Starting phenix.real_space_refine on Tue Mar 26 00:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/03_2024/8uz1_42830_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/03_2024/8uz1_42830.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/8uz1_42830/03_2024/8uz1_42830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/03_2024/8uz1_42830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/03_2024/8uz1_42830_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/03_2024/8uz1_42830_trim_updated.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= 0.002 sd= 0.062 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: 9 Type Number sf(0) Gaussians P 18 5.49 5 Mg 9 5.21 5 S 189 5.16 5 Be 9 3.05 5 C 16668 2.51 5 N 4455 2.21 5 O 5094 1.98 5 F 27 1.80 5 H 25860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 253": "OE1" <-> "OE2" Residue "L ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 288": "OD1" <-> "OD2" Residue "M ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52329 Number of models: 1 Model: "" Number of chains: 18 Chain: "J" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5782 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5782 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5783 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5783 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5782 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5783 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5782 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5782 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5782 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 21.91, per 1000 atoms: 0.42 Number of scatterers: 52329 At special positions: 0 Unit cell: (94.22, 102.296, 304.196, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 189 16.00 P 18 15.00 Mg 9 11.99 F 27 9.00 O 5094 8.00 N 4455 7.00 C 16668 6.00 Be 9 4.00 H 25860 1.00 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 40.42 Conformation dependent library (CDL) restraints added in 5.6 seconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 45 sheets defined 42.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.15 Creating SS restraints... Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 91 removed outlier: 4.354A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.937A pdb=" N TYR J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA J 144 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 182 through 196 Processing helix chain 'J' and resid 203 through 216 removed outlier: 3.506A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 231 Processing helix chain 'J' and resid 252 through 256 removed outlier: 3.841A pdb=" N ARG J 256 " --> pdb=" O GLU J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 261 Processing helix chain 'J' and resid 264 through 267 Processing helix chain 'J' and resid 274 through 284 Processing helix chain 'J' and resid 288 through 295 removed outlier: 4.073A pdb=" N LYS J 291 " --> pdb=" O ASP J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 304 No H-bonds generated for 'chain 'J' and resid 302 through 304' Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 338 through 348 removed outlier: 3.811A pdb=" N SER J 348 " --> pdb=" O SER J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 362 No H-bonds generated for 'chain 'J' and resid 359 through 362' Processing helix chain 'J' and resid 367 through 373 removed outlier: 4.039A pdb=" N HIS J 371 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 79 through 91 removed outlier: 4.384A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 113 through 125 Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.527A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 182 through 196 Processing helix chain 'K' and resid 203 through 216 removed outlier: 3.578A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 231 removed outlier: 3.797A pdb=" N ALA K 231 " --> pdb=" O MET K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 256 removed outlier: 4.044A pdb=" N ARG K 256 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 261 Processing helix chain 'K' and resid 264 through 267 Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 287 through 296 removed outlier: 4.478A pdb=" N LYS K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA K 295 " --> pdb=" O LYS K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 305 Processing helix chain 'K' and resid 309 through 320 Processing helix chain 'K' and resid 335 through 348 removed outlier: 5.940A pdb=" N VAL K 339 " --> pdb=" O LYS K 336 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY K 342 " --> pdb=" O VAL K 339 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA K 347 " --> pdb=" O SER K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 352 through 354 No H-bonds generated for 'chain 'K' and resid 352 through 354' Processing helix chain 'K' and resid 359 through 364 removed outlier: 5.055A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 373 removed outlier: 3.927A pdb=" N LYS K 373 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 64 removed outlier: 3.954A pdb=" N ARG L 62 " --> pdb=" O GLN L 59 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY L 63 " --> pdb=" O SER L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 91 removed outlier: 4.446A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 145 removed outlier: 3.624A pdb=" N SER L 141 " --> pdb=" O GLN L 137 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 142 " --> pdb=" O ALA L 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 144 " --> pdb=" O LEU L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 182 through 196 removed outlier: 3.775A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 removed outlier: 3.848A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE L 208 " --> pdb=" O ALA L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 231 removed outlier: 3.539A pdb=" N ALA L 231 " --> pdb=" O MET L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 256 removed outlier: 4.039A pdb=" N ARG L 256 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 261 Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 274 through 283 Processing helix chain 'L' and resid 290 through 296 Processing helix chain 'L' and resid 302 through 304 No H-bonds generated for 'chain 'L' and resid 302 through 304' Processing helix chain 'L' and resid 309 through 320 Processing helix chain 'L' and resid 338 through 346 Processing helix chain 'L' and