Starting phenix.real_space_refine on Tue Mar 26 00:48:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/03_2024/8uz0_42829_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/03_2024/8uz0_42829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/03_2024/8uz0_42829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/03_2024/8uz0_42829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/03_2024/8uz0_42829_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/03_2024/8uz0_42829_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.117 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: 7 Type Number sf(0) Gaussians P 18 5.49 5 Mg 9 5.21 5 S 189 5.16 5 C 16668 2.51 5 N 4455 2.21 5 O 5094 1.98 5 H 25857 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 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 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 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 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 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 253": "OE1" <-> "OE2" Residue "M ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 "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: 52290 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: 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: "M" 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.99, per 1000 atoms: 0.40 Number of scatterers: 52290 At special positions: 0 Unit cell: (92.874, 100.95, 302.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 189 16.00 P 18 15.00 Mg 9 11.99 O 5094 8.00 N 4455 7.00 C 16668 6.00 H 25857 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=0, symmetry=0 Time building additional restraints: 39.43 Conformation dependent library (CDL) restraints added in 5.2 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: 174 helices and 45 sheets defined 42.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.95 Creating SS restraints... Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 79 through 91 removed outlier: 4.301A 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: 3.556A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 196 removed outlier: 3.564A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 216 Processing helix chain 'J' and resid 223 through 231 removed outlier: 3.553A pdb=" N ALA J 231 " --> pdb=" O MET J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 256 removed outlier: 3.675A 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 287 through 296 removed outlier: 4.572A pdb=" N LYS J 291 " --> pdb=" O ILE J 287 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP J 292 " --> pdb=" O ASP J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 305 Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 333 through 336 removed outlier: 4.449A pdb=" N LYS J 336 " --> pdb=" O PRO J 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 333 through 336' Processing helix chain 'J' and resid 338 through 346 Processing helix chain 'J' and resid 350 through 352 No H-bonds generated for 'chain 'J' and resid 350 through 352' 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 372 removed outlier: 3.582A pdb=" N HIS J 371 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 64 removed outlier: 6.148A pdb=" N GLY K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 91 removed outlier: 3.836A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 125 Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.776A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.507A 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 removed outlier: 4.042A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 216 removed outlier: 3.809A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 231 Processing helix chain 'K' and resid 252 through 256 removed outlier: 3.866A 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 284 Processing helix chain 'K' and resid 287 through 296 removed outlier: 4.525A pdb=" N LYS K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA K 295 " --> pdb=" O LYS K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 304 No H-bonds generated for 'chain 'K' and resid 302 through 304' Processing helix chain 'K' and resid 309 through 320 Processing helix chain 'K' and resid 338 through 348 removed outlier: 3.534A pdb=" N SER K 348 " --> pdb=" O SER K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 354 removed outlier: 3.555A pdb=" N GLN K 353 " --> pdb=" O SER K 350 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 350 through 354' Processing helix chain 'K' and resid 359 through 362 No H-bonds generated for 'chain 'K' and resid 359 through 362' Processing helix chain 'K' and resid 367 through 373 removed outlier: 4.006A pdb=" N LYS K 373 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 64 removed outlier: 5.924A pdb=" N GLY L 63 " --> pdb=" O GLN L 59 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 91 removed outlier: 3.971A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 145 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: 3.813A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 removed outlier: 3.753A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 231 Processing helix chain 'L' and resid 252 through 256 removed outlier: 4.094A 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 284 Processing helix chain 'L' and resid 287 through 296 removed outlier: 4.468A pdb=" N LYS L 291 " --> pdb=" O ASP L 288 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR L 294 " --> pdb=" O LYS L 291 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA L 295 " --> pdb=" O ASP L 292 " (cutoff:3.500A) 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 335 