 Processing helix chain 'H' and resid 667 through 677 Processing helix chain 'I' and resid 6 through 17 Processing helix chain 'I' and resid 24 through 31 removed outlier: 3.544A pdb=" N LYS I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE I 30 " --> pdb=" O LEU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 49 removed outlier: 3.761A pdb=" N TYR I 43 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 69 Processing helix chain 'I' and resid 77 through 89 Processing helix chain 'I' and resid 123 through 130 Processing helix chain 'I' and resid 131 through 135 Processing helix chain 'I' and resid 172 through 182 removed outlier: 3.671A pdb=" N PHE I 176 " --> pdb=" O MET I 172 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER I 177 " --> pdb=" O ASP I 173 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 194 Processing helix chain 'I' and resid 198 through 202 Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 216 through 218 No H-bonds generated for 'chain 'I' and resid 216 through 218' Processing helix chain 'I' and resid 236 through 241 Processing helix chain 'I' and resid 254 through 259 Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 280 through 284 Processing helix chain 'I' and resid 290 through 302 removed outlier: 3.533A pdb=" N ILE I 294 " --> pdb=" O ASP I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 334 Processing helix chain 'I' and resid 341 through 345 Processing helix chain 'I' and resid 346 through 352 removed outlier: 3.658A pdb=" N ARG I 352 " --> pdb=" O ALA I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 362 No H-bonds generated for 'chain 'I' and resid 360 through 362' Processing helix chain 'I' and resid 366 through 370 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 395 through 400 removed outlier: 3.882A pdb=" N LYS I 399 " --> pdb=" O ASP I 395 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR I 400 " --> pdb=" O SER I 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 395 through 400' Processing helix chain 'I' and resid 408 through 427 Processing helix chain 'I' and resid 433 through 460 removed outlier: 3.548A pdb=" N VAL I 437 " --> pdb=" O ASN I 433 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL I 451 " --> pdb=" O VAL I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 537 through 554 Processing helix chain 'I' and resid 554 through 560 Processing helix chain 'I' and resid 563 through 565 No H-bonds generated for 'chain 'I' and resid 563 through 565' Processing helix chain 'I' and resid 585 through 599 Processing helix chain 'I' and resid 623 through 632 Processing helix chain 'I' and resid 642 through 652 removed outlier: 4.210A pdb=" N ALA I 647 " --> pdb=" O SER I 644 " (cutoff:3.500A) Proline residue: I 650 - end of helix Processing helix chain 'I' and resid 653 through 659 Processing helix chain 'I' and resid 667 through 677 Processing helix chain 'J' and resid 8 through 17 Processing helix chain 'J' and resid 23 through 30 removed outlier: 3.580A pdb=" N THR J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'J' and resid 53 through 71 removed outlier: 3.521A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.579A pdb=" N VAL J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 171 through 180 removed outlier: 3.968A pdb=" N LEU J 175 " --> pdb=" O ASN J 171 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA J 180 " --> pdb=" O PHE J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 194 Processing helix chain 'J' and resid 198 through 202 Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 216 through 218 No H-bonds generated for 'chain 'J' and resid 216 through 218' Processing helix chain 'J' and resid 236 through 241 Processing helix chain 'J' and resid 254 through 259 Processing helix chain 'J' and resid 269 through 272 Processing helix chain 'J' and resid 280 through 284 Processing helix chain 'J' and resid 290 through 302 Processing helix chain 'J' and resid 326 through 334 Processing helix chain 'J' and resid 341 through 345 Processing helix chain 'J' and resid 346 through 351 Processing helix chain 'J' and resid 366 through 370 Processing helix chain 'J' and resid 377 through 390 removed outlier: 3.751A pdb=" N LYS J 390 " --> pdb=" O ARG J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 400 removed outlier: 4.025A pdb=" N TYR J 400 " --> pdb=" O SER J 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 396 through 400' Processing helix chain 'J' and resid 408 through 427 Processing helix chain 'J' and resid 433 through 457 removed outlier: 3.766A pdb=" N VAL J 437 " --> pdb=" O ASN J 433 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL J 451 " --> pdb=" O VAL J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 554 Processing helix chain 'J' and resid 554 through 560 Processing helix chain 'J' and resid 563 through 565 No H-bonds generated for 'chain 'J' and resid 563 through 565' Processing helix chain 'J' and resid 585 through 599 Processing helix chain 'J' and resid 623 through 634 Processing helix chain 'J' and resid 644 through 649 removed outlier: 4.075A pdb=" N ALA J 647 " --> pdb=" O SER J 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 653 through 659 removed outlier: 3.640A pdb=" N LYS J 659 " --> pdb=" O GLU J 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 677 Processing helix chain 'K' and resid 8 through 17 Processing helix chain 'K' and resid 24 through 31 removed outlier: 3.510A pdb=" N ILE K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 45 removed outlier: 3.866A pdb=" N LEU K 41 " --> pdb=" O PRO K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 69 Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 77 through 89 removed outlier: 3.599A pdb=" N LYS K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU K 87 " --> pdb=" O SER K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 131 removed outlier: 3.683A pdb=" N GLU K 129 " --> pdb=" O GLY K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 181 removed outlier: 3.732A pdb=" N PHE K 176 " --> pdb=" O MET K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 195 removed outlier: 3.652A pdb=" N ILE K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 215 Processing helix chain 'K' and resid 216 through 218 No H-bonds generated for 'chain 'K' and resid 216 through 218' Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 269 through 272 Processing helix chain 'K' and resid 280 through 284 Processing helix chain 'K' and resid 290 through 302 Processing helix chain 'K' and resid 327 through 333 removed outlier: 3.535A pdb=" N VAL K 331 " --> pdb=" O VAL K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 345 Processing helix chain 'K' and resid 346 through 352 removed outlier: 4.261A pdb=" N ARG K 352 " --> pdb=" O ALA K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 370 Processing helix chain 'K' and resid 377 through 390 removed outlier: 3.584A pdb=" N LYS K 390 " --> pdb=" O ARG K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 400 removed outlier: 4.232A pdb=" N TYR K 400 " --> pdb=" O SER K 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 396 through 400' Processing helix chain 'K' and resid 408 through 427 Processing helix chain 'K' and resid 433 through 459 removed outlier: 3.621A pdb=" N VAL K 437 " --> pdb=" O ASN K 433 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL K 451 " --> pdb=" O VAL K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 537 through 554 Processing helix chain 'K' and resid 554 through 560 Processing helix chain 'K' and resid 563 through 565 No H-bonds generated for 'chain 'K' and resid 563 through 565' Processing helix chain 'K' and resid 585 through 599 Processing helix chain 'K' and resid 623 through 634 Processing helix chain 'K' and resid 642 through 649 removed outlier: 4.154A pdb=" N ALA K 647 " --> pdb=" O SER K 644 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 659 Processing helix chain 'K' and resid 667 through 677 Processing helix chain 'L' and resid 10 through 16 Processing helix chain 'L' and resid 24 through 29 removed outlier: 3.925A pdb=" N LYS L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 49 removed outlier: 3.668A pdb=" N LEU L 41 " --> pdb=" O PRO L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 69 Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 77 through 89 removed outlier: 3.537A pdb=" N VAL L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 131 through 135 removed outlier: 3.563A pdb=" N VAL L 135 " --> pdb=" O LYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 182 removed outlier: 3.716A pdb=" N LEU L 175 " --> pdb=" O ASN L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 195 Processing helix chain 'L' and resid 203 through 215 Processing helix chain 'L' and resid 216 through 218 No H-bonds generated for 'chain 'L' and resid 216 through 218' Processing helix chain 'L' and resid 235 through 241 Processing helix chain 'L' and resid 254 through 259 Processing helix chain 'L' and resid 269 through 272 Processing helix chain 'L' and resid 280 through 284 Processing helix chain 'L' and resid 289 through 302 removed outlier: 3.857A pdb=" N GLN L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 334 Processing helix chain 'L' and resid 341 through 345 removed outlier: 3.605A pdb=" N ILE L 345 " --> pdb=" O GLU L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 351 Processing helix chain 'L' and resid 366 through 370 Processing helix chain 'L' and resid 377 through 389 removed outlier: 3.900A pdb=" N GLU L 387 " --> pdb=" O GLU L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 400 removed outlier: 4.127A pdb=" N TYR L 400 " --> pdb=" O SER L 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 396 through 400' Processing helix chain 'L' and resid 408 through 427 Processing helix chain 'L' and resid 434 through 460 removed outlier: 3.528A pdb=" N VAL L 451 " --> pdb=" O VAL L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 464 Processing helix chain 'L' and resid 537 through 554 Processing helix chain 'L' and resid 554 through 560 Processing helix chain 'L' and resid 563 through 565 No H-bonds generated for 'chain 'L' and resid 563 through 565' Processing helix chain 'L' and resid 585 through 599 Processing helix chain 'L' and resid 623 through 634 Processing helix chain 'L' and resid 642 through 649 removed outlier: 4.285A pdb=" N ALA L 647 " --> pdb=" O SER L 644 " (cutoff:3.500A) Processing helix chain 'L' and resid 653 through 658 Processing helix chain 'L' and resid 667 through 677 Processing helix chain 'M' and resid 11 through 17 removed outlier: 3.803A pdb=" N HIS M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 32 removed outlier: 4.557A pdb=" N GLU M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 49 Processing helix chain 'M' and resid 53 through 69 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 123 through 130 Processing helix chain 'M' and resid 131 through 134 Processing helix chain 'M' and resid 171 through 182 removed outlier: 4.072A pdb=" N LEU M 175 " --> pdb=" O ASN M 171 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE M 176 " --> pdb=" O MET M 172 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 196 Processing helix chain 'M' and resid 198 through 202 Processing helix chain 'M' and resid 203 through 215 Processing helix chain 'M' and resid 216 through 218 No H-bonds generated for 'chain 'M' and resid 216 through 218' Processing helix chain 'M' and resid 233 through 241 removed outlier: 3.853A pdb=" N ILE M 237 " --> pdb=" O GLY M 233 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR M 238 " --> pdb=" O LYS M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 259 Processing helix chain 'M' and resid 269 through 272 Processing helix chain 'M' and resid 290 through 301 Processing helix chain 'M' and resid 326 through 334 Processing helix chain 'M' and resid 349 through 353 removed outlier: 3.686A pdb=" N PHE M 353 " --> pdb=" O PHE M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 370 Processing helix chain 'M' and resid 377 through 390 removed outlier: 4.231A pdb=" N LYS M 390 " --> pdb=" O ARG M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 408 through 427 Processing helix chain 'M' and resid 433 through 460 removed outlier: 3.693A pdb=" N CYS M 440 " --> pdb=" O ASP M 436 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR M 443 " --> pdb=" O GLN M 439 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL M 451 " --> pdb=" O VAL M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 464 removed outlier: 4.027A pdb=" N TYR M 464 " --> pdb=" O MET M 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 461 through 464' Processing helix chain 'M' and resid 537 through 554 Processing helix chain 'M' and resid 554 through 560 Processing helix chain 'M' and