resid 351 through 354 removed outlier: 4.077A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 351 through 354' Processing helix chain 'L' and resid 359 through 362 No H-bonds generated for 'chain 'L' and resid 359 through 362' Processing helix chain 'L' and resid 367 through 371 removed outlier: 3.661A pdb=" N HIS L 371 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 79 through 92 removed outlier: 4.385A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 125 Processing helix chain 'M' and resid 137 through 145 removed outlier: 3.569A pdb=" N LEU M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 144 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 182 through 196 removed outlier: 3.583A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 216 removed outlier: 3.982A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 231 Processing helix chain 'M' and resid 252 through 256 removed outlier: 3.632A pdb=" N ARG M 256 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 261 Processing helix chain 'M' and resid 264 through 267 Processing helix chain 'M' and resid 274 through 284 Processing helix chain 'M' and resid 287 through 295 removed outlier: 4.499A pdb=" N LYS M 291 " --> pdb=" O ASP M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 305 Processing helix chain 'M' and resid 309 through 320 Processing helix chain 'M' and resid 335 through 348 removed outlier: 5.955A pdb=" N VAL M 339 " --> pdb=" O LYS M 336 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE M 341 " --> pdb=" O SER M 338 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA M 347 " --> pdb=" O SER M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 364 removed outlier: 4.663A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.793A pdb=" N LYS M 373 " --> pdb=" O VAL M 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 79 through 91 removed outlier: 4.455A pdb=" N LYS N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 125 Processing helix chain 'N' and resid 137 through 145 removed outlier: 3.736A pdb=" N SER N 141 " --> pdb=" O GLN N 137 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU N 142 " --> pdb=" O ALA N 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 182 through 196 removed outlier: 3.835A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 216 removed outlier: 3.953A pdb=" N GLU N 207 " --> pdb=" O THR N 203 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE N 208 " --> pdb=" O ALA N 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 231 Processing helix chain 'N' and resid 252 through 254 No H-bonds generated for 'chain 'N' and resid 252 through 254' Processing helix chain 'N' and resid 258 through 261 Processing helix chain 'N' and resid 264 through 267 Processing helix chain 'N' and resid 274 through 284 Processing helix chain 'N' and resid 287 through 296 removed outlier: 3.500A pdb=" N ARG N 290 " --> pdb=" O ILE N 287 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS N 291 " --> pdb=" O ASP N 288 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR N 294 " --> pdb=" O LYS N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 305 Processing helix chain 'N' and resid 309 through 320 Processing helix chain 'N' and resid 338 through 348 removed outlier: 4.057A pdb=" N SER N 348 " --> pdb=" O SER N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 354 No H-bonds generated for 'chain 'N' and resid 352 through 354' Processing helix chain 'N' and resid 359 through 362 No H-bonds generated for 'chain 'N' and resid 359 through 362' Processing helix chain 'N' and resid 367 through 373 removed outlier: 3.613A pdb=" N HIS N 371 " --> pdb=" O SER N 368 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS N 373 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'O' and resid 79 through 91 removed outlier: 4.365A pdb=" N LYS O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 100 No H-bonds generated for 'chain 'O' and resid 98 through 100' Processing helix chain 'O' and resid 113 through 125 removed outlier: 3.518A pdb=" N MET O 123 " --> pdb=" O MET O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.524A pdb=" N SER O 141 " --> pdb=" O GLN O 137 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR O 143 " --> pdb=" O VAL O 139 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 196 removed outlier: 3.651A pdb=" N LYS O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 216 Processing helix chain 'O' and resid 223 through 231 removed outlier: 4.108A pdb=" N ALA O 231 " --> pdb=" O MET O 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 254 No H-bonds generated for 'chain 'O' and resid 252 through 254' Processing helix chain 'O' and resid 258 through 261 Processing helix chain 'O' and resid 264 through 267 Processing helix chain 'O' and resid 274 through 284 Processing helix chain 'O' and resid 287 through 296 removed outlier: 4.382A pdb=" N LYS O 291 " --> pdb=" O ASP O 288 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR O 294 " --> pdb=" O LYS O 291 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA O 295 " --> pdb=" O ASP O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 304 No H-bonds generated for 'chain 'O' and resid 302 through 304' Processing helix chain 'O' and resid 309 through 320 Processing helix chain 'O' and resid 338 through 348 removed outlier: 4.090A pdb=" N SER O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 364 removed outlier: 5.014A pdb=" N GLU O 364 " --> pdb=" O GLN O 360 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 373 removed outlier: 4.146A pdb=" N LYS O 373 " --> pdb=" O VAL O 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 60 Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'P' and resid 79 through 91 removed outlier: 4.473A pdb=" N LYS P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 100 No H-bonds generated for 'chain 'P' and resid 98 through 100' Processing helix chain 'P' and resid 113 through 125 Processing helix chain 'P' and resid 137 through 145 removed outlier: 3.575A pdb=" N LEU P 142 " --> pdb=" O ALA P 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 182 through 196 removed outlier: 3.890A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG P 196 " --> pdb=" O ILE P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 216 Processing helix chain 'P' and resid 223 through 229 Processing helix chain 'P' and resid 252 through 254 No H-bonds generated for 'chain 'P' and resid 252 through 254' Processing helix chain 'P' and resid 258 through 261 Processing