through 348 removed outlier: 5.805A pdb=" N VAL L 339 " --> pdb=" O LYS L 336 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE L 341 " --> pdb=" O SER L 338 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA L 347 " --> pdb=" O SER L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 352 No H-bonds generated for 'chain 'L' and resid 350 through 352' 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 Processing helix chain 'M' and resid 55 through 64 removed outlier: 3.611A pdb=" N GLN M 59 " --> pdb=" O ASP M 56 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER M 60 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG M 62 " --> pdb=" O GLN M 59 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 91 removed outlier: 3.650A 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: 3.704A pdb=" N LEU M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 196 removed outlier: 3.569A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 216 removed outlier: 3.693A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.010A 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 296 removed outlier: 4.760A pdb=" N LYS M 291 " --> pdb=" O ILE M 287 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP M 292 " --> pdb=" O ASP M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 304 No H-bonds generated for 'chain 'M' and resid 302 through 304' Processing helix chain 'M' and resid 309 through 320 Processing helix chain 'M' and resid 338 through 348 removed outlier: 3.649A pdb=" N SER M 348 " --> pdb=" O SER M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 352 No H-bonds generated for 'chain 'M' and resid 350 through 352' Processing helix chain 'M' and resid 359 through 364 removed outlier: 4.285A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 373 removed outlier: 4.323A pdb=" N LYS M 373 " --> pdb=" O VAL M 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 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: 3.957A 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: 3.603A pdb=" N LEU N 142 " --> pdb=" O ALA N 138 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.548A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 216 removed outlier: 3.783A pdb=" N GLU N 207 " --> pdb=" O THR N 203 " (cutoff:3.500A) removed outlier: 3.684A 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 256 removed outlier: 4.088A pdb=" N ARG N 256 " --> pdb=" O GLU N 253 " (cutoff:3.500A) 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 294 removed outlier: 4.569A pdb=" N LYS N 291 " --> pdb=" O ILE N 287 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP N 292 " --> pdb=" O ASP N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 304 No H-bonds generated for 'chain 'N' and resid 302 through 304' Processing helix chain 'N' and resid 309 through 320 Processing helix chain 'N' and resid 335 through 348 removed outlier: 6.021A pdb=" N VAL N 339 " --> pdb=" O LYS N 336 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY N 342 " --> pdb=" O VAL N 339 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA N 347 " --> pdb=" O SER N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 352 No H-bonds generated for 'chain 'N' and resid 350 through 352' 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: 3.627A pdb=" N HIS N 371 " --> pdb=" O SER N 368 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS N 373 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 64 removed outlier: 5.983A pdb=" N GLY O 63 " --> pdb=" O GLN O 59 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 91 removed outlier: 3.959A pdb=" N LYS O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 125 Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.522A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR O 143 " --> pdb=" O VAL O 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER O 145 " --> pdb=" O SER O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 182 through 196 removed outlier: 3.585A pdb=" N THR O 194 " --> pdb=" O MET O 190 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 216 removed outlier: 3.704A pdb=" N GLU O 207 " --> pdb=" O THR O 203 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 231 Processing helix chain 'O' and resid 252 through 256 removed outlier: 3.872A pdb=" N ARG O 256 " --> pdb=" O GLU O 253 " (cutoff:3.500A) 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 283 Processing helix chain 'O' and resid 290 through 296 removed outlier: 3.540A pdb=" N ASN O 296 " --> pdb=" O ASP O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 305 Processing helix chain 'O' and resid 309 through 320 Processing helix chain 'O' and resid 335 through 348 removed outlier: 5.826A pdb=" N VAL O 339 " --> pdb=" O LYS O 336 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY O 342 " --> pdb=" O VAL O 339 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA O 347 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 352 No H-bonds generated for 'chain 'O' and resid 350 through 352' Processing helix chain 'O' and resid 359 through 363 Processing helix chain 'O' and resid 367 through 373 removed outlier: 3.758A 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: 3.615A pdb=" N LYS P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 125 Processing helix chain 'P' and resid 137 through 145 removed outlier: 3.648A 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: 3.820A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG P 196 " --> pdb=" O ILE P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 216 removed outlier: 3.985A pdb=" N GLU P 207 " --> pdb=" O THR P 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 231 Processing helix chain 'P' and