resid 563 through 565 No H-bonds generated for 'chain 'M' and resid 563 through 565' Processing helix chain 'M' and resid 585 through 599 Processing helix chain 'M' and resid 623 through 635 Processing helix chain 'M' and resid 643 through 647 removed outlier: 4.283A pdb=" N ALA M 647 " --> pdb=" O MET M 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 643 through 647' Processing helix chain 'M' and resid 653 through 659 removed outlier: 3.602A pdb=" N LYS M 659 " --> pdb=" O GLU M 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 667 through 677 Processing helix chain 'N' and resid 10 through 17 Processing helix chain 'N' and resid 25 through 31 removed outlier: 3.575A pdb=" N LEU N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 49 removed outlier: 3.669A pdb=" N LEU N 41 " --> pdb=" O PRO N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 72 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 77 through 89 removed outlier: 3.815A pdb=" N ARG N 86 " --> pdb=" O LYS N 82 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG N 88 " --> pdb=" O LEU N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 130 Processing helix chain 'N' and resid 131 through 135 Processing helix chain 'N' and resid 171 through 182 removed outlier: 3.642A pdb=" N LEU N 175 " --> pdb=" O ASN N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 194 Processing helix chain 'N' and resid 198 through 202 Processing helix chain 'N' and resid 203 through 215 Processing helix chain 'N' and resid 216 through 218 No H-bonds generated for 'chain 'N' and resid 216 through 218' Processing helix chain 'N' and resid 233 through 240 removed outlier: 3.871A pdb=" N ILE N 237 " --> pdb=" O GLY N 233 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR N 238 " --> pdb=" O LYS N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 259 Processing helix chain 'N' and resid 269 through 272 Processing helix chain 'N' and resid 280 through 284 Processing helix chain 'N' and resid 290 through 302 Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 341 through 345 Processing helix chain 'N' and resid 346 through 352 removed outlier: 3.813A pdb=" N ARG N 352 " --> pdb=" O ALA N 348 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 370 Processing helix chain 'N' and resid 377 through 390 removed outlier: 4.002A pdb=" N LYS N 390 " --> pdb=" O ARG N 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 395 through 400 removed outlier: 4.094A pdb=" N LYS N 399 " --> pdb=" O ASP N 395 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR N 400 " --> pdb=" O SER N 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 395 through 400' Processing helix chain 'N' and resid 408 through 427 Processing helix chain 'N' and resid 433 through 460 removed outlier: 3.603A pdb=" N VAL N 437 " --> pdb=" O ASN N 433 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL N 451 " --> pdb=" O VAL N 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 464 removed outlier: 4.082A pdb=" N TYR N 464 " --> pdb=" O MET N 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 461 through 464' Processing helix chain 'N' and resid 537 through 554 Processing helix chain 'N' and resid 554 through 560 removed outlier: 3.730A pdb=" N ILE N 558 " --> pdb=" O ASN N 554 " (cutoff:3.500A) Processing helix chain 'N' and resid 563 through 565 No H-bonds generated for 'chain 'N' and resid 563 through 565' Processing helix chain 'N' and resid 585 through 599 Processing helix chain 'N' and resid 623 through 635 Processing helix chain 'N' and resid 644 through 649 removed outlier: 4.024A pdb=" N ALA N 647 " --> pdb=" O SER N 644 " (cutoff:3.500A) Processing helix chain 'N' and resid 653 through 659 removed outlier: 3.591A pdb=" N LYS N 659 " --> pdb=" O GLU N 655 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 102 removed outlier: 4.291A pdb=" N TYR A 108 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU A 121 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU A 161 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 143 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 162 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 141 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TRP A 139 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.854A pdb=" N CYS A 225 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA7, first strand: chain 'A' and resid 501 through 507 removed outlier: 6.372A pdb=" N ALA A 530 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 573 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER A 532 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLU A 575 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 608 removed outlier: 6.685A pdb=" N VAL A 607 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 611 through 612 removed outlier: 3.835A pdb=" N ASP A 611 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 102 removed outlier: 4.351A pdb=" N TYR B 108 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLU B 121 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N LEU B 161 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 143 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 162 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 141 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP B 139 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.801A pdb=" N CYS B 225 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB4, first strand: chain 'B' and resid 303 through 306 Processing sheet with id=AB5, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AB6, first strand: chain 'B' and resid 529 through 532 removed outlier: 6.361A pdb=" N ALA B 530 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL B 573 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER B 532 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLU B 575 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N PHE B 501 " --> pdb=" O MET B 606 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N VAL B 608 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N TYR B 503 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 607 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 611 through 612 removed outlier: 3.861A pdb=" N ASP B 611 " --> pdb=" O THR B 619 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 90 through 102 removed outlier: 4.329A pdb=" N TYR C 108 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU C 121 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LEU C 161 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR C 143 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 162 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 141 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TRP C 139 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 245 through 248 removed outlier: 6.758A pdb=" N CYS C 225 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 260 through 261 Processing sheet with id=AC3, first strand: chain 'C' and resid 303 through 306 Processing sheet with id=AC4, first strand: chain 'C' and resid 401 through 403 Processing sheet with id=AC5, first strand: chain 'C' and resid 501 through 507 removed outlier: 6.285A pdb=" N ALA C 530 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL C 573 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER C 532 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLU C 575 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 606 through 608 removed outlier: 6.611A pdb=" N VAL C 607 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 611 through 612 removed outlier: 3.851A pdb=" N ASP C 611 " --> pdb=" O THR C 619 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AC9, first strand: chain 'D' and resid 90 through 102 removed outlier: 4.570A pdb=" N TYR D 108 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLU D 121 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LEU D 161 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR D 143 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU D 162 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE D 141 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N TRP D 139 " --> pdb=" O PRO D 164 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR D 91 " --> pdb=" O LEU D 144 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 245 through 246 removed outlier: 6.675A pdb=" N ILE D 246 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP D 279 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS D 225 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.608A pdb=" N ARG D 266 " --> pdb=" O ASN D 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 303 through 306 Processing sheet with id=AD4, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AD5, first strand: chain 'D' and resid 529 through 532 removed outlier: 6.372A pdb=" N ALA D 530 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL D 573 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER D 532 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLU D 575 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N PHE D 501 " --> pdb=" O MET D 606 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL D 608 " --> pdb=" O PHE D 501 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR D 503 " --> pdb=" O VAL D 608 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 611 through 612 removed outlier: 3.735A pdb=" N ASP D 611 " --> pdb=" O THR D 619 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AD8, first strand: chain 'E' and resid 90 through 102 removed outlier: 4.337A pdb=" N TYR E 108 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU E 121 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N LEU E 161 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR E 143 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU E 162 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE E 141 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TRP E 139 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 245 through 248 removed outlier: 6.720A pdb=" N CYS E 225 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AE2, first strand: chain 'E' and resid 303 through 306 Processing sheet with id=AE3, first strand: chain 'E' and resid 401 through 403 Processing sheet with id=AE4, first strand: chain 'E' and resid 529 through 532 removed outlier: 10.101A pdb=" N PHE E 501 " --> pdb=" O MET E 606 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N VAL E 608 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR E 503 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL E 607 " --> pdb=" O ALA E 640 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 611 through 612 removed outlier: 3.841A pdb=" N ASP E 611 " --> pdb=" O THR E 619 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AE7, first strand: chain 'F' and resid 90 through 102 removed outlier: 4.304A pdb=" N TYR F 108 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU F 121 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU F 161 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR F 143 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU F 162 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE F 141 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N TRP F 139 " --> pdb=" O PRO F 164 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 245 through 248 removed outlier: 3.643A pdb=" N ASP F 279 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS F 225 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 260 through 261 Processing sheet with id=AF1, first strand: chain 'F' and resid 303 through 306 Processing sheet with id=AF2, first strand: chain 'F' and resid 401 through 403 removed outlier: 3.697A pdb=" N HIS F 479 " --> pdb=" O TYR F 470 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 501 through 507 removed outlier: 6.455A pdb=" N ALA F 530 " --> pdb=" O LEU F 571 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL F 573 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER F 532 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLU F 575 " --> pdb=" O SER F 532 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 606 through 608 removed outlier: 6.475A pdb=" N VAL F 607 " --> pdb=" O ALA F 640 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 611 through 612 removed outlier: 3.972A pdb=" N ASP F 611 " --> pdb=" O THR F 619 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AF7, first strand: chain 'G' and resid 90 through 101 removed outlier: 4.418A pdb=" N TYR G 108 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 122 " --> pdb=" O TYR G 108 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU G 121 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N LEU G 161 " --> pdb=" O GLU G 121 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL G 159 