helix chain 'P' and resid 264 through 267 Processing helix chain 'P' and resid 274 through 283 Processing helix chain 'P' and resid 287 through 295 removed outlier: 4.592A pdb=" N LYS P 291 " --> pdb=" O ILE P 287 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP P 292 " --> pdb=" O ASP P 288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 302 through 305 Processing helix chain 'P' and resid 309 through 320 Processing helix chain 'P' and resid 335 through 348 removed outlier: 5.815A pdb=" N VAL P 339 " --> pdb=" O LYS P 336 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA P 347 " --> pdb=" O SER P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 352 No H-bonds generated for 'chain 'P' and resid 350 through 352' Processing helix chain 'P' and resid 359 through 362 No H-bonds generated for 'chain 'P' and resid 359 through 362' Processing helix chain 'P' and resid 367 through 373 removed outlier: 3.581A pdb=" N HIS P 371 " --> pdb=" O SER P 368 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS P 373 " --> pdb=" O VAL P 370 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'Q' and resid 79 through 91 removed outlier: 4.676A pdb=" N LYS Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'Q' and resid 113 through 125 Processing helix chain 'Q' and resid 137 through 145 removed outlier: 3.571A pdb=" N LEU Q 142 " --> pdb=" O ALA Q 138 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR Q 143 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA Q 144 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER Q 145 " --> pdb=" O SER Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 182 through 195 removed outlier: 3.886A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 216 removed outlier: 3.848A pdb=" N GLU Q 207 " --> pdb=" O THR Q 203 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE Q 208 " --> pdb=" O ALA Q 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 231 Processing helix chain 'Q' and resid 252 through 254 No H-bonds generated for 'chain 'Q' and resid 252 through 254' Processing helix chain 'Q' and resid 258 through 261 Processing helix chain 'Q' and resid 264 through 267 Processing helix chain 'Q' and resid 274 through 283 Processing helix chain 'Q' and resid 290 through 293 No H-bonds generated for 'chain 'Q' and resid 290 through 293' Processing helix chain 'Q' and resid 302 through 305 Processing helix chain 'Q' and resid 309 through 320 Processing helix chain 'Q' and resid 335 through 348 removed outlier: 5.913A pdb=" N VAL Q 339 " --> pdb=" O LYS Q 336 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE Q 341 " --> pdb=" O SER Q 338 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA Q 347 " --> pdb=" O SER Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 364 removed outlier: 4.684A pdb=" N GLU Q 364 " --> pdb=" O GLN Q 360 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 373 removed outlier: 3.680A pdb=" N HIS Q 371 " --> pdb=" O SER Q 368 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS Q 373 " --> pdb=" O VAL Q 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 60 Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 79 through 91 removed outlier: 4.344A pdb=" N LYS R 84 " --> pdb=" O ASP R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 125 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.958A pdb=" N SER R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 182 through 196 removed outlier: 3.743A pdb=" N THR R 194 " --> pdb=" O MET R 190 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 216 removed outlier: 4.011A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 231 removed outlier: 3.825A pdb=" N ALA R 231 " --> pdb=" O MET R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 256 Processing helix chain 'R' and resid 258 through 261 Processing helix chain 'R' and resid 264 through 267 Processing helix chain 'R' and resid 274 through 283 Processing helix chain 'R' and resid 287 through 296 removed outlier: 4.461A pdb=" N LYS R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP R 292 " --> pdb=" O ASP R 288 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA R 295 " --> pdb=" O LYS R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 305 Processing helix chain 'R' and resid 309 through 320 Processing helix chain 'R' and resid 333 through 336 removed outlier: 4.501A pdb=" N LYS R 336 " --> pdb=" O PRO R 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 333 through 336' Processing helix chain 'R' and resid 338 through 348 removed outlier: 3.714A pdb=" N SER R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 362 No H-bonds generated for 'chain 'R' and resid 359 through 362' Processing helix chain 'R' and resid 367 through 373 removed outlier: 3.878A pdb=" N HIS R 371 " --> pdb=" O SER R 368 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS R 373 " --> pdb=" O VAL R 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'J' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'J' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'J' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'J' and resid 297 through 300 removed outlier: 6.389A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'K' and resid 8 through 11 Processing sheet with id= G, first strand: chain 'K' and resid 35 through 38 Processing sheet with id= H, first strand: chain 'K' and resid 103 through 107 removed outlier: 3.688A pdb=" N TYR K 133 " --> pdb=" O THR K 103 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 297 through 300 removed outlier: 6.209A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'L' and resid 8 through 11 removed outlier: 4.373A pdb=" N GLY L 15 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'L' and resid 103 through 107 removed outlier: 3.583A pdb=" N ALA L 135 " --> pdb=" O LEU L 105 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 298 through 300 Processing sheet with id= O, first strand: chain 'L' and resid 238 through 241 Processing sheet with id= P, first strand: chain 'M' and resid 8 through 11 Processing sheet with id= Q, first strand: chain 'M' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'M' and resid 103 through 107 removed outlier: 3.856A pdb=" N ALA M 135 " --> pdb=" O LEU M 105 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 297 through 300 removed outlier: 6.236A pdb=" N ILE M 151 " --> pdb=" O VAL M 298 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER M 300 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU M 153 " --> pdb=" O SER M 