resid 253 through 256 No H-bonds generated for 'chain 'P' and resid 253 through 256' 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 284 Processing helix chain 'P' and resid 287 through 296 removed outlier: 4.407A pdb=" N LYS P 291 " --> pdb=" O ASP P 288 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR P 294 " --> pdb=" O LYS P 291 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA P 295 " --> pdb=" O ASP P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 302 through 304 No H-bonds generated for 'chain 'P' and resid 302 through 304' Processing helix chain 'P' and resid 309 through 320 Processing helix chain 'P' and resid 338 through 348 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: 3.632A pdb=" N LYS P 373 " --> pdb=" O VAL P 370 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 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: 3.985A pdb=" N LYS Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 125 Processing helix chain 'Q' and resid 137 through 145 removed outlier: 3.505A pdb=" N LEU Q 142 " --> pdb=" O ALA Q 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR Q 143 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 196 removed outlier: 3.704A pdb=" N THR Q 194 " --> pdb=" O MET Q 190 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG Q 196 " --> pdb=" O ILE Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 216 removed outlier: 3.528A 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 256 removed outlier: 3.824A pdb=" N ARG Q 256 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) 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 284 Processing helix chain 'Q' and resid 287 through 295 removed outlier: 4.290A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA Q 295 " --> pdb=" O LYS Q 291 " (cutoff:3.500A) 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: 5.975A pdb=" N VAL Q 339 " --> pdb=" O LYS Q 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE Q 341 " --> pdb=" O SER Q 338 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA Q 347 " --> pdb=" O SER Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 354 removed outlier: 4.165A pdb=" N GLN Q 354 " --> pdb=" O THR Q 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 351 through 354' Processing helix chain 'Q' and resid 359 through 362 No H-bonds generated for 'chain 'Q' and resid 359 through 362' Processing helix chain 'Q' and resid 367 through 373 removed outlier: 3.847A pdb=" N HIS Q 371 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 64 removed outlier: 5.870A pdb=" N GLY R 63 " --> pdb=" O GLN R 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 91 removed outlier: 4.195A 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: 3.846A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 144 " --> pdb=" O LEU R 140 " (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: 4.027A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 216 removed outlier: 3.699A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 231 Processing helix chain 'R' and resid 252 through 256 removed outlier: 3.889A pdb=" N ARG R 256 " --> pdb=" O GLU R 253 " (cutoff:3.500A) 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 295 removed outlier: 4.323A pdb=" N LYS R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP R 292 " --> pdb=" O ASP R 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA R 295 " --> pdb=" O LYS R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 304 No H-bonds generated for 'chain 'R' and resid 302 through 304' Processing helix chain 'R' and resid 309 through 320 Processing helix chain 'R' and resid 333 through 336 removed outlier: 4.502A 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 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: 3.984A pdb=" N HIS R 371 " --> pdb=" O SER R 368 " (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: 6.335A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 6.610A 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 Processing sheet with id= I, first strand: chain 'K' and resid 297 through 300 removed outlier: 6.165A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.563A 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 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 Processing sheet with id= N, first strand: chain 'L' and resid 297 through 300 removed outlier: 6.189A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) 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 12 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 Processing sheet with id= S, first strand: chain 'M' and resid 297 through 300 removed outlier: 6.275A pdb=" N ILE M 151 " --> pdb=" O VAL M 298 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER M 300 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 6.458A 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 34 through 38 Processing sheet with id= W, first strand: chain 'N' and resid 103 through 107 Processing sheet with id= X, first strand: chain 'N' and resid 297 through 300 removed outlier: 6.217A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (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 12 removed outlier: 4.197A pdb=" N GLY O 15 " --> pdb=" O SER O 33 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 35 through 38 Processing sheet with id= AB, first strand: chain 'O' and resid 103 through 107 Processing sheet with id= AC, first strand: chain 'O' and resid 297 through 300 removed outlier: 6.502A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) 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 12 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 Processing sheet with id= AH, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.144A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (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 297 through 300 removed outlier: 6.329A pdb=" N ILE Q 151 " --> pdb=" O VAL Q 298 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER Q 300 " --> pdb=" O ILE Q 151 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU Q 153 " --> pdb=" O SER Q 300 " (cutoff:3.500A) 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 297 through 300 removed outlier: 6.282A pdb=" N ILE R 151 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER R 300 " --> pdb=" O ILE R 151 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU R 153 " --> pdb=" O SER R 300 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'R' and resid 238 through 241 946 hydrogen bonds defined for protein. 