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER G 145 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU G 161 " --> pdb=" O THR G 143 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR G 91 " --> pdb=" O LEU G 144 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 245 through 248 removed outlier: 6.666A pdb=" N ILE G 246 " --> pdb=" O ALA G 277 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP G 279 " --> pdb=" O ILE G 246 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL G 248 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS G 225 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 260 through 261 Processing sheet with id=AG1, first strand: chain 'G' and resid 303 through 306 Processing sheet with id=AG2, first strand: chain 'G' and resid 401 through 403 Processing sheet with id=AG3, first strand: chain 'G' and resid 502 through 507 removed outlier: 6.329A pdb=" N ALA G 530 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL G 573 " --> pdb=" O ALA G 530 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER G 532 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLU G 575 " --> pdb=" O SER G 532 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 606 through 608 removed outlier: 6.623A pdb=" N VAL G 607 " --> pdb=" O ALA G 640 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL G 639 " --> pdb=" O GLN G 661 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'G' and resid 611 through 612 removed outlier: 3.879A pdb=" N ASP G 611 " --> pdb=" O THR G 619 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 116 through 120 removed outlier: 5.196A pdb=" N LYS H 118 " --> pdb=" O PHE H 112 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE H 112 " --> pdb=" O LYS H 118 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP H 95 " --> pdb=" O VAL H 140 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 224 through 228 Processing sheet with id=AG8, first strand: chain 'H' and resid 252 through 253 removed outlier: 3.815A pdb=" N THR H 253 " --> pdb=" O SER H 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'H' and resid 260 through 261 Processing sheet with id=AH1, first strand: chain 'H' and resid 303 through 306 Processing sheet with id=AH2, first strand: chain 'H' and resid 401 through 403 Processing sheet with id=AH3, first strand: chain 'H' and resid 529 through 532 removed outlier: 6.488A pdb=" N ALA H 530 " --> pdb=" O LEU H 571 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL H 573 " --> pdb=" O ALA H 530 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER H 532 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N GLU H 575 " --> pdb=" O SER H 532 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N VAL H 608 " --> pdb=" O PHE H 501 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR H 503 " --> pdb=" O VAL H 608 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 611 through 612 removed outlier: 4.165A pdb=" N ASP H 611 " --> pdb=" O THR H 619 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 638 through 639 Processing sheet with id=AH6, first strand: chain 'I' and resid 90 through 102 removed outlier: 4.230A pdb=" N TYR I 108 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR I 143 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU I 162 " --> pdb=" O ILE I 141 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE I 141 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TRP I 139 " --> pdb=" O PRO I 164 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL I 97 " --> pdb=" O ILE I 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 245 through 248 removed outlier: 3.670A pdb=" N LEU I 227 " --> pdb=" O ILE I 357 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.558A pdb=" N ARG I 266 " --> pdb=" O ASN I 261 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 303 through 306 Processing sheet with id=AI1, first strand: chain 'I' and resid 401 through 403 Processing sheet with id=AI2, first strand: chain 'I' and resid 501 through 507 removed outlier: 6.489A pdb=" N ALA I 530 " --> pdb=" O LEU I 571 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL I 573 " --> pdb=" O ALA I 530 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER I 532 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLU I 575 " --> pdb=" O SER I 532 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 606 through 608 removed outlier: 7.115A pdb=" N VAL I 607 " --> pdb=" O ALA I 640 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 611 through 612 removed outlier: 4.111A pdb=" N ASP I 611 " --> pdb=" O THR I 619 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 90 through 102 removed outlier: 4.400A pdb=" N TYR J 108 " --> pdb=" O ILE J 122 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR J 143 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU J 162 " --> pdb=" O ILE J 141 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE J 141 " --> pdb=" O LEU J 162 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 245 through 248 removed outlier: 6.540A pdb=" N ILE J 246 " --> pdb=" O ALA J 277 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL J 276 " --> pdb=" O VAL J 318 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL J 320 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE J 278 " --> pdb=" O VAL J 320 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ASN J 322 " --> pdb=" O PHE J 278 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 227 " --> pdb=" O ILE J 357 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 252 through 253 Processing sheet with id=AI8, first strand: chain 'J' and resid 260 through 261 removed outlier: 3.843A pdb=" N ARG J 266 " --> pdb=" O ASN J 261 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 303 through 306 Processing sheet with id=AJ1, first strand: chain 'J' and resid 401 through 403 Processing sheet with id=AJ2, first strand: chain 'J' and resid 501 through 507 removed outlier: 6.498A pdb=" N ALA J 530 " --> pdb=" O LEU J 571 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL J 573 " --> pdb=" O ALA J 530 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER J 532 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N GLU J 575 " --> pdb=" O SER J 532 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'J' and resid 611 through 612 removed outlier: 4.160A pdb=" N ASP J 611 " --> pdb=" O THR J 619 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 638 through 642 removed outlier: 6.770A pdb=" N VAL J 639 " --> pdb=" O SER J 663 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR J 665 " --> pdb=" O VAL J 639 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU J 641 " --> pdb=" O TYR J 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AJ6, first strand: chain 'K' and resid 101 through 102 removed outlier: 3.800A pdb=" N ASN K 102 " --> pdb=" O LYS K 107 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS K 107 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR K 108 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLU K 121 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU K 161 " --> pdb=" O GLU K 121 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR K 143 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU K 162 " --> pdb=" O ILE K 141 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE K 141 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TRP K 139 " --> pdb=" O PRO K 164 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 245 through 248 Processing sheet with id=AJ8, first strand: chain 'K' and resid 260 through 261 removed outlier: 3.650A pdb=" N ARG K 266 " --> pdb=" O ASN K 261 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'K' and resid 303 through 306 Processing sheet with id=AK1, first strand: chain 'K' and resid 401 through 403 Processing sheet with id=AK2, first strand: chain 'K' and resid 529 through 532 removed outlier: 6.473A pdb=" N ALA K 530 " --> pdb=" O LEU K 571 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL K 573 " --> pdb=" O ALA K 530 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER K 532 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU K 575 " --> pdb=" O SER K 532 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR K 503 " --> pdb=" O VAL K 608 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL K 607 " --> pdb=" O ALA K 640 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL K 639 " --> pdb=" O GLN K 661 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'K' and resid 611 through 612 removed outlier: 4.200A pdb=" N ASP K 611 " --> pdb=" O THR K 619 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 90 through 100 removed outlier: 6.662A pdb=" N GLU L 121 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU L 161 " --> pdb=" O GLU L 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR L 143 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU L 162 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE L 141 " --> pdb=" O LEU L 162 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'L' and resid 245 through 249 removed outlier: 5.839A pdb=" N ILE L 246 " --> pdb=" O ALA L 277 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP L 279 " --> pdb=" O ILE L 246 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL L 248 " --> pdb=" O ASP L 279 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU L 227 " --> pdb=" O ILE L 357 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 260 through 261 Processing sheet with id=AK7, first strand: chain 'L' and resid 303 through 306 Processing sheet with id=AK8, first strand: chain 'L' and resid 401 through 403 Processing sheet with id=AK9, first strand: chain 'L' and resid 529 through 532 removed outlier: 6.420A pdb=" N ALA L 530 " --> pdb=" O LEU L 571 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL L 573 " --> pdb=" O ALA L 530 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER L 532 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLU L 575 " --> pdb=" O SER L 532 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N PHE L 501 " --> pdb=" O MET L 606 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N VAL L 608 " --> pdb=" O PHE L 501 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR L 503 " --> pdb=" O VAL L 608 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL L 607 " --> pdb=" O ALA L 640 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL L 639 " --> pdb=" O SER L 663 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'L' and resid 611 through 612 removed outlier: 4.279A pdb=" N ASP L 611 " --> pdb=" O THR L 619 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'M' and resid 21 through 23 Processing sheet with id=AL3, first strand: chain 'M' and resid 90 through 102 removed outlier: 4.288A pdb=" N TYR M 108 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU M 121 " --> pdb=" O VAL M 159 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU M 161 " --> pdb=" O GLU M 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR M 143 " --> pdb=" O SER M 160 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU M 162 " --> pdb=" O ILE M 141 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE M 141 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.574A pdb=" N VAL M 276 " --> pdb=" O VAL M 318 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL M 320 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE M 278 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASN M 322 " --> pdb=" O PHE M 278 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU M 227 " --> pdb=" O ILE M 357 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'M' and resid 260 through 261 Processing sheet with id=AL6, first strand: chain 'M' and resid 303 through 305 Processing sheet with id=AL7, first strand: chain 'M' and resid 469 through 470 Processing sheet with id=AL8, first strand: chain 'M' and resid 529 through 532 removed outlier: 6.428A pdb=" N ALA M 530 " --> pdb=" O LEU M 571 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL M 573 " --> pdb=" O ALA M 530 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER M 532 " --> pdb=" O VAL M 573 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLU M 575 " --> pdb=" O SER M 532 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N PHE M 501 " --> pdb=" O MET M 606 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N VAL M 608 " --> pdb=" O PHE M 501 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR M 503 " --> pdb=" O VAL M 608 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL M 607 " --> pdb=" O ALA M 640 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'M' and resid 611 through 612 removed outlier: 4.139A pdb=" N ASP M 611 " --> pdb=" O THR M 619 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AM2, first strand: chain 'N' and resid 90 through 102 removed outlier: 4.205A pdb=" N TYR N 108 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU N 121 " --> pdb=" O VAL N 159 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEU N 161 " --> pdb=" O GLU N 121 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR N 143 " --> pdb=" O SER N 160 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU N 162 " --> pdb=" O ILE N 141 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE N 141 " --> pdb=" O LEU N 162 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TRP N 139 " --> pdb=" O PRO N 164 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'N' and resid 245 through 248 removed outlier: 3.988A pdb=" N LEU N 227 " --> pdb=" O ILE N 357 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'N' and resid 260 through 261 Processing sheet with id=AM5, first strand: chain 'N' and resid 303 through 306 Processing sheet with id=AM6, first strand: chain 'N' and resid 401 through 403 removed outlier: 4.490A pdb=" N PHE N 468 " --> pdb=" O VAL N 481 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'N' and resid 501 through 502 removed outlier: 3.505A pdb=" N LEU N 502 " --> pdb=" O LEU N 518 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA N 530 " --> pdb=" O LEU N 571 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL N 573 " --> pdb=" O ALA N 530 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER N 532 " --> pdb=" O VAL N 573 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'N' and resid 606 through 608 removed outlier: 6.440A pdb=" N VAL N 607 " --> pdb=" O ALA N 640 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'N' and resid 611 through 612 removed outlier: 4.041A pdb=" N ASP N 611 " --> pdb=" O THR N 619 " (cutoff:3.500A) 3383 hydrogen bonds defined for protein. 