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'N' and resid 8 through 11 Processing sheet with id= V, first strand: chain 'N' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'N' and resid 103 through 107 removed outlier: 3.614A pdb=" N ALA N 135 " --> pdb=" O LEU N 105 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 297 through 300 removed outlier: 6.350A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL N 152 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL N 163 " --> pdb=" O VAL N 152 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 238 through 241 Processing sheet with id= Z, first strand: chain 'O' and resid 8 through 11 Processing sheet with id= AA, first strand: chain 'O' and resid 34 through 38 Processing sheet with id= AB, first strand: chain 'O' and resid 103 through 107 removed outlier: 3.598A pdb=" N ALA O 135 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 298 through 300 Processing sheet with id= AD, first strand: chain 'O' and resid 238 through 241 Processing sheet with id= AE, first strand: chain 'P' and resid 8 through 11 Processing sheet with id= AF, first strand: chain 'P' and resid 35 through 38 Processing sheet with id= AG, first strand: chain 'P' and resid 103 through 107 removed outlier: 3.823A pdb=" N ALA P 135 " --> pdb=" O LEU P 105 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.032A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL P 152 " --> pdb=" O VAL P 163 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'P' and resid 238 through 241 Processing sheet with id= AJ, first strand: chain 'Q' and resid 8 through 11 Processing sheet with id= AK, first strand: chain 'Q' and resid 35 through 38 Processing sheet with id= AL, first strand: chain 'Q' and resid 103 through 107 Processing sheet with id= AM, first strand: chain 'Q' and resid 298 through 300 Processing sheet with id= AN, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id= AO, first strand: chain 'R' and resid 8 through 11 Processing sheet with id= AP, first strand: chain 'R' and resid 35 through 38 Processing sheet with id= AQ, first strand: chain 'R' and resid 103 through 107 Processing sheet with id= AR, first strand: chain 'R' and resid 150 through 155 Processing sheet with id= AS, first strand: chain 'R' and resid 238 through 241 925 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.27 Time building geometry restraints manager: 42.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 25815 1.12 - 1.30: 4562 1.30 - 1.47: 10064 1.47 - 1.64: 12122 1.64 - 1.82: 333 Bond restraints: 52896 Sorted by residual: bond pdb=" N ILE J 212 " pdb=" H ILE J 212 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N VAL J 209 " pdb=" H VAL J 209 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA O 365 " pdb=" H ALA O 365 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE ARG J 312 " pdb=" HE ARG J 312 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP L 288 " pdb=" H ASP L 288 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 52891 not shown) Histogram of bond angle deviations from ideal: 94.66 - 102.71: 292 102.71 - 110.76: 52966 110.76 - 118.80: 20111 118.80 - 126.85: 21748 126.85 - 134.89: 451 Bond angle restraints: 95568 Sorted by residual: angle pdb=" CA ASP N 80 " pdb=" CB ASP N 80 " pdb=" CG ASP N 80 " ideal model delta sigma weight residual 112.60 119.54 -6.94 1.00e+00 1.00e+00 4.81e+01 angle pdb=" CA ASP Q 244 " pdb=" CB ASP Q 244 " pdb=" CG ASP Q 244 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" CA ASP M 244 " pdb=" CB ASP M 244 " pdb=" CG ASP M 244 " ideal model delta sigma weight residual 112.60 118.97 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASP L 244 " pdb=" CB ASP L 244 " pdb=" CG ASP L 244 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.90e+01 angle pdb=" CA ASP N 244 " pdb=" CB ASP N 244 " pdb=" CG ASP N 244 " ideal model delta sigma weight residual 112.60 118.78 -6.18 1.00e+00 1.00e+00 3.82e+01 ... (remaining 95563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 23560 27.95 - 55.89: 1059 55.89 - 83.84: 274 83.84 - 111.78: 15 111.78 - 139.73: 25 Dihedral angle restraints: 24933 sinusoidal: 13707 harmonic: 11226 Sorted by residual: dihedral pdb=" C GLU M 93 " pdb=" N GLU M 93 " pdb=" CA GLU M 93 " pdb=" CB GLU M 93 " ideal model delta harmonic sigma weight residual -122.60 -141.76 19.16 0 2.50e+00 1.60e-01 5.88e+01 dihedral pdb=" N GLU M 93 " pdb=" C GLU M 93 " pdb=" CA GLU M 93 " pdb=" CB GLU M 93 " ideal model delta harmonic sigma weight residual 122.80 140.48 -17.68 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" C GLU P 93 " pdb=" N GLU P 93 " pdb=" CA GLU P 93 " pdb=" CB GLU P 93 " ideal model delta harmonic sigma weight residual -122.60 -140.02 17.42 0 2.50e+00 1.60e-01 4.86e+01 ... (remaining 24930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 3578 0.153 - 0.306: 443 0.306 - 0.460: 34 0.460 - 0.613: 11 0.613 - 0.766: 2 Chirality restraints: 4068 Sorted by residual: chirality pdb=" CA GLU M 93 " pdb=" N GLU M 93 " pdb=" C GLU M 93 " pdb=" CB GLU M 93 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA GLU P 93 " pdb=" N GLU P 93 " pdb=" C GLU P 93 " pdb=" CB GLU P 93 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA GLU O 93 " pdb=" N GLU O 93 " pdb=" C GLU O 93 " pdb=" CB GLU O 93 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.22e+00 ... (remaining 4065 not shown) Planarity restraints: 7848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 340 " 0.244 2.00e-02 2.50e+03 9.46e-02 3.58e+02 pdb=" CG TRP P 340 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP P 340 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP P 340 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP P 340 " -0.109 2.00e-02 2.50e+03 pdb=" CE2 TRP P 340 " -0.084 2.00e-02 2.50e+03 pdb=" CE3 TRP P 340 " -0.093 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 340 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP P 340 " 0.051 2.00e-02 2.50e+03 pdb=" HD1 TRP P 340 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 TRP P 340 " 0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP P 340 " -0.128 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 340 " 0.033 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 340 " 0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP P 340 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 340 " 0.252 2.00e-02 2.50e+03 9.08e-02 3.30e+02 pdb=" CG TRP J 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP J 340 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP J 340 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP J 340 " -0.099 2.00e-02 2.50e+03 pdb=" CE2 TRP J 340 " -0.069 2.00e-02 2.50e+03 pdb=" CE3 TRP J 340 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 340 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 340 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP J 340 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP J 340 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP J 340 " -0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP J 340 " -0.119 2.00e-02 2.50e+03 pdb=" HZ2 TRP J 340 " 0.067 2.00e-02 2.50e+03 pdb=" HZ3 TRP J 340 " 0.029 2.00e-02 2.50e+03 pdb=" HH2 TRP J 340 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 62 " 0.055 9.50e-02 1.11e+02 1.19e-01 3.11e+02 pdb=" NE ARG R 62 " 0.110 2.00e-02 2.50e+03 pdb=" CZ ARG R 62 " 0.097 2.00e-02 2.50e+03 pdb=" NH1 ARG R 62 " 0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG R 62 " 0.073 2.00e-02 2.50e+03 pdb="HH11 ARG R 62 " -0.205 2.00e-02 2.50e+03 pdb="HH12 ARG R 62 " 0.034 2.00e-02 2.50e+03 pdb="HH21 ARG R 62 " -0.219 2.00e-02 2.50e+03 pdb="HH22 ARG R 62 " 0.045 2.00e-02 2.50e+03 ... (remaining 7845 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1616 2.01 - 2.66: 62239 2.66 - 3.30: 160748 3.30 - 3.95: 208189 3.95 - 4.60: 316826 Nonbonded interactions: 749618 Sorted by model distance: nonbonded pdb=" HE2 HIS M 173 " pdb=" HE2 HIS O 40 " model vdw 1.360 2.100 nonbonded pdb=" HE2 HIS O 173 " pdb=" HE2 HIS Q 40 " model vdw 1.483 2.100 nonbonded pdb=" OE2 GLU N 270 " pdb=" HG1 THR O 66 " model vdw 1.600 1.850 nonbonded pdb=" OE2 GLU O 270 " pdb=" HG1 THR P 66 " model vdw 1.603 1.850 nonbonded pdb=" HH TYR M 69 " pdb=" OE2 GLU M 207 " model vdw 1.609 1.850 ... (remaining 749613 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 'J' selection = chain 'K' selection = (chain 'L' and (resid 4 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 174 through 375 or resid 401 through 403)) selection = (chain 'M' and (resid 4 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 174 through 375 or resid 401 through 403)) selection = chain 'N' selection = (chain 'O' and (resid 4 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 174 through 375 or resid 401 through 403)) selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.770 Extract box with map and model: 6.530 Check model and map are aligned: 0.740 Set scattering table: 0.430 Process input model: 157.370 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.310 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.143 27036 Z= 0.821 Angle : 1.908 18.446 36684 Z= 1.211 Chirality : 0.106 0.766 4068 Planarity : 0.014 0.116 4689 Dihedral : 15.162 139.725 10053 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.91 % Rotamer: Outliers : 1.34 % Allowed : 5.13 % Favored : 93.52 % Cbeta Deviations : 0.97 % 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: -1.77 (0.13), residues: 3303 helix: -1.94 (0.12), residues: 1341 sheet: -0.13 (0.24), residues: 360 loop : -0.55 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.169 0.033 TRP J 340 HIS 0.011 0.004 HIS L 101 PHE 0.068 0.010 PHE L 31 TYR 0.098 0.016 TYR L 53 ARG 0.015 0.001 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 499 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8256 (tpt) cc_final: 0.7858 (tpt) REVERT: J 137 GLN cc_start: 0.7550 (mt0) cc_final: 0.7347 (mt0) REVERT: J 176 MET cc_start: 0.7982 (mmm) cc_final: 0.7771 (mmt) REVERT: L 244 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7387 (p0) REVERT: M 82 MET cc_start: 0.9287 (tpt) cc_final: 0.8873 (tpt) REVERT: M 157 ASP cc_start: 0.8483 (t70) cc_final: 0.8154 (t0) REVERT: M 176 MET cc_start: 0.8814 (mmt) cc_final: 0.8488 (mmt) REVERT: N 47 MET cc_start: 0.5402 (ttp) cc_final: 0.5184 (ttt) REVERT: N 82 MET cc_start: 0.8888 (tpt) cc_final: 0.8670 (tpt) REVERT: N 190 MET cc_start: 0.8384 (mtm) cc_final: 0.7890 (mtm) REVERT: N 227 MET cc_start: 0.8893 (mmm) cc_final: 0.8652 (mmm) REVERT: O 82 MET cc_start: 0.9049 (tpt) cc_final: 0.8260 (tpt) REVERT: O 123 MET cc_start: 0.8201 (tpp) cc_final: 0.7988 (mmt) REVERT: O 244 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7991 (p0) REVERT: O 269 MET cc_start: 0.8234 (ptp) cc_final: 0.7964 (ptm) REVERT: O 283 MET cc_start: 0.8618 (mmt) cc_final: 0.8361 (mmm) REVERT: P 93 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: P 132 MET cc_start: 0.8767 (ptm) cc_final: 0.8558 (ppp) REVERT: P 176 MET cc_start: 0.8846 (mmt) cc_final: 0.8546 (mmt) REVERT: P 227 MET cc_start: 0.8939 (mmm) cc_final: 0.8521 (mmm) REVERT: P 374 CYS cc_start: 0.7936 (m) cc_final: 0.7599 (m) REVERT: Q 82 MET cc_start: 0.9028 (tpt) cc_final: 0.8827 (tpt) REVERT: Q 244 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7916 (p0) REVERT: Q 291 LYS cc_start: 0.6249 (mmtt) cc_final: 0.5442 (mptt) REVERT: R 41 GLN cc_start: 0.7870 (tt0) cc_final: 0.7552 (tt0) REVERT: R 330 ILE cc_start: 0.9272 (tp) cc_final: 0.9005 (mt) outliers start: 38 outliers final: 15 residues processed: 532 average time/residue: 0.8166 time to fit residues: 706.1659 Evaluate side-chains 327 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 308 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 93 GLU Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 162 ASN O 41 GLN O 162 ASN P 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27036 Z= 0.198 Angle : 0.652 6.382 36684 Z= 0.327 Chirality : 0.045 0.164 4068 Planarity : 0.004 0.034 4689 Dihedral : 11.802 124.471 3797 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 8.17 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.14), residues: 3303 helix: -0.84 (0.14), residues: 1350 sheet: -0.44 (0.21), residues: 558 loop : 0.20 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 356 HIS 0.005 0.001 HIS L 275 PHE 0.011 0.001 PHE P 262 TYR 0.011 0.001 TYR L 294 ARG 0.003 0.000 ARG K 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 356 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8452 (tpt) cc_final: 0.7848 (tpt) REVERT: J 324 THR cc_start: 0.8010 (m) cc_final: 0.7698 (m) REVERT: K 244 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7157 (p0) REVERT: L 253 GLU cc_start: 0.8271 (pm20) cc_final: 0.7950 (pm20) REVERT: M 82 MET cc_start: 0.9333 (tpt) cc_final: 0.8872 (tpt) REVERT: M 93 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: M 157 ASP cc_start: 0.8314 (t70) cc_final: 0.7897 (t0) REVERT: M 176 MET cc_start: 0.8865 (mmt) cc_final: 0.8619 (mmt) REVERT: N 123 MET cc_start: 0.8822 (tpp) cc_final: 