9384 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: 37.15 Time building geometry restraints manager: 23.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23804 1.34 - 1.46: 14461 1.46 - 1.58: 35927 1.58 - 1.70: 2 1.70 - 1.82: 658 Bond restraints: 74852 Sorted by residual: bond pdb=" CA ILE B 649 " pdb=" CB ILE B 649 " ideal model delta sigma weight residual 1.539 1.522 0.017 5.40e-03 3.43e+04 1.03e+01 bond pdb=" CA TYR B 72 " pdb=" CB TYR B 72 " ideal model delta sigma weight residual 1.529 1.486 0.043 1.34e-02 5.57e+03 1.01e+01 bond pdb=" CB PRO M 168 " pdb=" CG PRO M 168 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.76e+00 bond pdb=" CB PRO F 339 " pdb=" CG PRO F 339 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.22e+00 bond pdb=" C VAL H 215 " pdb=" N PRO H 216 " ideal model delta sigma weight residual 1.333 1.362 -0.029 1.44e-02 4.82e+03 4.00e+00 ... (remaining 74847 not shown) Histogram of bond angle deviations from ideal: 94.67 - 102.55: 353 102.55 - 110.43: 17901 110.43 - 118.30: 38628 118.30 - 126.18: 43246 126.18 - 134.06: 872 Bond angle restraints: 101000 Sorted by residual: angle pdb=" CA PRO M 168 " pdb=" N PRO M 168 " pdb=" CD PRO M 168 " ideal model delta sigma weight residual 112.00 101.71 10.29 1.40e+00 5.10e-01 5.40e+01 angle pdb=" N ILE N 165 " pdb=" CA ILE N 165 " pdb=" C ILE N 165 " ideal model delta sigma weight residual 113.47 106.75 6.72 1.01e+00 9.80e-01 4.43e+01 angle pdb=" CA PRO F 339 " pdb=" N PRO F 339 " pdb=" CD PRO F 339 " ideal model delta sigma weight residual 112.00 103.26 8.74 1.40e+00 5.10e-01 3.90e+01 angle pdb=" C GLN A 166 " pdb=" N MET A 167 " pdb=" CA MET A 167 " ideal model delta sigma weight residual 120.67 112.32 8.35 1.34e+00 5.57e-01 3.89e+01 angle pdb=" N VAL E 466 " pdb=" CA VAL E 466 " pdb=" C VAL E 466 " ideal model delta sigma weight residual 113.10 107.70 5.40 9.70e-01 1.06e+00 3.10e+01 ... (remaining 100995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 41519 17.87 - 35.74: 2951 35.74 - 53.61: 474 53.61 - 71.48: 118 71.48 - 89.35: 55 Dihedral angle restraints: 45117 sinusoidal: 18244 harmonic: 26873 Sorted by residual: dihedral pdb=" CA TYR D 72 " pdb=" C TYR D 72 " pdb=" N VAL D 73 " pdb=" CA VAL D 73 " ideal model delta harmonic sigma weight residual -180.00 -148.78 -31.22 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ILE J 492 " pdb=" C ILE J 492 " pdb=" N PRO J 493 " pdb=" CA PRO J 493 " ideal model delta harmonic sigma weight residual 180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASN G 169 " pdb=" C ASN G 169 " pdb=" N MET G 170 " pdb=" CA MET G 170 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 45114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 9309 0.059 - 0.117: 1644 0.117 - 0.176: 113 0.176 - 0.234: 4 0.234 - 0.293: 2 Chirality restraints: 11072 Sorted by residual: chirality pdb=" CB VAL F 73 " pdb=" CA VAL F 73 " pdb=" CG1 VAL F 73 " pdb=" CG2 VAL F 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE E 345 " pdb=" CA ILE E 345 " pdb=" CG1 ILE E 345 " pdb=" CG2 ILE E 345 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE G 345 " pdb=" CA ILE G 345 " pdb=" CG1 ILE G 345 " pdb=" CG2 ILE G 345 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 11069 not shown) Planarity restraints: 13037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET M 167 " 0.113 5.00e-02 4.00e+02 1.62e-01 4.19e+01 pdb=" N PRO M 168 " -0.280 5.00e-02 4.00e+02 pdb=" CA PRO M 168 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO M 168 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 53 " -0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO B 54 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 667 " -0.058 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO L 668 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO L 668 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO L 668 " -0.047 5.00e-02 4.00e+02 ... (remaining 13034 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 682 2.58 - 3.16: 62512 3.16 - 3.74: 115294 3.74 - 4.32: 160541 4.32 - 4.90: 263154 Nonbonded interactions: 602183 Sorted by model distance: nonbonded pdb=" OH TYR D 516 " pdb=" O GLY D 580 " model vdw 1.997 2.440 nonbonded pdb=" OH TYR B 516 " pdb=" O GLY B 580 " model vdw 2.032 2.440 nonbonded pdb=" OH TYR E 516 " pdb=" O GLY E 580 " model vdw 2.033 2.440 nonbonded pdb=" OH TYR C 516 " pdb=" O GLY C 580 " model vdw 2.055 2.440 nonbonded pdb=" OH TYR G 516 " pdb=" O GLY G 580 " model vdw 2.062 2.440 ... (remaining 602178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'B' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'C' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'D' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'E' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'F' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'G' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'H' and (resid 10 through 485 or resid 496 through 677)) selection = (chain 'I' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'J' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'K' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'L' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'M' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) selection = (chain 'N' and (resid 10 through 376 or resid 378 through 485 or resid 496 throu \ gh 677)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 14.560 Check model and map are aligned: 0.810 Set scattering table: 0.520 Process input model: 156.960 Find NCS groups from input model: 5.220 Set up NCS constraints: 0.250 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.004 0.120 74852 Z= 0.268 Angle : 0.731 11.425 101000 Z= 0.430 Chirality : 0.043 0.293 11072 Planarity : 0.005 0.162 13037 Dihedral : 13.020 89.348 27893 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.70 % Favored : 95.01 % Rotamer: Outliers : 0.01 % Allowed : 0.21 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.09), residues: 9270 helix: 0.86 (0.09), residues: 3619 sheet: 0.47 (0.14), residues: 1366 loop : -0.29 (0.10), residues: 4285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 535 HIS 0.010 0.001 HIS M 572 PHE 0.050 0.002 PHE D 593 TYR 0.032 0.002 TYR D 72 ARG 0.010 0.001 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 6.507 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: B 606 MET cc_start: 0.8093 (tpt) cc_final: 0.7818 (tpt) REVERT: B 612 MET cc_start: 0.6475 (ppp) cc_final: 0.6005 (ptt) REVERT: C 606 MET cc_start: 0.8518 (ptt) cc_final: 0.7616 (tmm) REVERT: D 299 MET cc_start: 0.7742 (mtm) cc_final: 0.7531 (mtm) REVERT: D 311 MET cc_start: 0.7339 (mpp) cc_final: 0.6868 (mtt) REVERT: D 606 MET cc_start: 0.8633 (ttm) cc_final: 0.7805 (tpp) REVERT: D 612 MET cc_start: 0.7311 (ppp) cc_final: 0.6823 (ptt) REVERT: E 606 MET cc_start: 0.8740 (ttm) cc_final: 0.7916 (tpp) REVERT: F 464 TYR cc_start: 0.5789 (p90) cc_final: 0.5488 (p90) REVERT: F 606 MET cc_start: 0.9320 (ptt) cc_final: 0.8814 (ttm) REVERT: G 606 MET cc_start: 0.8275 (ptm) cc_final: 0.7561 (tmm) REVERT: H 167 MET cc_start: 0.9228 (ppp) cc_final: 0.8931 (ppp) REVERT: H 299 MET cc_start: 0.8276 (mpp) cc_final: 0.7485 (mmm) REVERT: H 423 MET cc_start: 0.9185 (tpp) cc_final: 0.8851 (tpp) REVERT: H 512 MET cc_start: 0.8894 (ttm) cc_final: 0.8634 (tpp) REVERT: I 295 MET cc_start: 0.9299 (mtm) cc_final: 0.8586 (mpp) REVERT: I 299 MET cc_start: 0.7747 (mpp) cc_final: 0.7421 (mmm) REVERT: I 344 MET cc_start: 0.6821 (mpp) cc_final: 0.6601 (mpp) REVERT: I 423 MET cc_start: 0.9207 (tpp) cc_final: 0.8893 (tpp) REVERT: I 461 MET cc_start: 0.8265 (tpt) cc_final: 0.8041 (tpt) REVERT: I 565 MET cc_start: 0.6590 (mmt) cc_final: 0.6046 (mpp) REVERT: I 606 MET cc_start: 0.5910 (tpt) cc_final: 0.5659 (tpt) REVERT: I 612 MET cc_start: 0.3249 (ptt) cc_final: 0.2662 (ptt) REVERT: J 47 MET cc_start: 0.6379 (ptt) cc_final: 0.6025 (ptp) REVERT: J 172 MET cc_start: 0.7933 (pmm) cc_final: 0.7423 (mmt) REVERT: J 388 MET cc_start: 0.8712 (mmp) cc_final: 0.8449 (mmm) REVERT: J 423 MET cc_start: 0.8912 (tpt) cc_final: 0.8539 (tpp) REVERT: J 565 MET cc_start: 0.6844 (mmp) cc_final: 0.6519 (mpp) REVERT: J 606 MET cc_start: 0.4913 (mmp) cc_final: 0.3178 (tpp) REVERT: K 172 MET cc_start: 0.8438 (mpp) cc_final: 0.8031 (mtp) REVERT: K 317 MET cc_start: 0.8343 (mtp) cc_final: 0.8038 (mtm) REVERT: K 388 MET cc_start: 0.8876 (mmp) cc_final: 0.8661 (mmm) REVERT: L 47 MET cc_start: 0.5968 (mmt) cc_final: 0.5683 (ptm) REVERT: L 606 MET cc_start: 0.6840 (tpt) cc_final: 0.6413 (tpt) REVERT: M 295 MET cc_start: 0.9229 (mtm) cc_final: 0.8782 (mtm) REVERT: M 612 MET cc_start: 0.4072 (ppp) cc_final: 0.3054 (ptt) REVERT: N 170 MET cc_start: 0.5277 (ppp) cc_final: 0.5004 (tmm) REVERT: N 295 MET cc_start: 0.9303 (mtm) cc_final: 0.8950 (mtm) REVERT: N 299 MET cc_start: 0.7805 (mpp) cc_final: 0.7093 (mmm) REVERT: N 423 MET cc_start: 0.9221 (tpp) cc_final: 0.8530 (tpp) REVERT: N 612 MET cc_start: 0.3102 (ptm) cc_final: 0.2630 (ppp) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.7275 time to fit residues: 473.1152 Evaluate side-chains 320 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 6.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 781 optimal weight: 30.0000 chunk 701 optimal weight: 9.9990 chunk 389 optimal weight: 20.0000 chunk 239 optimal weight: 0.9980 chunk 472 optimal weight: 9.9990 chunk 374 optimal weight: 7.9990 chunk 725 optimal weight: 10.0000 chunk 280 optimal weight: 9.9990 chunk 440 optimal weight: 0.9990 chunk 539 optimal weight: 20.0000 chunk 840 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 446 GLN B 35 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN C 293 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN D 293 GLN D 446 GLN F 293 GLN ** F 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 661 GLN ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 ASN N 578 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 74852 Z= 0.297 Angle : 0.604 11.693 101000 Z= 0.314 Chirality : 0.042 0.232 11072 Planarity : 0.004 0.090 13037 Dihedral : 4.415 32.686 10097 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 0.24 % Allowed : 4.22 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 9270 helix: 1.20 (0.09), residues: 3648 sheet: 0.49 (0.14), residues: 1350 loop : -0.34 (0.10), residues: 4272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 535 HIS 0.008 0.001 HIS L 479 PHE 0.040 0.002 PHE D 593 TYR 0.042 0.002 TYR K 72 ARG 0.005 0.001 ARG F 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 324 time to evaluate : 6.722 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: A 612 MET cc_start: 0.7070 (ptt) cc_final: 0.5573 (ptt) REVERT: B 512 MET cc_start: 0.9208 (tmm) cc_final: 0.8784 (tmm) REVERT: B 606 MET cc_start: 0.8203 (tpt) cc_final: 0.7859 (tpt) REVERT: C 299 MET cc_start: 0.8062 (mtt) cc_final: 0.7833 (mtt) REVERT: C 606 MET cc_start: 0.8548 (ptt) cc_final: 0.7744 (tmm) REVERT: D 311 MET cc_start: 0.7388 (mpp) cc_final: 0.6825 (mtm) REVERT: D 612 MET cc_start: 0.7208 (ppp) cc_final: 0.6718 (ptt) REVERT: E 512 MET cc_start: 0.9037 (tmm) cc_final: 0.8669 (tmm) REVERT: E 606 MET cc_start: 0.8857 (ttm) cc_final: 0.8033 (tpp) REVERT: F 464 TYR cc_start: 0.5985 (p90) cc_final: 0.5685 (p90) REVERT: F 512 MET cc_start: 0.8472 (ppp) cc_final: 0.8024 (tmm) REVERT: F 606 MET cc_start: 0.9375 (ptt) cc_final: 0.8814 (ttm) REVERT: G 606 MET cc_start: 0.8338 (ptm) cc_final: 0.7633 (tmm) REVERT: H 167 MET cc_start: 0.9270 (ppp) cc_final: 0.8920 (ppp) REVERT: H 172 MET cc_start: 0.4162 (ttt) cc_final: 0.3881 (tpt) REVERT: H 295 MET cc_start: 0.9184 (mtm) cc_final: 0.8389 (mtm) REVERT: H 299 MET cc_start: 0.8298 (mpp) cc_final: 0.7827 (mmm) REVERT: H 423 MET cc_start: 0.9126 (tpp) cc_final: 0.8774 (tpp) REVERT: H 512 MET cc_start: 0.9005 (ttm) cc_final: 0.8706 (tpp) REVERT: H 606 MET cc_start: 0.4267 (tpp) cc_final: 0.3978 (tpp) REVERT: I 344 MET cc_start: 0.6886 (mpp) cc_final: 0.6671 (mpp) REVERT: I 423 MET cc_start: 0.9307 (tpp) cc_final: 0.8940 (tpp) REVERT: I 461 MET cc_start: 0.8370 (tpt) cc_final: 0.8082 (tpt) REVERT: I 606 MET cc_start: 0.5995 (tpt) cc_final: 0.5664 (tpt) REVERT: J 47 MET cc_start: 0.6339 (ptt) cc_final: 0.5647 (ptp) REVERT: J 172 MET cc_start: 0.8100 (pmm) cc_final: 0.7560 (mmt) REVERT: J 214 MET cc_start: 0.8663 (mmp) cc_final: 0.8428 (mmp) REVERT: J 423 MET cc_start: 0.8971 (tpt) cc_final: 0.8559 (tpp) REVERT: J 606 MET cc_start: 0.5037 (mmp) cc_final: 0.3635 (tpp) REVERT: K 461 MET cc_start: 0.8517 (mmm) cc_final: 0.8221 (mmm) REVERT: L 167 MET cc_start: 0.8623 (mmm) cc_final: 0.7995 (mmm) REVERT: L 295 MET cc_start: 0.9076 (tpp) cc_final: 0.8596 (tpp) REVERT: L 299 MET cc_start: 0.8465 (mmt) cc_final: 0.7651 (mmm) REVERT: L 423 MET cc_start: 0.8537 (ppp) cc_final: 0.8199 (ppp) REVERT: L 606 MET cc_start: 0.6878 (tpt) cc_final: 0.6570 (tpp) REVERT: M 167 MET cc_start: 0.7342 (ppp) cc_final: 0.7084 (tmm) REVERT: M 295 MET cc_start: 0.9241 (mtm) cc_final: 0.8716 (mtt) REVERT: M 299 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7250 (mmm) REVERT: M 423 MET cc_start: 0.9364 (tpt) cc_final: 0.8653 (tpp) REVERT: M 606 MET cc_start: 0.6974 (mmm) cc_final: 0.5768 (mmm) REVERT: M 612 MET cc_start: 0.4397 (ppp) cc_final: 0.3072 (ptt) REVERT: N 170 MET cc_start: 0.5761 (ppp) cc_final: 0.5108 (tmm) REVERT: N 295 MET cc_start: 0.9317 (mtm) cc_final: 0.8892 (mtm) REVERT: N 299 MET cc_start: 0.7767 (mpp) cc_final: 0.7084 (mmm) REVERT: N 423 MET cc_start: 0.9291 (tpp) cc_final: 0.8655 (tpp) REVERT: N 512 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8081 (pmm) REVERT: N 612 MET cc_start: 0.3118 (ptm) cc_final: 0.2832 (ppp) outliers start: 19 outliers final: 6 residues processed: 331 average time/residue: 0.6955 time to fit residues: 403.8681 Evaluate side-chains 326 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 318 time to evaluate : 6.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain L residue 614 LEU Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain N residue 512 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 466 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 699 optimal weight: 10.0000 chunk 571 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 841 optimal weight: 40.0000 chunk 909 optimal weight: 9.9990 chunk 749 optimal weight: 20.0000 chunk 834 optimal weight: 20.0000 chunk 286 optimal weight: 0.9990 chunk 675 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 661 GLN G 59 GLN G 257 ASN ** G 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 GLN J 409 GLN K 409 GLN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 578 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 74852 Z= 0.383 Angle : 0.634 12.476 101000 Z= 0.328 Chirality : 0.043 0.218 11072 Planarity : 0.004 0.078 13037 Dihedral : 4.540 33.395 10097 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.13 % Favored : 94.61 % Rotamer: Outliers : 0.75 % Allowed : 6.62 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.09), residues: 9270 helix: 1.13 (0.09), residues: 3661 sheet: 0.32 (0.14), residues: 1367 loop : -0.46 (0.10), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 535 HIS 0.007 0.001 HIS F 467 PHE 0.033 0.002 PHE D 593 TYR 0.034 0.002 TYR K 72 ARG 0.005 0.001 ARG G 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 321 time to evaluate : 6.638 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: A 39 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7482 (p90) REVERT: A 606 MET cc_start: 0.9194 (ttm) cc_final: 0.8209 (tpp) REVERT: A 612 MET cc_start: 0.7050 (ptt) cc_final: 0.5717 (ptt) REVERT: B 197 MET cc_start: 0.7672 (mmt) cc_final: 0.6741 (mmt) REVERT: B 512 MET cc_start: 0.9308 (tmm) cc_final: 0.8830 (tmm) REVERT: B 612 MET cc_start: 0.7046 (ppp) cc_final: 0.6306 (ptt) REVERT: C 197 MET cc_start: 0.8050 (mmt) cc_final: 0.7442 (mmt) REVERT: C 365 MET cc_start: 0.7862 (mmt) cc_final: 0.7482 (mmt) REVERT: C 512 MET cc_start: 0.9124 (tmm) cc_final: 0.8804 (tmm) REVERT: C 606 MET cc_start: 0.8818 (ptt) cc_final: 0.8102 (tmm) REVERT: D 197 MET cc_start: 0.8045 (mmt) cc_final: 0.6414 (mmt) REVERT: D 262 MET cc_start: 0.7758 (pmm) cc_final: 0.7221 (pmm) REVERT: D 612 MET cc_start: 0.7167 (ppp) cc_final: 0.6803 (ptt) REVERT: E 365 MET cc_start: 0.7231 (mmt) cc_final: 0.6931 (mmt) REVERT: E 606 MET cc_start: 0.9047 (ttm) cc_final: 0.8201 (tpp) REVERT: F 464 TYR cc_start: 0.6163 (p90) cc_final: 0.5788 (p90) REVERT: F 606 MET cc_start: 0.9325 (ptt) cc_final: 0.8917 (ttm) REVERT: G 262 MET cc_start: 0.7813 (pmm) cc_final: 0.7479 (pmm) REVERT: G 365 MET cc_start: 0.7052 (mmt) cc_final: 0.6802 (mmt) REVERT: G 453 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: G 512 MET cc_start: 0.8910 (tmm) cc_final: 0.8671 (tmm) REVERT: G 606 MET cc_start: 0.8365 (ptm) cc_final: 0.7850 (tmm) REVERT: H 167 MET cc_start: 0.9232 (ppp) cc_final: 0.8955 (ppp) REVERT: H 172 MET cc_start: 0.3899 (ttt) cc_final: 0.3645 (tpt) REVERT: H 299 MET cc_start: 0.8430 (mpp) cc_final: 0.8086 (mmm) REVERT: H 423 MET cc_start: 0.9164 (tpp) cc_final: 0.8776 (tpp) REVERT: H 512 MET cc_start: 0.9059 (ttm) cc_final: 0.8756 (tpp) REVERT: I 167 MET cc_start: 0.7512 (mmp) cc_final: 0.7079 (mmm) REVERT: I 317 MET cc_start: 0.8387 (mtp) cc_final: 0.7485 (mtp) REVERT: I 344 MET cc_start: 0.6946 (mpp) cc_final: 0.6737 (mpp) REVERT: I 423 MET cc_start: 0.9343 (tpp) cc_final: 0.8831 (tpp) REVERT: I 461 MET cc_start: 0.8448 (tpt) cc_final: 0.8163 (tpt) REVERT: I 606 MET cc_start: 0.6292 (tpt) cc_final: 0.5847 (tpt) REVERT: I 612 MET cc_start: 0.3192 (ptt) cc_final: 0.2488 (ptt) REVERT: J 47 MET cc_start: 0.6738 (ptt) cc_final: 0.5893 (ptp) REVERT: J 170 MET cc_start: 0.7751 (ppp) cc_final: 0.6476 (ppp) REVERT: J 317 MET cc_start: 0.8333 (mmm) cc_final: 0.8130 (mmm) REVERT: J 423 MET cc_start: 0.9029 (tpt) cc_final: 0.8538 (tpp) REVERT: J 606 MET cc_start: 0.4910 (mmp) cc_final: 0.3705 (tpp) REVERT: K 388 MET cc_start: 0.9176 (mmm) cc_final: 0.8821 (mmm) REVERT: K 461 MET cc_start: 0.8463 (mmm) cc_final: 0.8186 (mmm) REVERT: K 612 MET cc_start: 0.3315 (ptt) cc_final: 0.3108 (ptt) REVERT: L 172 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7235 (mmp) REVERT: L 295 MET cc_start: 0.9177 (tpp) cc_final: 0.8553 (tpp) REVERT: L 299 MET cc_start: 0.8747 (mmt) cc_final: 0.7806 (mmm) REVERT: L 423 MET cc_start: 0.8343 (ppp) cc_final: 0.8064 (ppp) REVERT: L 606 MET cc_start: 0.7241 (tpt) cc_final: 0.6943 (tpp) REVERT: M 170 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6203 (tmm) REVERT: M 295 MET cc_start: 0.9219 (mtm) cc_final: 0.8704 (mtt) REVERT: M 299 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7376 (mmm) REVERT: M 388 MET cc_start: 0.9330 (tpp) cc_final: 0.9074 (tpp) REVERT: M 423 MET cc_start: 0.9378 (tpt) cc_final: 0.8527 (tpp) REVERT: M 612 MET cc_start: 0.4362 (ppp) cc_final: 0.2985 (ptt) REVERT: N 170 MET cc_start: 0.6002 (ppp) cc_final: 0.5434 (ppp) REVERT: N 295 MET cc_start: 0.9306 (mtm) cc_final: 0.8904 (mtm) REVERT: N 299 MET cc_start: 0.7926 (mpp) cc_final: 0.7240 (mmm) REVERT: N 423 MET cc_start: 0.9347 (tpp) cc_final: 0.8699 (tpp) REVERT: N 512 MET cc_start: 0.8620 (mpp) cc_final: 0.8382 (pmm) REVERT: N 606 MET cc_start: 0.3169 (tpt) cc_final: 0.2394 (tpp) REVERT: N 612 MET cc_start: 0.3303 (ptm) cc_final: 0.2861 (ppp) outliers start: 60 outliers final: 24 residues processed: 365 average time/residue: 0.6724 time to fit residues: 436.1943 Evaluate side-chains 343 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 314 time to evaluate : 6.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 317 MET Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain M residue 170 MET Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain M residue 565 MET Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 377 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 831 optimal weight: 20.0000 chunk 632 optimal weight: 7.9990 chunk 436 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 565 optimal weight: 2.9990 chunk 844 optimal weight: 50.0000 chunk 894 optimal weight: 0.0370 chunk 441 optimal weight: 8.9990 chunk 800 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 ASN C 446 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 GLN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 74852 Z= 0.181 Angle : 0.529 12.040 101000 Z= 0.273 Chirality : 0.040 0.207 11072 Planarity : 0.004 0.065 13037 Dihedral : 4.278 28.813 10097 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.36 % Favored : 95.37 % Rotamer: Outliers : 0.82 % Allowed : 7.95 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.09), residues: 9270 helix: 1.44 (0.09), residues: 3641 sheet: 0.43 (0.14), residues: 1374 loop : -0.35 (0.10), residues: 4255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 535 HIS 0.005 0.001 HIS N 429 PHE 0.023 0.001 PHE D 593 TYR 0.032 0.001 TYR K 72 ARG 0.003 0.000 ARG L 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 318 time to evaluate : 6.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7404 (p90) REVERT: A 365 MET cc_start: 0.6530 (mmt) cc_final: 0.6270 (mmt) REVERT: A 512 MET cc_start: 0.8933 (tmm) cc_final: 0.8528 (tmm) REVERT: A 606 MET cc_start: 0.9166 (ttm) cc_final: 0.8149 (tpp) REVERT: A 612 MET cc_start: 0.7103 (ptt) cc_final: 0.5795 (ptt) REVERT: B 197 MET cc_start: 0.7510 (mmt) cc_final: 0.6722 (mmt) REVERT: B 512 MET cc_start: 0.9282 (tmm) cc_final: 0.8976 (tmm) REVERT: B 612 MET cc_start: 0.6767 (ppp) cc_final: 0.6130 (ptt) REVERT: C 197 MET cc_start: 0.7901 (mmt) cc_final: 0.7255 (mmt) REVERT: C 365 MET cc_start: 0.7810 (mmt) cc_final: 0.7319 (mmt) REVERT: C 512 MET cc_start: 0.9132 (tmm) cc_final: 0.8899 (tmm) REVERT: C 606 MET cc_start: 0.8774 (ptt) cc_final: 0.8017 (tmm) REVERT: D 39 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7833 (p90) REVERT: D 197 MET cc_start: 0.7867 (mmt) cc_final: 0.6291 (mmt) REVERT: D 612 MET cc_start: 0.7282 (ppp) cc_final: 0.6845 (ptt) REVERT: E 365 MET cc_start: 0.7407 (mmt) cc_final: 0.7120 (mmt) REVERT: E 512 MET cc_start: 0.9110 (tmm) cc_final: 0.8856 (tmm) REVERT: E 606 MET cc_start: 0.8984 (ttm) cc_final: 0.8146 (tpp) REVERT: E 612 MET cc_start: 0.7346 (ptt) cc_final: 0.5947 (ptt) REVERT: F 197 MET cc_start: 0.7755 (mmt) cc_final: 0.7020 (mmt) REVERT: F 464 TYR cc_start: 0.6178 (p90) cc_final: 0.5866 (p90) REVERT: F 606 MET cc_start: 0.9396 (ptt) cc_final: 0.8993 (ttm) REVERT: G 135 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8512 (t) REVERT: G 365 MET cc_start: 0.7516 (mmt) cc_final: 0.6709 (mmt) REVERT: G 453 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: G 606 MET cc_start: 0.8293 (ptm) cc_final: 0.7757 (tmm) REVERT: H 167 MET cc_start: 0.9196 (ppp) cc_final: 0.8867 (ppp) REVERT: H 172 MET cc_start: 0.4059 (ttt) cc_final: 0.3723 (tpt) REVERT: H 295 MET cc_start: 0.9184 (mtm) cc_final: 0.8281 (mtm) REVERT: H 423 MET cc_start: 0.9210 (tpp) cc_final: 0.8852 (tpp) REVERT: H 512 MET cc_start: 0.9051 (ttm) cc_final: 0.8735 (tpp) REVERT: I 167 MET cc_start: 0.7486 (mmp) cc_final: 0.7058 (mmm) REVERT: I 344 MET cc_start: 0.7139 (mpp) cc_final: 0.6936 (mpp) REVERT: I 388 MET cc_start: 0.9022 (mmm) cc_final: 0.8784 (tpp) REVERT: I 423 MET cc_start: 0.9342 (tpp) cc_final: 0.8815 (tpp) REVERT: I 461 MET cc_start: 0.8329 (tpt) cc_final: 0.8128 (tpt) REVERT: I 606 MET cc_start: 0.5993 (tpt) cc_final: 0.5069 (tpp) REVERT: I 612 MET cc_start: 0.3156 (ptt) cc_final: 0.2387 (ptt) REVERT: J 47 MET cc_start: 0.6653 (ptt) cc_final: 0.6216 (ptt) REVERT: J 170 MET cc_start: 0.7878 (ppp) cc_final: 0.7368 (ppp) REVERT: J 295 MET cc_start: 0.9392 (tpp) cc_final: 0.9160 (tpp) REVERT: J 423 MET cc_start: 0.9013 (tpt) cc_final: 0.8515 (tpp) REVERT: J 606 MET cc_start: 0.4736 (mmp) cc_final: 0.3392 (tpp) REVERT: K 47 MET cc_start: 0.4360 (mmp) cc_final: 0.2810 (ptt) REVERT: K 388 MET cc_start: 0.9090 (mmm) cc_final: 0.8718 (mmm) REVERT: K 612 MET cc_start: 0.3296 (ptt) cc_final: 0.2999 (ptt) REVERT: L 167 MET cc_start: 0.8761 (mmm) cc_final: 0.8168 (mmm) REVERT: L 172 MET cc_start: 0.7856 (mmp) cc_final: 0.7404 (mmp) REVERT: L 295 MET cc_start: 0.9170 (tpp) cc_final: 0.8897 (tpp) REVERT: L 299 MET cc_start: 0.8712 (mmt) cc_final: 0.7701 (mmm) REVERT: L 423 MET cc_start: 0.8207 (ppp) cc_final: 0.7960 (ppp) REVERT: L 606 MET cc_start: 0.6991 (tpt) cc_final: 0.6696 (tpp) REVERT: M 167 MET cc_start: 0.7461 (ppp) cc_final: 0.7235 (ppp) REVERT: M 295 MET cc_start: 0.9230 (mtm) cc_final: 0.8720 (mtt) REVERT: M 388 MET cc_start: 0.9255 (tpp) cc_final: 0.8917 (tpp) REVERT: M 423 MET cc_start: 0.9385 (tpt) cc_final: 0.8547 (tpp) REVERT: M 606 MET cc_start: 0.7023 (tpp) cc_final: 0.6679 (mmm) REVERT: M 612 MET cc_start: 0.4554 (ppp) cc_final: 0.3204 (ptt) REVERT: N 170 MET cc_start: 0.5936 (ppp) cc_final: 0.5250 (tmm) REVERT: N 172 MET cc_start: 0.5692 (mmm) cc_final: 0.5146 (mmp) REVERT: N 197 MET cc_start: 0.4470 (mmp) cc_final: 0.4205 (mmp) REVERT: N 295 MET cc_start: 0.9266 (mtm) cc_final: 0.8901 (mtm) REVERT: N 299 MET cc_start: 0.8061 (mpp) cc_final: 0.7435 (mmm) REVERT: N 423 MET cc_start: 0.9355 (tpp) cc_final: 0.8695 (tpp) REVERT: N 461 MET cc_start: 0.8219 (mmm) cc_final: 0.7636 (mmm) REVERT: N 512 MET cc_start: 0.8560 (mpp) cc_final: 0.8350 (pmm) REVERT: N 606 MET cc_start: 0.2791 (tpt) cc_final: 0.1944 (tpp) REVERT: N 612 MET cc_start: 0.3157 (ptm) cc_final: 0.2865 (ppp) outliers start: 65 outliers final: 31 residues processed: 366 average time/residue: 0.6535 time to fit residues: 424.9377 Evaluate side-chains 348 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 313 time to evaluate : 6.