0.8216 (mmm) REVERT: N 190 MET cc_start: 0.8277 (mtm) cc_final: 0.7882 (mtp) REVERT: N 227 MET cc_start: 0.8631 (mmm) cc_final: 0.8348 (mmm) REVERT: O 82 MET cc_start: 0.9044 (tpt) cc_final: 0.8321 (tpt) REVERT: O 123 MET cc_start: 0.8102 (tpp) cc_final: 0.7803 (mmt) REVERT: O 269 MET cc_start: 0.8313 (ptp) cc_final: 0.8079 (ptm) REVERT: P 227 MET cc_start: 0.8811 (mmm) cc_final: 0.8345 (mmm) REVERT: Q 93 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6015 (pm20) REVERT: Q 291 LYS cc_start: 0.5887 (mmtt) cc_final: 0.5384 (mmtt) REVERT: R 270 GLU cc_start: 0.6732 (mp0) cc_final: 0.6355 (mt-10) REVERT: R 330 ILE cc_start: 0.9010 (tp) cc_final: 0.8726 (mt) outliers start: 43 outliers final: 21 residues processed: 386 average time/residue: 0.7158 time to fit residues: 464.6988 Evaluate side-chains 302 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 205 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 GLN K 137 GLN L 137 GLN N 40 HIS N 137 GLN ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Q 12 ASN ** R 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27036 Z= 0.314 Angle : 0.646 7.628 36684 Z= 0.322 Chirality : 0.045 0.170 4068 Planarity : 0.004 0.036 4689 Dihedral : 10.917 144.152 3774 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.73 % Allowed : 9.94 % Favored : 88.32 % 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: -0.51 (0.15), residues: 3303 helix: -0.50 (0.14), residues: 1359 sheet: -0.54 (0.22), residues: 558 loop : 0.21 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 356 HIS 0.003 0.001 HIS R 87 PHE 0.014 0.001 PHE L 31 TYR 0.011 0.001 TYR N 198 ARG 0.003 0.000 ARG J 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 283 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8482 (tpt) cc_final: 0.8081 (tpt) REVERT: K 82 MET cc_start: 0.8816 (tpt) cc_final: 0.8469 (tpt) REVERT: L 80 ASP cc_start: 0.7679 (t0) cc_final: 0.7425 (t0) REVERT: L 137 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: L 176 MET cc_start: 0.9013 (tpp) cc_final: 0.8806 (mmt) REVERT: M 157 ASP cc_start: 0.8282 (t70) cc_final: 0.7967 (t0) REVERT: N 121 GLN cc_start: 0.8491 (tt0) cc_final: 0.8197 (tt0) REVERT: N 123 MET cc_start: 0.8765 (tpp) cc_final: 0.8503 (mmm) REVERT: N 190 MET cc_start: 0.8405 (mtm) cc_final: 0.8097 (mtp) REVERT: N 227 MET cc_start: 0.8664 (mmm) cc_final: 0.8448 (mmm) REVERT: O 82 MET cc_start: 0.9068 (tpt) cc_final: 0.8470 (tpt) REVERT: P 54 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8963 (m) REVERT: P 93 GLU cc_start: 0.7420 (pm20) cc_final: 0.6550 (pt0) REVERT: P 227 MET cc_start: 0.8732 (mmm) cc_final: 0.8379 (mmm) REVERT: Q 81 ASP cc_start: 0.7727 (m-30) cc_final: 0.7437 (m-30) REVERT: Q 82 MET cc_start: 0.8791 (tpt) cc_final: 0.8538 (tpt) REVERT: Q 205 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8192 (mt-10) REVERT: Q 244 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8180 (p0) REVERT: Q 291 LYS cc_start: 0.5886 (mmtt) cc_final: 0.5440 (mptt) REVERT: R 244 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8764 (p0) REVERT: R 330 ILE cc_start: 0.9081 (tp) cc_final: 0.8726 (mt) outliers start: 49 outliers final: 36 residues processed: 327 average time/residue: 0.7496 time to fit residues: 410.7926 Evaluate side-chains 305 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 265 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 137 GLN Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 157 optimal weight: 0.0370 chunk 33 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 GLN L 137 GLN N 41 GLN Q 12 ASN R 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27036 Z= 0.301 Angle : 0.615 6.915 36684 Z= 0.301 Chirality : 0.044 0.163 4068 Planarity : 0.004 0.039 4689 Dihedral : 10.526 147.177 3774 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.98 % Allowed : 10.54 % Favored : 87.47 % 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: -0.40 (0.15), residues: 3303 helix: -0.33 (0.14), residues: 1359 sheet: -0.57 (0.22), residues: 558 loop : 0.21 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 356 HIS 0.003 0.001 HIS Q 101 PHE 0.012 0.001 PHE L 31 TYR 0.010 0.001 TYR M 133 ARG 0.002 0.000 ARG M 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 277 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8480 (tpt) cc_final: 0.8098 (tpt) REVERT: J 259 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: K 244 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7147 (p0) REVERT: L 176 MET cc_start: 0.8978 (tpp) cc_final: 0.8759 (mmt) REVERT: L 277 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9205 (t) REVERT: M 82 MET cc_start: 0.9332 (tpt) cc_final: 0.8826 (tpt) REVERT: M 334 GLU cc_start: 0.8042 (pp20) cc_final: 0.7794 (pp20) REVERT: N 121 GLN cc_start: 0.8391 (tt0) cc_final: 0.8071 (tt0) REVERT: N 190 MET cc_start: 0.8413 (mtm) cc_final: 0.8141 (mtp) REVERT: O 82 MET cc_start: 0.8998 (tpt) cc_final: 0.8540 (tpt) REVERT: P 93 GLU cc_start: 0.7442 (pm20) cc_final: 0.6802 (pt0) REVERT: P 325 MET cc_start: 0.8218 (ptp) cc_final: 0.7853 (ptp) REVERT: Q 81 ASP cc_start: 0.7593 (m-30) cc_final: 0.7378 (m-30) REVERT: Q 244 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8092 (p0) REVERT: Q 291 LYS cc_start: 0.5910 (mmtt) cc_final: 0.5450 (mptt) REVERT: R 244 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8428 (p0) outliers start: 56 outliers final: 42 residues processed: 325 average time/residue: 0.7376 time to fit residues: 403.0780 Evaluate side-chains 311 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 264 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 259 GLU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 259 GLU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Q 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27036 Z= 0.340 Angle : 0.625 7.541 36684 Z= 0.306 Chirality : 0.045 0.180 4068 Planarity : 0.004 0.040 4689 Dihedral : 10.290 150.508 3774 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.05 % Allowed : 10.97 % Favored : 86.98 % 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: -0.45 (0.15), residues: 3303 helix: -0.27 (0.14), residues: 1377 sheet: -0.61 (0.22), residues: 558 loop : 0.09 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 356 HIS 0.003 0.001 HIS Q 101 PHE 0.012 0.001 PHE L 31 TYR 0.011 0.001 TYR M 133 ARG 0.003 0.000 ARG K 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 267 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8475 (tpt) cc_final: 0.7938 (tpt) REVERT: J 259 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: K 93 GLU cc_start: 0.6724 (pm20) cc_final: 0.6160 (pt0) REVERT: K 244 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7247 (p0) REVERT: L 277 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9230 (t) REVERT: M 82 MET cc_start: 0.9335 (tpt) cc_final: 0.8811 (tpt) REVERT: M 93 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: N 121 GLN cc_start: 0.8425 (tt0) cc_final: 0.8091 (tt0) REVERT: N 190 MET cc_start: 0.8425 (mtm) cc_final: 0.8138 (mtp) REVERT: O 77 THR cc_start: 0.9188 (p) cc_final: 0.8796 (t) REVERT: O 82 MET cc_start: 0.8982 (tpt) cc_final: 0.8581 (tpt) REVERT: P 93 GLU cc_start: 0.7318 (pm20) cc_final: 0.7024 (pt0) REVERT: P 325 MET cc_start: 0.8218 (ptp) cc_final: 0.7808 (ptp) REVERT: Q 81 ASP cc_start: 0.7652 (m-30) cc_final: 0.7427 (m-30) REVERT: Q 93 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6634 (pt0) REVERT: Q 244 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8085 (p0) REVERT: Q 291 LYS cc_start: 0.5918 (mmtt) cc_final: 0.5546 (mptt) REVERT: R 244 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8489 (p0) outliers start: 58 outliers final: 45 residues processed: 319 average time/residue: 0.7358 time to fit residues: 395.4268 Evaluate side-chains 311 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 259 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 259 GLU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 259 GLU Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 137 GLN Q 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27036 Z= 0.256 Angle : 0.585 6.766 36684 Z= 0.282 Chirality : 0.044 0.153 4068 Planarity : 0.003 0.041 4689 Dihedral : 9.940 145.576 3774 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.95 % Allowed : 11.75 % Favored : 86.31 % 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: -0.30 (0.15), residues: 3303 helix: -0.12 (0.14), residues: 1377 sheet: -0.59 (0.22), residues: 558 loop : 0.15 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.002 0.001 HIS N 101 PHE 0.010 0.001 PHE L 31 TYR 0.010 0.001 TYR N 198 ARG 0.005 0.000 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 270 time to evaluate : 4.091 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: J 82 MET cc_start: 0.8470 (tpt) cc_final: 0.7987 (tpt) REVERT: J 259 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8284 (tm-30) REVERT: J 313 MET cc_start: 0.8615 (mmm) cc_final: 0.8261 (mtp) REVERT: K 93 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5921 (pt0) REVERT: K 244 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7227 (p0) REVERT: N 121 GLN cc_start: 0.8416 (tt0) cc_final: 0.8090 (tt0) REVERT: N 190 MET cc_start: 0.8329 (mtm) cc_final: 0.8050 (mtp) REVERT: O 77 THR cc_start: 0.9180 (p) cc_final: 0.8794 (t) REVERT: O 82 MET cc_start: 0.8981 (tpt) cc_final: 0.8270 (tpt) REVERT: P 325 MET cc_start: 0.8174 (ptp) cc_final: 0.7742 (ptp) REVERT: Q 93 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: Q 244 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8073 (p0) REVERT: Q 291 LYS cc_start: 0.6126 (mmtt) cc_final: 0.5631 (mptt) REVERT: R 244 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8426 (p0) outliers start: 55 outliers final: 37 residues processed: 317 average time/residue: 0.7260 time to fit residues: 390.0280 Evaluate side-chains 300 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 257 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 259 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 259 GLU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 271 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 27036 Z= 0.376 Angle : 0.628 7.932 36684 Z= 0.308 Chirality : 0.045 0.186 4068 Planarity : 0.004 0.040 4689 Dihedral : 9.886 146.490 3770 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.16 % Allowed : 12.14 % Favored : 85.70 % 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: -0.46 (0.15), residues: 3303 helix: -0.21 (0.14), residues: 1377 sheet: -0.66 (0.22), residues: 558 loop : 0.02 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 356 HIS 0.003 0.001 HIS N 40 PHE 0.012 0.001 PHE L 31 TYR 0.011 0.001 TYR M 133 ARG 0.003 0.000 ARG M 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 259 time to evaluate : 3.718 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: J 82 MET cc_start: 0.8480 (tpt) cc_final: 0.8009 (tpt) REVERT: J 259 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: J 313 MET cc_start: 0.8635 (mmm) cc_final: 0.8291 (mtp) REVERT: K 93 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5873 (pt0) REVERT: K 244 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7491 (p0) REVERT: M 82 MET cc_start: 0.9314 (tpt) cc_final: 0.8953 (tpt) REVERT: N 121 GLN cc_start: 0.8435 (tt0) cc_final: 0.8094 (tt0) REVERT: N 190 MET cc_start: 0.8352 (mtm) cc_final: 0.8066 (mtp) REVERT: O 77 THR cc_start: 0.9203 (p) cc_final: 0.8839 (t) REVERT: P 132 MET cc_start: 0.9099 (ppp) cc_final: 0.8741 (ppp) REVERT: P 325 MET cc_start: 0.8258 (ptp) cc_final: 0.7889 (ptp) REVERT: Q 244 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8076 (p0) REVERT: Q 291 LYS cc_start: 0.6150 (mmtt) cc_final: 0.5607 (mptt) REVERT: R 41 GLN cc_start: 0.7894 (tt0) cc_final: 0.7564 (tt0) REVERT: R 244 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8490 (p0) outliers start: 61 outliers final: 50 residues processed: 311 average time/residue: 0.7136 time to fit residues: 376.3671 Evaluate side-chains 310 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 259 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 259 GLU Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 201 VAL Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27036 Z= 0.272 Angle : 0.586 6.693 36684 Z= 0.282 Chirality : 0.044 0.160 4068 Planarity : 0.003 0.042 4689 Dihedral : 9.624 150.151 3767 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.09 % Allowed : 12.60 % Favored : 85.31 % 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: -0.42 (0.15), residues: 3303 helix: -0.18 (0.14), residues: 1431 sheet: -0.63 (0.22), residues: 558 loop : 0.05 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.003 0.001 HIS Q 101 PHE 0.010 0.001 PHE L 31 TYR 0.010 0.001 TYR N 198 ARG 0.003 0.000 ARG M 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 266 time to evaluate : 3.840 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: J 82 MET cc_start: 0.8461 (tpt) cc_final: 0.8014 (tpt) REVERT: J 259 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: J 313 MET cc_start: 0.8600 (mmm) cc_final: 0.8264 (mtp) REVERT: K 93 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5785 (pt0) REVERT: K 244 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7448 (p0) REVERT: L 47 MET cc_start: 0.5610 (tmm) cc_final: 0.5083 (tmm) REVERT: M 82 MET cc_start: 0.9320 (tpt) cc_final: 0.8927 (tpt) REVERT: N 121 GLN cc_start: 0.8417 (tt0) cc_final: 0.8089 (tt0) REVERT: N 190 MET cc_start: 0.8328 (mtm) cc_final: 0.8035 (mtp) REVERT: O 77 THR cc_start: 0.9187 (p) cc_final: 0.8817 (t) REVERT: P 325 MET cc_start: 0.8222 (ptp) cc_final: 0.7837 (ptp) REVERT: Q 244 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8058 (p0) REVERT: Q 291 LYS cc_start: 0.5845 (mmtt) cc_final: 0.5268 (mptt) REVERT: R 41 GLN cc_start: 0.7903 (tt0) cc_final: 0.7580 (tt0) REVERT: R 244 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8440 (p0) outliers start: 59 outliers final: 47 residues processed: 317 average time/residue: 0.7013 time to fit residues: 378.4934 Evaluate side-chains 307 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 255 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 259 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 259 GLU Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.9990 chunk 307 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 180 optimal weight: 0.0070 chunk 130 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27036 Z= 0.262 Angle : 0.582 7.051 36684 Z= 0.279 Chirality : 0.044 0.195 4068 Planarity : 0.003 0.043 4689 Dihedral : 9.456 150.966 3767 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.09 % Allowed : 12.67 % Favored : 85.24 % 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: -0.37 (0.15), residues: 3303 helix: -0.12 (0.14), residues: 1431 sheet: -0.59 (0.22), residues: 558 loop : 0.06 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.003 0.001 HIS N 275 PHE 0.009 0.001 PHE L 31 TYR 0.010 0.001 TYR J 169 ARG 0.002 0.000 ARG N 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 266 time to evaluate : 4.054 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: J 82 MET cc_start: 0.8418 (tpt) cc_final: 0.8009 (tpt) REVERT: J 259 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: J 313 MET cc_start: 0.8586 (mmm) cc_final: 0.8263 (mtp) REVERT: K 93 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5764 (pt0) REVERT: K 244 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7450 (p0) REVERT: M 82 MET cc_start: 0.9310 (tpt) cc_final: 0.8975 (tpt) REVERT: N 121 GLN cc_start: 0.8411 (tt0) cc_final: 0.8088 (tt0) REVERT: N 190 MET cc_start: 0.8314 (mtm) cc_final: 0.8033 (mtp) REVERT: O 77 THR cc_start: 0.9186 (p) cc_final: 0.8816 (t) REVERT: P 325 MET cc_start: 0.8224 (ptp) cc_final: 0.7899 (ptp) REVERT: Q 244 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8064 (p0) REVERT: Q 291 LYS cc_start: 0.5836 (mmtt) cc_final: 0.5300 (mptt) REVERT: R 244 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8465 (p0) outliers start: 59 outliers final: 50 residues processed: 318 average time/residue: 0.6925 time to fit residues: 373.9910 Evaluate side-chains 315 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 260 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 259 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 259 GLU Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 288 ASP Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 150 optimal weight: 0.2980 chunk 219 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 305 optimal weight: 0.3980 chunk 264 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27036 Z= 0.253 Angle : 0.576 6.713 36684 Z= 0.276 Chirality : 0.043 0.157 4068 Planarity : 0.003 0.043 4689 Dihedral : 9.325 151.420 3767 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.88 % Allowed : 13.20 % Favored : 84.93 % 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: -0.41 (0.15), residues: 3303 helix: -0.18 (0.14), residues: 1476 sheet: -0.50 (0.22), residues: 585 loop : 0.04 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.005 0.001 HIS N 275 PHE 0.008 0.001 PHE L 31 TYR 0.009 0.001 TYR M 133 ARG 0.002 0.000 ARG N 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 268 time to evaluate : 4.129 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: J 82 MET cc_start: 0.8411 (tpt) cc_final: 0.8005 (tpt) REVERT: J 259 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: J 313 MET cc_start: 0.8576 (mmm) cc_final: 0.8255 (mtp) REVERT: K 93 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5780 (pt0) REVERT: K 244 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7449 (p0) REVERT: M 82 MET cc_start: 0.9302 (tpt) cc_final: 0.8987 (tpt) REVERT: N 121 GLN cc_start: 0.8402 (tt0) cc_final: 0.8077 (tt0) REVERT: N 190 MET cc_start: 0.8306 (mtm) cc_final: 0.8013 (mtp) REVERT: O 77 THR cc_start: 0.9167 (p) cc_final: 0.8793 (t) REVERT: P 325 MET cc_start: 0.8227 (ptp) cc_final: 0.7958 (ptp) REVERT: Q 244 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8070 (p0) REVERT: Q 291 LYS cc_start: 0.5824 (mmtt) cc_final: 0.5321 (mptt) REVERT: R 41 GLN cc_start: 0.7958 (tt0) cc_final: 0.7639 (tt0) REVERT: R 244 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8408 (p0) outliers start: 53 outliers final: 48 residues processed: 315 average time/residue: 0.6979 time to fit residues: 375.9635 Evaluate side-chains 315 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 262 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 259 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 259 GLU Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 0.7980 chunk 281 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104820 restraints weight = 113273.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109060 restraints weight = 40308.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111385 restraints weight = 18967.643| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27036 Z= 0.186 Angle : 0.550 7.200 36684 Z= 0.260 Chirality : 0.043 0.177 4068 Planarity : 0.003 0.044 4689 Dihedral : 9.019 150.089 3767 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.52 % Allowed : 13.55 % Favored : 84.93 % 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: -0.24 (0.15), residues: 3303 helix: -0.04 (0.14), residues: 1476 sheet: -0.56 (0.22), residues: 603 loop : 0.22 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.003 0.001 HIS M 275 PHE 0.010 0.001 PHE Q 124 TYR 0.009 0.001 TYR N 198 ARG 0.005 0.000 ARG O 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9073.06 seconds wall clock time: 161 minutes 24.11 seconds (9684.11 seconds total)