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain L residue 614 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 565 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 744 optimal weight: 10.0000 chunk 507 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 665 optimal weight: 1.9990 chunk 368 optimal weight: 0.8980 chunk 762 optimal weight: 40.0000 chunk 618 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 456 optimal weight: 40.0000 chunk 802 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 372 ASN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 74852 Z= 0.201 Angle : 0.525 11.100 101000 Z= 0.269 Chirality : 0.040 0.211 11072 Planarity : 0.004 0.063 13037 Dihedral : 4.179 28.189 10097 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.79 % Favored : 94.94 % Rotamer: Outliers : 0.93 % Allowed : 8.83 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.09), residues: 9270 helix: 1.53 (0.09), residues: 3646 sheet: 0.39 (0.14), residues: 1383 loop : -0.31 (0.10), residues: 4241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.005 0.001 HIS N 429 PHE 0.020 0.001 PHE D 593 TYR 0.029 0.001 TYR K 72 ARG 0.004 0.000 ARG L 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 316 time to evaluate : 6.595 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: A 39 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7384 (p90) REVERT: A 606 MET cc_start: 0.9188 (ttm) cc_final: 0.8165 (tpp) REVERT: A 612 MET cc_start: 0.7076 (ptt) cc_final: 0.5811 (ptt) REVERT: B 197 MET cc_start: 0.7565 (mmt) cc_final: 0.6815 (mmt) REVERT: B 512 MET cc_start: 0.9300 (tmm) cc_final: 0.8995 (tmm) REVERT: B 656 LEU cc_start: 0.7867 (tp) cc_final: 0.7527 (tp) REVERT: C 197 MET cc_start: 0.7879 (mmt) cc_final: 0.7229 (mmt) REVERT: C 365 MET cc_start: 0.7903 (mmt) cc_final: 0.7558 (mmt) REVERT: C 512 MET cc_start: 0.9129 (tmm) cc_final: 0.8924 (tmm) REVERT: C 606 MET cc_start: 0.8780 (ptt) cc_final: 0.8037 (tmm) REVERT: C 632 PHE cc_start: 0.9062 (m-80) cc_final: 0.8762 (m-10) REVERT: D 39 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7834 (p90) REVERT: D 197 MET cc_start: 0.7877 (mmt) cc_final: 0.6249 (mmt) REVERT: D 612 MET cc_start: 0.7182 (ppp) cc_final: 0.6794 (ptt) REVERT: E 197 MET cc_start: 0.7639 (mmt) cc_final: 0.6376 (mmt) REVERT: E 512 MET cc_start: 0.9188 (tmm) cc_final: 0.8848 (tmm) REVERT: E 606 MET cc_start: 0.9017 (ttm) cc_final: 0.8185 (tpp) REVERT: E 612 MET cc_start: 0.7306 (ptt) cc_final: 0.5977 (ptt) REVERT: F 464 TYR cc_start: 0.6185 (p90) cc_final: 0.5892 (p90) REVERT: F 512 MET cc_start: 0.8323 (ppp) cc_final: 0.8033 (ppp) REVERT: F 606 MET cc_start: 0.9381 (ptt) cc_final: 0.8126 (tmm) REVERT: G 135 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8474 (t) REVERT: G 365 MET cc_start: 0.7684 (mmt) cc_final: 0.7286 (mmt) REVERT: G 453 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: H 167 MET cc_start: 0.9192 (ppp) cc_final: 0.8818 (ppp) REVERT: H 172 MET cc_start: 0.4094 (ttt) cc_final: 0.3759 (tpt) REVERT: H 317 MET cc_start: 0.8299 (ptp) cc_final: 0.7748 (ptp) REVERT: H 423 MET cc_start: 0.9179 (tpp) cc_final: 0.8837 (tpp) REVERT: H 512 MET cc_start: 0.9086 (ttm) cc_final: 0.8767 (tpp) REVERT: I 167 MET cc_start: 0.7437 (mmp) cc_final: 0.7006 (mmm) REVERT: I 423 MET cc_start: 0.9344 (tpp) cc_final: 0.8804 (tpp) REVERT: I 461 MET cc_start: 0.8331 (tpt) cc_final: 0.8099 (tpt) REVERT: I 606 MET cc_start: 0.6069 (tpt) cc_final: 0.5171 (tpp) REVERT: I 612 MET cc_start: 0.3094 (ptt) cc_final: 0.2243 (ptt) REVERT: J 47 MET cc_start: 0.6763 (ptt) cc_final: 0.6311 (ptt) REVERT: J 170 MET cc_start: 0.7890 (ppp) cc_final: 0.7459 (ppp) REVERT: J 214 MET cc_start: 0.8697 (mmp) cc_final: 0.8308 (mmp) REVERT: J 423 MET cc_start: 0.9072 (tpt) cc_final: 0.8588 (tpp) REVERT: J 606 MET cc_start: 0.4553 (mmp) cc_final: 0.3469 (tpp) REVERT: K 47 MET cc_start: 0.4361 (mmp) cc_final: 0.2912 (ptt) REVERT: K 299 MET cc_start: 0.8218 (mmm) cc_final: 0.7416 (mmm) REVERT: K 388 MET cc_start: 0.9109 (mmm) cc_final: 0.8726 (mmm) REVERT: K 612 MET cc_start: 0.3255 (ptt) cc_final: 0.2890 (ptt) REVERT: L 167 MET cc_start: 0.8667 (mmm) cc_final: 0.8381 (mmm) REVERT: L 172 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7428 (mmp) REVERT: L 423 MET cc_start: 0.8204 (ppp) cc_final: 0.7923 (ppp) REVERT: L 606 MET cc_start: 0.6963 (tpt) cc_final: 0.6676 (tpp) REVERT: M 388 MET cc_start: 0.9193 (tpp) cc_final: 0.8904 (tpp) REVERT: M 423 MET cc_start: 0.9393 (tpt) cc_final: 0.8555 (tpp) REVERT: M 606 MET cc_start: 0.7092 (tpp) cc_final: 0.6675 (mmm) REVERT: M 612 MET cc_start: 0.4540 (ppp) cc_final: 0.3077 (ptt) REVERT: N 170 MET cc_start: 0.5945 (ppp) cc_final: 0.5465 (ppp) REVERT: N 197 MET cc_start: 0.4801 (mmp) cc_final: 0.4552 (mmp) REVERT: N 295 MET cc_start: 0.9273 (mtm) cc_final: 0.8922 (mtm) REVERT: N 299 MET cc_start: 0.8107 (mpp) cc_final: 0.7473 (mmm) REVERT: N 423 MET cc_start: 0.9358 (tpp) cc_final: 0.8627 (tpp) REVERT: N 461 MET cc_start: 0.8072 (mmm) cc_final: 0.7425 (mmm) REVERT: N 512 MET cc_start: 0.8576 (mpp) cc_final: 0.8190 (pmm) REVERT: N 606 MET cc_start: 0.2757 (tpt) cc_final: 0.1909 (tpp) outliers start: 74 outliers final: 38 residues processed: 376 average time/residue: 0.6510 time to fit residues: 435.9134 Evaluate side-chains 354 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 311 time to evaluate : 6.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain L residue 614 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 565 MET Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 300 optimal weight: 3.9990 chunk 805 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 524 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 894 optimal weight: 40.0000 chunk 742 optimal weight: 3.9990 chunk 414 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 296 optimal weight: 8.9990 chunk 469 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 605 GLN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 223 ASN ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 74852 Z= 0.188 Angle : 0.521 10.695 101000 Z= 0.267 Chirality : 0.040 0.209 11072 Planarity : 0.004 0.061 13037 Dihedral : 4.127 27.334 10097 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 0.90 % Allowed : 9.69 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.09), residues: 9270 helix: 1.59 (0.09), residues: 3642 sheet: 0.46 (0.14), residues: 1371 loop : -0.28 (0.10), residues: 4257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 535 HIS 0.005 0.001 HIS N 429 PHE 0.025 0.001 PHE A 632 TYR 0.028 0.001 TYR K 72 ARG 0.009 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 314 time to evaluate : 6.606 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: A 39 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7407 (p90) REVERT: A 606 MET cc_start: 0.9204 (ttm) cc_final: 0.8179 (tpp) REVERT: A 612 MET cc_start: 0.7110 (ptt) cc_final: 0.5887 (ptt) REVERT: B 197 MET cc_start: 0.7515 (mmt) cc_final: 0.6800 (mmt) REVERT: B 299 MET cc_start: 0.7778 (mtm) cc_final: 0.7350 (mtm) REVERT: B 512 MET cc_start: 0.9303 (tmm) cc_final: 0.9005 (tmm) REVERT: C 197 MET cc_start: 0.7913 (mmt) cc_final: 0.7196 (mmt) REVERT: C 299 MET cc_start: 0.7988 (mtm) cc_final: 0.7677 (mtm) REVERT: C 365 MET cc_start: 0.7873 (mmt) cc_final: 0.7593 (mmt) REVERT: C 512 MET cc_start: 0.9141 (tmm) cc_final: 0.8935 (tmm) REVERT: C 606 MET cc_start: 0.8774 (ptt) cc_final: 0.8098 (tmm) REVERT: D 39 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7840 (p90) REVERT: D 365 MET cc_start: 0.7737 (mmt) cc_final: 0.7265 (mmt) REVERT: D 612 MET cc_start: 0.7161 (ppp) cc_final: 0.6751 (ptt) REVERT: D 632 PHE cc_start: 0.9065 (m-80) cc_final: 0.8807 (m-10) REVERT: E 170 MET cc_start: 0.7520 (ttt) cc_final: 0.7311 (ptm) REVERT: E 197 MET cc_start: 0.7638 (mmt) cc_final: 0.6225 (mmt) REVERT: E 262 MET cc_start: 0.8110 (pmm) cc_final: 0.7904 (pmm) REVERT: E 512 MET cc_start: 0.9202 (tmm) cc_final: 0.8853 (tmm) REVERT: E 606 MET cc_start: 0.8997 (ttm) cc_final: 0.8205 (tpp) REVERT: E 612 MET cc_start: 0.7386 (ptt) cc_final: 0.6074 (ptt) REVERT: F 197 MET cc_start: 0.7892 (mmt) cc_final: 0.7292 (mmt) REVERT: F 464 TYR cc_start: 0.6180 (p90) cc_final: 0.5907 (p90) REVERT: F 512 MET cc_start: 0.8363 (ppp) cc_final: 0.8016 (ppp) REVERT: F 534 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8303 (pp) REVERT: F 606 MET cc_start: 0.9376 (ptt) cc_final: 0.8128 (tmm) REVERT: G 135 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8472 (t) REVERT: G 365 MET cc_start: 0.7635 (mmt) cc_final: 0.6888 (mmt) REVERT: G 453 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: G 512 MET cc_start: 0.8789 (tmm) cc_final: 0.8554 (tmm) REVERT: H 167 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8777 (ppp) REVERT: H 172 MET cc_start: 0.3951 (ttt) cc_final: 0.3622 (tpt) REVERT: H 423 MET cc_start: 0.9167 (tpp) cc_final: 0.8825 (tpp) REVERT: H 512 MET cc_start: 0.9087 (ttm) cc_final: 0.8751 (tpp) REVERT: I 167 MET cc_start: 0.7369 (mmp) cc_final: 0.6865 (mmm) REVERT: I 170 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7744 (mmm) REVERT: I 423 MET cc_start: 0.9345 (tpp) cc_final: 0.8796 (tpp) REVERT: I 461 MET cc_start: 0.8365 (tpt) cc_final: 0.8111 (tpt) REVERT: I 606 MET cc_start: 0.6253 (tpt) cc_final: 0.5408 (tpp) REVERT: I 612 MET cc_start: 0.3179 (ptt) cc_final: 0.2294 (ptt) REVERT: J 47 MET cc_start: 0.6551 (ptt) cc_final: 0.6192 (ptt) REVERT: J 172 MET cc_start: 0.7969 (pmm) cc_final: 0.7638 (mmp) REVERT: J 214 MET cc_start: 0.8645 (mmp) cc_final: 0.8224 (mmp) REVERT: J 423 MET cc_start: 0.9108 (tpt) cc_final: 0.8528 (tpp) REVERT: J 512 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8762 (ptp) REVERT: J 606 MET cc_start: 0.4559 (mmp) cc_final: 0.3551 (tpp) REVERT: K 47 MET cc_start: 0.4190 (mmp) cc_final: 0.2752 (ptt) REVERT: K 299 MET cc_start: 0.8315 (mmm) cc_final: 0.7623 (mmm) REVERT: K 388 MET cc_start: 0.9092 (mmm) cc_final: 0.8754 (mmm) REVERT: K 565 MET cc_start: 0.8554 (mpp) cc_final: 0.7606 (mmp) REVERT: K 612 MET cc_start: 0.3238 (ptt) cc_final: 0.2809 (ptt) REVERT: L 167 MET cc_start: 0.8650 (mmm) cc_final: 0.8394 (mmm) REVERT: L 172 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7474 (mmp) REVERT: L 423 MET cc_start: 0.8182 (ppp) cc_final: 0.7894 (ppp) REVERT: L 606 MET cc_start: 0.6747 (tpt) cc_final: 0.6431 (tpp) REVERT: M 388 MET cc_start: 0.9168 (tpp) cc_final: 0.8788 (tpp) REVERT: M 423 MET cc_start: 0.9403 (tpt) cc_final: 0.8576 (tpp) REVERT: M 612 MET cc_start: 0.4746 (ppp) cc_final: 0.3123 (ptt) REVERT: N 170 MET cc_start: 0.5964 (ppp) cc_final: 0.5478 (ppp) REVERT: N 197 MET cc_start: 0.4802 (mmp) cc_final: 0.4518 (mmp) REVERT: N 295 MET cc_start: 0.9289 (mtm) cc_final: 0.8953 (mtm) REVERT: N 299 MET cc_start: 0.8134 (mpp) cc_final: 0.7495 (mmm) REVERT: N 423 MET cc_start: 0.9372 (tpp) cc_final: 0.8674 (tpp) REVERT: N 461 MET cc_start: 0.8141 (mmm) cc_final: 0.7534 (mmm) REVERT: N 512 MET cc_start: 0.8610 (mpp) cc_final: 0.8358 (pmm) REVERT: N 606 MET cc_start: 0.2737 (tpt) cc_final: 0.1873 (tpp) outliers start: 72 outliers final: 42 residues processed: 372 average time/residue: 0.6465 time to fit residues: 429.0646 Evaluate side-chains 362 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 311 time to evaluate : 6.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain L residue 614 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 565 MET Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 862 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 509 optimal weight: 50.0000 chunk 653 optimal weight: 30.0000 chunk 506 optimal weight: 5.9990 chunk 753 optimal weight: 10.0000 chunk 499 optimal weight: 30.0000 chunk 891 optimal weight: 8.9990 chunk 557 optimal weight: 8.9990 chunk 543 optimal weight: 10.0000 chunk 411 optimal weight: 0.4980 overall best weight: 6.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 236 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS C 236 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 236 HIS F 14 ASN F 59 GLN G 236 HIS ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN H 11 GLN ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 GLN K 409 GLN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 252 GLN L 409 GLN L 603 GLN M 584 HIS ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 74852 Z= 0.407 Angle : 0.646 12.534 101000 Z= 0.331 Chirality : 0.043 0.228 11072 Planarity : 0.004 0.065 13037 Dihedral : 4.498 35.211 10097 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.52 % Favored : 94.25 % Rotamer: Outliers : 1.21 % Allowed : 10.10 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 9270 helix: 1.27 (0.09), residues: 3651 sheet: 0.33 (0.14), residues: 1351 loop : -0.43 (0.10), residues: 4268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 208 HIS 0.009 0.001 HIS H 429 PHE 0.036 0.002 PHE E 632 TYR 0.025 0.002 TYR A 298 ARG 0.005 0.001 ARG H 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 311 time to evaluate : 6.700 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: A 39 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7629 (p90) REVERT: A 365 MET cc_start: 0.7747 (mmt) cc_final: 0.6838 (mmt) REVERT: A 512 MET cc_start: 0.8983 (tmm) cc_final: 0.8639 (tmm) REVERT: A 606 MET cc_start: 0.9267 (ttm) cc_final: 0.8421 (tpp) REVERT: A 612 MET cc_start: 0.7171 (ptt) cc_final: 0.5930 (ptt) REVERT: B 197 MET cc_start: 0.7747 (mmt) cc_final: 0.7412 (mmt) REVERT: B 512 MET cc_start: 0.9338 (tmm) cc_final: 0.9102 (tmm) REVERT: C 39 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: C 365 MET cc_start: 0.7900 (mmt) cc_final: 0.7336 (mmt) REVERT: C 606 MET cc_start: 0.8903 (ptt) cc_final: 0.8211 (tmm) REVERT: D 39 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7942 (p90) REVERT: D 197 MET cc_start: 0.7854 (mmt) cc_final: 0.6819 (mmt) REVERT: D 606 MET cc_start: 0.9003 (ttm) cc_final: 0.8108 (tpp) REVERT: D 612 MET cc_start: 0.7272 (ppp) cc_final: 0.6882 (ptt) REVERT: D 632 PHE cc_start: 0.9101 (m-80) cc_final: 0.8777 (m-10) REVERT: E 197 MET cc_start: 0.7993 (mmt) cc_final: 0.6847 (mmt) REVERT: E 512 MET cc_start: 0.9258 (tmm) cc_final: 0.8930 (tmm) REVERT: E 612 MET cc_start: 0.7499 (ptt) cc_final: 0.6328 (ptt) REVERT: F 197 MET cc_start: 0.7946 (mmt) cc_final: 0.7201 (mmt) REVERT: F 534 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8229 (pp) REVERT: F 606 MET cc_start: 0.9342 (ptt) cc_final: 0.8136 (tmm) REVERT: G 365 MET cc_start: 0.7890 (mmt) cc_final: 0.7183 (mmt) REVERT: G 453 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: H 167 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8865 (ppp) REVERT: H 172 MET cc_start: 0.3713 (ttt) cc_final: 0.3279 (tpt) REVERT: H 423 MET cc_start: 0.9214 (tpp) cc_final: 0.8877 (tpp) REVERT: H 512 MET cc_start: 0.9089 (ttm) cc_final: 0.8809 (tpp) REVERT: I 170 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7419 (mmm) REVERT: I 423 MET cc_start: 0.9401 (tpp) cc_final: 0.8749 (tpp) REVERT: I 606 MET cc_start: 0.6841 (tpt) cc_final: 0.6308 (tpt) REVERT: I 612 MET cc_start: 0.3487 (ptt) cc_final: 0.2524 (ptt) REVERT: J 47 MET cc_start: 0.6746 (ptt) cc_final: 0.6234 (ptt) REVERT: J 214 MET cc_start: 0.8706 (mmp) cc_final: 0.8314 (mmp) REVERT: J 295 MET cc_start: 0.9470 (tpp) cc_final: 0.8763 (tpp) REVERT: J 299 MET cc_start: 0.7736 (mmm) cc_final: 0.6763 (mmm) REVERT: J 311 MET cc_start: 0.8557 (mmm) cc_final: 0.8328 (mpp) REVERT: J 423 MET cc_start: 0.9337 (tpt) cc_final: 0.8683 (tpp) REVERT: J 606 MET cc_start: 0.4839 (mmp) cc_final: 0.4018 (tpp) REVERT: K 47 MET cc_start: 0.4758 (mmp) cc_final: 0.2959 (ptt) REVERT: K 565 MET cc_start: 0.8532 (mpp) cc_final: 0.7551 (mmp) REVERT: K 612 MET cc_start: 0.3693 (ptt) cc_final: 0.3202 (ptt) REVERT: L 167 MET cc_start: 0.8697 (mmm) cc_final: 0.8454 (mmm) REVERT: L 172 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7239 (mmp) REVERT: L 299 MET cc_start: 0.8639 (mmp) cc_final: 0.7694 (mmm) REVERT: L 423 MET cc_start: 0.8343 (ppp) cc_final: 0.8033 (ppp) REVERT: L 606 MET cc_start: 0.7187 (tpt) cc_final: 0.6884 (tpp) REVERT: L 612 MET cc_start: 0.3710 (ptt) cc_final: 0.3303 (ptt) REVERT: M 388 MET cc_start: 0.9208 (tpp) cc_final: 0.9007 (tpp) REVERT: M 423 MET cc_start: 0.9472 (tpt) cc_final: 0.8634 (tpp) REVERT: M 612 MET cc_start: 0.5148 (ppp) cc_final: 0.3405 (ptt) REVERT: N 170 MET cc_start: 0.6181 (ppp) cc_final: 0.5684 (ppp) REVERT: N 197 MET cc_start: 0.5145 (mmp) cc_final: 0.4877 (mmp) REVERT: N 295 MET cc_start: 0.9259 (mtm) cc_final: 0.8942 (mtm) REVERT: N 299 MET cc_start: 0.8097 (mpp) cc_final: 0.7457 (mmm) REVERT: N 423 MET cc_start: 0.9354 (tpp) cc_final: 0.8615 (tpp) REVERT: N 461 MET cc_start: 0.8176 (mmm) cc_final: 0.7620 (mmm) REVERT: N 512 MET cc_start: 0.8755 (mpp) cc_final: 0.8525 (pmm) REVERT: N 606 MET cc_start: 0.3509 (tpt) cc_final: 0.2687 (tpp) outliers start: 96 outliers final: 61 residues processed: 389 average time/residue: 0.6490 time to fit residues: 451.5023 Evaluate side-chains 378 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 309 time to evaluate : 6.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 656 LEU Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 565 MET Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 377 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 551 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 532 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 566 optimal weight: 20.0000 chunk 607 optimal weight: 6.9990 chunk 440 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 700 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 35 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN D 236 HIS E 446 GLN F 14 ASN F 223 ASN G 293 GLN ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 ASN ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 74852 Z= 0.149 Angle : 0.534 11.494 101000 Z= 0.273 Chirality : 0.041 0.209 11072 Planarity : 0.004 0.063 13037 Dihedral : 4.189 27.797 10097 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.21 % Favored : 95.56 % Rotamer: Outliers : 0.88 % Allowed : 10.64 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.09), residues: 9270 helix: 1.57 (0.09), residues: 3645 sheet: 0.43 (0.14), residues: 1357 loop : -0.28 (0.10), residues: 4268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 535 HIS 0.011 0.001 HIS B 236 PHE 0.017 0.001 PHE B 632 TYR 0.037 0.001 TYR I 43 ARG 0.004 0.000 ARG L 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 310 time to evaluate : 6.690 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: A 39 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7495 (p90) REVERT: A 197 MET cc_start: 0.7601 (mmt) cc_final: 0.7386 (mmt) REVERT: A 365 MET cc_start: 0.7966 (mmt) cc_final: 0.7262 (mmt) REVERT: A 512 MET cc_start: 0.8946 (tmm) cc_final: 0.8645 (tmm) REVERT: A 606 MET cc_start: 0.9199 (ttm) cc_final: 0.8231 (tpp) REVERT: A 612 MET cc_start: 0.7113 (ptt) cc_final: 0.5918 (ptt) REVERT: B 197 MET cc_start: 0.7431 (mmt) cc_final: 0.6811 (mmt) REVERT: B 299 MET cc_start: 0.7719 (mtm) cc_final: 0.7297 (mtm) REVERT: B 512 MET cc_start: 0.9300 (tmm) cc_final: 0.9063 (tmm) REVERT: C 197 MET cc_start: 0.7768 (mmt) cc_final: 0.7237 (mmt) REVERT: C 365 MET cc_start: 0.7798 (mmt) cc_final: 0.7570 (mmt) REVERT: C 606 MET cc_start: 0.8779 (ptt) cc_final: 0.8215 (tmm) REVERT: D 197 MET cc_start: 0.7756 (mmt) cc_final: 0.6666 (mmt) REVERT: D 612 MET cc_start: 0.7142 (ppp) cc_final: 0.6774 (ptt) REVERT: D 632 PHE cc_start: 0.9161 (m-80) cc_final: 0.8931 (m-10) REVERT: E 197 MET cc_start: 0.7749 (mmt) cc_final: 0.6574 (mmt) REVERT: E 512 MET cc_start: 0.9236 (tmm) cc_final: 0.8906 (tmm) REVERT: E 606 MET cc_start: 0.9062 (ttm) cc_final: 0.8232 (tpp) REVERT: E 612 MET cc_start: 0.7296 (ptt) cc_final: 0.6077 (ptt) REVERT: F 534 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8078 (pp) REVERT: F 606 MET cc_start: 0.9356 (ptt) cc_final: 0.8183 (tmm) REVERT: F 612 MET cc_start: 0.5885 (ttp) cc_final: 0.5601 (ttp) REVERT: G 135 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8597 (t) REVERT: G 197 MET cc_start: 0.7539 (mmt) cc_final: 0.6177 (mmt) REVERT: G 453 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: H 167 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8769 (ppp) REVERT: H 170 MET cc_start: 0.6584 (ttm) cc_final: 0.5160 (ttm) REVERT: H 172 MET cc_start: 0.4148 (ttt) cc_final: 0.3702 (tpt) REVERT: H 423 MET cc_start: 0.9231 (tpp) cc_final: 0.8880 (tpp) REVERT: H 442 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: H 512 MET cc_start: 0.9061 (ttm) cc_final: 0.8757 (tpp) REVERT: I 167 MET cc_start: 0.6981 (mmp) cc_final: 0.6216 (mmm) REVERT: I 170 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7263 (mmm) REVERT: I 299 MET cc_start: 0.7726 (mmm) cc_final: 0.7038 (mmm) REVERT: I 423 MET cc_start: 0.9351 (tpp) cc_final: 0.8758 (tpp) REVERT: I 606 MET cc_start: 0.6578 (tpt) cc_final: 0.6052 (tpt) REVERT: I 612 MET cc_start: 0.3171 (ptt) cc_final: 0.2320 (ptt) REVERT: J 47 MET cc_start: 0.6669 (ptt) cc_final: 0.6326 (ptt) REVERT: J 214 MET cc_start: 0.8745 (mmp) cc_final: 0.8237 (mmp) REVERT: J 295 MET cc_start: 0.9423 (tpp) cc_final: 0.8712 (tpp) REVERT: J 299 MET cc_start: 0.7682 (mmm) cc_final: 0.6843 (mmm) REVERT: J 311 MET cc_start: 0.8516 (mmm) cc_final: 0.8294 (mpp) REVERT: J 388 MET cc_start: 0.8559 (mmm) cc_final: 0.8221 (mmm) REVERT: J 423 MET cc_start: 0.9291 (tpt) cc_final: 0.8756 (tpp) REVERT: J 606 MET cc_start: 0.4406 (mmp) cc_final: 0.3648 (tpp) REVERT: K 47 MET cc_start: 0.4821 (mmp) cc_final: 0.3424 (ptt) REVERT: K 299 MET cc_start: 0.8259 (mmm) cc_final: 0.7361 (mmm) REVERT: K 565 MET cc_start: 0.8498 (mpp) cc_final: 0.7484 (mmp) REVERT: K 606 MET cc_start: 0.5265 (tpp) cc_final: 0.4441 (mmm) REVERT: K 612 MET cc_start: 0.3300 (ptt) cc_final: 0.2816 (ptt) REVERT: L 172 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7454 (mmp) REVERT: L 423 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7932 (ppp) REVERT: L 606 MET cc_start: 0.6634 (tpt) cc_final: 0.6309 (tpp) REVERT: M 167 MET cc_start: 0.7552 (ppp) cc_final: 0.7342 (tmm) REVERT: M 387 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8115 (pp20) REVERT: M 388 MET cc_start: 0.9149 (tpp) cc_final: 0.8733 (tpp) REVERT: M 423 MET cc_start: 0.9402 (tpt) cc_final: 0.8567 (tpp) REVERT: M 606 MET cc_start: 0.6793 (tpp) cc_final: 0.5895 (mmm) REVERT: M 612 MET cc_start: 0.5093 (ppp) cc_final: 0.3366 (ptt) REVERT: N 170 MET cc_start: 0.6099 (ppp) cc_final: 0.5585 (ppp) REVERT: N 197 MET cc_start: 0.4764 (mmp) cc_final: 0.4466 (mmp) REVERT: N 295 MET cc_start: 0.9252 (mtm) cc_final: 0.8930 (mtm) REVERT: N 299 MET cc_start: 0.8242 (mpp) cc_final: 0.7603 (mmm) REVERT: N 423 MET cc_start: 0.9391 (tpp) cc_final: 0.8665 (tpp) REVERT: N 461 MET cc_start: 0.8223 (mmm) cc_final: 0.7908 (mmm) REVERT: N 518 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8035 (tt) REVERT: N 606 MET cc_start: 0.3058 (tpt) cc_final: 0.2153 (tpp) outliers start: 70 outliers final: 45 residues processed: 367 average time/residue: 0.6649 time to fit residues: 435.6030 Evaluate side-chains 365 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 309 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 236 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 387 GLU Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 423 MET Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 387 GLU Chi-restraints excluded: chain M residue 565 MET Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 811 optimal weight: 20.0000 chunk 854 optimal weight: 40.0000 chunk 779 optimal weight: 8.9990 chunk 830 optimal weight: 4.9990 chunk 853 optimal weight: 30.0000 chunk 500 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 652 optimal weight: 6.9990 chunk 254 optimal weight: 50.0000 chunk 750 optimal weight: 20.0000 chunk 785 optimal weight: 20.0000 overall best weight: 6.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN D 236 HIS ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 GLN F 14 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 HIS ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 74852 Z= 0.383 Angle : 0.636 12.583 101000 Z= 0.322 Chirality : 0.042 0.217 11072 Planarity : 0.004 0.063 13037 Dihedral : 4.380 31.539 10097 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 1.04 % Allowed : 10.75 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 9270 helix: 1.40 (0.09), residues: 3657 sheet: 0.28 (0.14), residues: 1354 loop : -0.38 (0.10), residues: 4259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 208 HIS 0.008 0.001 HIS D 236 PHE 0.018 0.001 PHE K 385 TYR 0.026 0.002 TYR K 72 ARG 0.006 0.000 ARG K 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 308 time to evaluate : 6.580 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: A 39 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7610 (p90) REVERT: A 365 MET cc_start: 0.7980 (mmt) cc_final: 0.7110 (mmt) REVERT: A 512 MET cc_start: 0.8967 (tmm) cc_final: 0.8740 (tmm) REVERT: A 612 MET cc_start: 0.7106 (ptt) cc_final: 0.5900 (ptt) REVERT: B 197 MET cc_start: 0.7658 (mmt) cc_final: 0.7298 (mmt) REVERT: B 512 MET cc_start: 0.9342 (tmm) cc_final: 0.9124 (tmm) REVERT: B 612 MET cc_start: 0.6721 (ttp) cc_final: 0.5654 (ptm) REVERT: C 39 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7650 (m-10) REVERT: C 365 MET cc_start: 0.7815 (mmt) cc_final: 0.7446 (mmt) REVERT: C 606 MET cc_start: 0.8978 (ptt) cc_final: 0.8315 (tmm) REVERT: D 197 MET cc_start: 0.7814 (mmt) cc_final: 0.6657 (mmt) REVERT: D 606 MET cc_start: 0.9021 (ttm) cc_final: 0.8128 (tpp) REVERT: D 612 MET cc_start: 0.7306 (ppp) cc_final: 0.6999 (ptt) REVERT: E 197 MET cc_start: 0.8030 (mmt) cc_final: 0.6793 (mmt) REVERT: E 512 MET cc_start: 0.9241 (tmm) cc_final: 0.8901 (tmm) REVERT: E 612 MET cc_start: 0.7402 (ptt) cc_final: 0.6348 (ptt) REVERT: F 534 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8378 (pp) REVERT: F 606 MET cc_start: 0.9386 (ptt) cc_final: 0.8198 (tmm) REVERT: F 612 MET cc_start: 0.5885 (ttp) cc_final: 0.5591 (ttp) REVERT: G 135 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8692 (t) REVERT: G 365 MET cc_start: 0.7916 (mmt) cc_final: 0.7603 (mmt) REVERT: G 453 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: H 167 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8843 (ppp) REVERT: H 172 MET cc_start: 0.3712 (ttt) cc_final: 0.3190 (tpp) REVERT: H 423 MET cc_start: 0.9249 (tpp) cc_final: 0.8873 (tpp) REVERT: H 512 MET cc_start: 0.9087 (ttm) cc_final: 0.8780 (tpp) REVERT: I 167 MET cc_start: 0.7022 (mmp) cc_final: 0.6799 (mmp) REVERT: I 170 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7333 (mmm) REVERT: I 423 MET cc_start: 0.9380 (tpp) cc_final: 0.8789 (tpp) REVERT: I 606 MET cc_start: 0.6947 (tpt) cc_final: 0.6432 (tpt) REVERT: I 612 MET cc_start: 0.3461 (ptt) cc_final: 0.2513 (ptt) REVERT: J 47 MET cc_start: 0.6870 (ptt) cc_final: 0.6385 (ptt) REVERT: J 172 MET cc_start: 0.7967 (pmm) cc_final: 0.7556 (mmt) REVERT: J 214 MET cc_start: 0.8611 (mmp) cc_final: 0.8232 (mmp) REVERT: J 295 MET cc_start: 0.9452 (tpp) cc_final: 0.8770 (tpp) REVERT: J 299 MET cc_start: 0.7878 (mmm) cc_final: 0.6953 (mmm) REVERT: J 423 MET cc_start: 0.9334 (tpt) cc_final: 0.8769 (tpp) REVERT: J 606 MET cc_start: 0.5182 (mmp) cc_final: 0.4500 (tpp) REVERT: K 47 MET cc_start: 0.4772 (mmp) cc_final: 0.3130 (ptt) REVERT: K 299 MET cc_start: 0.8218 (mmm) cc_final: 0.7286 (mmm) REVERT: K 565 MET cc_start: 0.8524 (mpp) cc_final: 0.7496 (mmp) REVERT: K 612 MET cc_start: 0.3550 (ptt) cc_final: 0.2997 (ptt) REVERT: L 167 MET cc_start: 0.8687 (mmm) cc_final: 0.8404 (mmm) REVERT: L 172 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7420 (mmp) REVERT: L 423 MET cc_start: 0.8350 (ppp) cc_final: 0.8031 (ppp) REVERT: L 606 MET cc_start: 0.6998 (tpt) cc_final: 0.6677 (tpp) REVERT: M 423 MET cc_start: 0.9445 (tpt) cc_final: 0.8637 (tpp) REVERT: M 606 MET cc_start: 0.6962 (tpp) cc_final: 0.6019 (mmm) REVERT: M 612 MET cc_start: 0.5257 (ppp) cc_final: 0.3586 (ptt) REVERT: N 170 MET cc_start: 0.6046 (ppp) cc_final: 0.5604 (ppp) REVERT: N 197 MET cc_start: 0.4814 (mmp) cc_final: 0.4518 (mmp) REVERT: N 295 MET cc_start: 0.9279 (mtm) cc_final: 0.8968 (mtm) REVERT: N 299 MET cc_start: 0.8202 (mpp) cc_final: 0.7579 (mmm) REVERT: N 423 MET cc_start: 0.9388 (tpp) cc_final: 0.8644 (tpp) REVERT: N 461 MET cc_start: 0.8242 (mmm) cc_final: 0.7987 (mmm) REVERT: N 518 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8119 (tt) REVERT: N 606 MET cc_start: 0.3458 (tpt) cc_final: 0.2631 (tpp) outliers start: 83 outliers final: 57 residues processed: 374 average time/residue: 0.6381 time to fit residues: 427.8709 Evaluate side-chains 373 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 307 time to evaluate : 8.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 236 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 632 PHE Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 344 MET Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 565 MET Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 827 optimal weight: 3.9990 chunk 545 optimal weight: 4.9990 chunk 878 optimal weight: 6.9990 chunk 536 optimal weight: 10.0000 chunk 416 optimal weight: 5.9990 chunk 610 optimal weight: 2.9990 chunk 921 optimal weight: 20.0000 chunk 848 optimal weight: 8.9990 chunk 733 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 566 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 236 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 GLN F 14 ASN ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 252 GLN ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 74852 Z= 0.246 Angle : 0.576 13.145 101000 Z= 0.291 Chirality : 0.041 0.287 11072 Planarity : 0.004 0.062 13037 Dihedral : 4.309 28.365 10097 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.65 % Favored : 95.10 % Rotamer: Outliers : 0.88 % Allowed : 10.86 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.09), residues: 9270 helix: 1.47 (0.09), residues: 3654 sheet: 0.36 (0.14), residues: 1333 loop : -0.35 (0.10), residues: 4283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 535 HIS 0.006 0.001 HIS H 429 PHE 0.017 0.001 PHE K 385 TYR 0.030 0.001 TYR C 72 ARG 0.005 0.000 ARG M 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18540 Ramachandran restraints generated. 9270 Oldfield, 0 Emsley, 9270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 310 time to evaluate : 6.679 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: A 39 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7541 (p90) REVERT: A 365 MET cc_start: 0.8079 (mmt) cc_final: 0.7346 (mmt) REVERT: A 512 MET cc_start: 0.8912 (tmm) cc_final: 0.8700 (tmm) REVERT: A 606 MET cc_start: 0.9277 (ttm) cc_final: 0.8367 (tpp) REVERT: A 612 MET cc_start: 0.7071 (ptt) cc_final: 0.5897 (ptt) REVERT: B 39 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7642 (p90) REVERT: B 197 MET cc_start: 0.7608 (mmt) cc_final: 0.7176 (mmt) REVERT: B 299 MET cc_start: 0.7768 (mtm) cc_final: 0.7317 (mtm) REVERT: B 512 MET cc_start: 0.9325 (tmm) cc_final: 0.9120 (tmm) REVERT: B 612 MET cc_start: 0.6478 (ttp) cc_final: 0.5431 (ptm) REVERT: C 197 MET cc_start: 0.7821 (mmt) cc_final: 0.6297 (mmt) REVERT: C 606 MET cc_start: 0.8939 (ptt) cc_final: 0.8308 (tmm) REVERT: D 197 MET cc_start: 0.7681 (mmt) cc_final: 0.6653 (mmt) REVERT: D 512 MET cc_start: 0.8924 (tmm) cc_final: 0.8716 (pmm) REVERT: D 612 MET cc_start: 0.7273 (ppp) cc_final: 0.6972 (ptt) REVERT: E 197 MET cc_start: 0.7975 (mmt) cc_final: 0.6725 (mmt) REVERT: E 262 MET cc_start: 0.8150 (pmm) cc_final: 0.7945 (pmm) REVERT: E 512 MET cc_start: 0.9237 (tmm) cc_final: 0.8894 (tmm) REVERT: E 606 MET cc_start: 0.9183 (ttm) cc_final: 0.8277 (tpp) REVERT: E 612 MET cc_start: 0.7538 (ptt) cc_final: 0.6429 (ptt) REVERT: F 344 MET cc_start: 0.8106 (tpp) cc_final: 0.7375 (ttp) REVERT: F 534 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8270 (pp) REVERT: F 606 MET cc_start: 0.9362 (ptt) cc_final: 0.8187 (tmm) REVERT: F 612 MET cc_start: 0.5620 (ttp) cc_final: 0.5300 (ttp) REVERT: G 135 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8656 (t) REVERT: G 365 MET cc_start: 0.7878 (mmt) cc_final: 0.7224 (mmt) REVERT: G 453 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: H 167 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8795 (ppp) REVERT: H 172 MET cc_start: 0.3992 (ttt) cc_final: 0.3416 (tpp) REVERT: H 423 MET cc_start: 0.9241 (tpp) cc_final: 0.8858 (tpp) REVERT: H 512 MET cc_start: 0.9098 (ttm) cc_final: 0.8782 (tpp) REVERT: I 170 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7351 (mmm) REVERT: I 423 MET cc_start: 0.9405 (tpp) cc_final: 0.8775 (tpp) REVERT: I 606 MET cc_start: 0.6870 (tpt) cc_final: 0.6343 (tpt) REVERT: I 612 MET cc_start: 0.3377 (ptt) cc_final: 0.2455 (ptt) REVERT: J 47 MET cc_start: 0.6869 (ptt) cc_final: 0.6439 (ptt) REVERT: J 167 MET cc_start: 0.8014 (ptp) cc_final: 0.7287 (pmm) REVERT: J 172 MET cc_start: 0.7965 (pmm) cc_final: 0.7559 (mmt) REVERT: J 214 MET cc_start: 0.8650 (mmp) cc_final: 0.8235 (mmp) REVERT: J 295 MET cc_start: 0.9442 (tpp) cc_final: 0.8752 (tpp) REVERT: J 299 MET cc_start: 0.7745 (mmm) cc_final: 0.6852 (mmm) REVERT: J 388 MET cc_start: 0.8587 (mmm) cc_final: 0.8125 (mmm) REVERT: J 423 MET cc_start: 0.9317 (tpt) cc_final: 0.8780 (tpp) REVERT: J 606 MET cc_start: 0.5098 (mmp) cc_final: 0.4371 (tpp) REVERT: K 47 MET cc_start: 0.4918 (mmp) cc_final: 0.3388 (ptt) REVERT: K 299 MET cc_start: 0.8188 (mmm) cc_final: 0.7276 (mmm) REVERT: K 388 MET cc_start: 0.8943 (mmp) cc_final: 0.8619 (mmm) REVERT: K 565 MET cc_start: 0.8490 (mpp) cc_final: 0.7435 (mmp) REVERT: K 606 MET cc_start: 0.5552 (tpp) cc_final: 0.4512 (mmm) REVERT: K 612 MET cc_start: 0.3400 (ptt) cc_final: 0.2831 (ptt) REVERT: L 167 MET cc_start: 0.8591 (mmm) cc_final: 0.8324 (mmm) REVERT: L 423 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7998 (ppp) REVERT: L 606 MET cc_start: 0.6934 (tpt) cc_final: 0.6620 (tpp) REVERT: M 423 MET cc_start: 0.9419 (tpt) cc_final: 0.8612 (tpp) REVERT: M 606 MET cc_start: 0.6860 (tpp) cc_final: 0.5974 (mmm) REVERT: M 612 MET cc_start: 0.5266 (ppp) cc_final: 0.3555 (ptt) REVERT: N 170 MET cc_start: 0.6106 (ppp) cc_final: 0.5607 (ppp) REVERT: N 197 MET cc_start: 0.5045 (mmp) cc_final: 0.4739 (mmp) REVERT: N 295 MET cc_start: 0.9249 (mtm) cc_final: 0.8948 (mtm) REVERT: N 299 MET cc_start: 0.8206 (mpp) cc_final: 0.7567 (mmm) REVERT: N 423 MET cc_start: 0.9383 (tpp) cc_final: 0.8631 (tpp) REVERT: N 461 MET cc_start: 0.8195 (mmm) cc_final: 0.7949 (mmm) REVERT: N 518 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8124 (tt) outliers start: 70 outliers final: 57 residues processed: 364 average time/residue: 0.6506 time to fit residues: 425.1456 Evaluate side-chains 375 residues out of total 7964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 309 time to evaluate : 6.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 436 ASP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 436 ASP Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain H residue 167 MET Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 387 GLU Chi-restraints excluded: chain J residue 262 MET Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 240 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 423 MET Chi-restraints excluded: chain L residue 565 MET Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 565 MET Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 925 random chunks: chunk 449 optimal weight: 20.0000 chunk 582 optimal weight: 1.9990 chunk 781 optimal weight: 30.0000 chunk 224 optimal weight: 2.9990 chunk 676 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 203 optimal weight: 0.7980 chunk 734 optimal weight: 7.9990 chunk 307 optimal weight: 1.9990 chunk 754 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN D 236 HIS ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 252 GLN ** N 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.055908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.037214 restraints weight = 618932.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.038279 restraints weight = 277268.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.039040 restraints weight = 172294.939| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 74852 Z= 0.159 Angle : 0.545 13.182 101000 Z= 0.275 Chirality : 0.041 0.212 11072 Planarity : 0.004 0.061 13037 Dihedral : 4.152 27.544 10097 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.61 % Favored : 95.17 % Rotamer: Outliers : 0.89 % Allowed : 11.01 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 9270 helix: 1.59 (0.09), residues: 3669 sheet: 0.39 (0.14), residues: 1345 loop : -0.29 (0.10), residues: 4256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.008 0.001 HIS A 236 PHE 0.017 0.001 PHE D 660 TYR 0.027 0.001 TYR K 72 ARG 0.003 0.000 ARG L 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10359.55 seconds wall clock time: 188 minutes 29.94 seconds (11309.94 seconds total)