2391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.11 Time building geometry restraints manager: 41.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.10: 25812 1.10 - 1.28: 4410 1.28 - 1.46: 8663 1.46 - 1.64: 13648 1.64 - 1.82: 333 Bond restraints: 52866 Sorted by residual: bond pdb=" N MET R 47 " pdb=" H MET R 47 " 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 R 108 " pdb=" H ALA R 108 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 HIS R 371 " pdb=" HE2 HIS R 371 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD1 TYR P 169 " pdb=" HD1 TYR P 169 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 HIS R 161 " pdb=" HE1 HIS R 161 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 52861 not shown) Histogram of bond angle deviations from ideal: 94.93 - 103.21: 381 103.21 - 111.50: 55896 111.50 - 119.79: 23072 119.79 - 128.08: 16024 128.08 - 136.36: 162 Bond angle restraints: 95535 Sorted by residual: angle pdb=" CA ASP P 244 " pdb=" CB ASP P 244 " pdb=" CG ASP P 244 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.43e+01 angle pdb=" CA ASP R 244 " pdb=" CB ASP R 244 " pdb=" CG ASP R 244 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA ASP L 244 " pdb=" CB ASP L 244 " pdb=" CG ASP L 244 " ideal model delta sigma weight residual 112.60 118.92 -6.32 1.00e+00 1.00e+00 3.99e+01 angle pdb=" C ILE M 330 " pdb=" CA ILE M 330 " pdb=" CB ILE M 330 " ideal model delta sigma weight residual 111.53 119.74 -8.21 1.30e+00 5.92e-01 3.98e+01 angle pdb=" CA ASP O 244 " pdb=" CB ASP O 244 " pdb=" CG ASP O 244 " ideal model delta sigma weight residual 112.60 118.89 -6.29 1.00e+00 1.00e+00 3.95e+01 ... (remaining 95530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 23787 33.64 - 67.27: 1044 67.27 - 100.91: 81 100.91 - 134.55: 9 134.55 - 168.19: 9 Dihedral angle restraints: 24930 sinusoidal: 13707 harmonic: 11223 Sorted by residual: dihedral pdb=" C GLU Q 93 " pdb=" N GLU Q 93 " pdb=" CA GLU Q 93 " pdb=" CB GLU Q 93 " ideal model delta harmonic sigma weight residual -122.60 -142.81 20.21 0 2.50e+00 1.60e-01 6.53e+01 dihedral pdb=" C GLU L 93 " pdb=" N GLU L 93 " pdb=" CA GLU L 93 " pdb=" CB GLU L 93 " ideal model delta harmonic sigma weight residual -122.60 -142.05 19.45 0 2.50e+00 1.60e-01 6.05e+01 dihedral pdb=" N GLU Q 93 " pdb=" C GLU Q 93 " pdb=" CA GLU Q 93 " pdb=" CB GLU Q 93 " ideal model delta harmonic sigma weight residual 122.80 141.69 -18.89 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 24927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 3587 0.161 - 0.322: 429 0.322 - 0.483: 38 0.483 - 0.644: 10 0.644 - 0.805: 4 Chirality restraints: 4068 Sorted by residual: chirality pdb=" CA GLU Q 93 " pdb=" N GLU Q 93 " pdb=" C GLU Q 93 " pdb=" CB GLU Q 93 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA GLU L 93 " pdb=" N GLU L 93 " pdb=" C GLU L 93 " pdb=" CB GLU L 93 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA GLU N 93 " pdb=" N GLU N 93 " pdb=" C GLU N 93 " pdb=" CB GLU N 93 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4065 not shown) Planarity restraints: 7848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 340 " 0.308 2.00e-02 2.50e+03 1.17e-01 5.49e+02 pdb=" CG TRP J 340 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP J 340 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP J 340 " -0.115 2.00e-02 2.50e+03 pdb=" NE1 TRP J 340 " -0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP J 340 " -0.092 2.00e-02 2.50e+03 pdb=" CE3 TRP J 340 " -0.122 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 340 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP J 340 " 0.061 2.00e-02 2.50e+03 pdb=" HD1 TRP J 340 " 0.079 2.00e-02 2.50e+03 pdb=" HE1 TRP J 340 " -0.024 2.00e-02 2.50e+03 pdb=" HE3 TRP J 340 " -0.165 2.00e-02 2.50e+03 pdb=" HZ2 TRP J 340 " 0.058 2.00e-02 2.50e+03 pdb=" HZ3 TRP J 340 " 0.037 2.00e-02 2.50e+03 pdb=" HH2 TRP J 340 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 340 " 0.288 2.00e-02 2.50e+03 1.12e-01 5.00e+02 pdb=" CG TRP O 340 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP O 340 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP O 340 " -0.118 2.00e-02 2.50e+03 pdb=" NE1 TRP O 340 " -0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP O 340 " -0.100 2.00e-02 2.50e+03 pdb=" CE3 TRP O 340 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 340 " -0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP O 340 " 0.058 2.00e-02 2.50e+03 pdb=" HD1 TRP O 340 " 0.085 2.00e-02 2.50e+03 pdb=" HE1 TRP O 340 " -0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP O 340 " -0.152 2.00e-02 2.50e+03 pdb=" HZ2 TRP O 340 " 0.047 2.00e-02 2.50e+03 pdb=" HZ3 TRP O 340 " 0.048 2.00e-02 2.50e+03 pdb=" HH2 TRP O 340 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 340 " 0.297 2.00e-02 2.50e+03 1.08e-01 4.70e+02 pdb=" CG TRP P 340 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP P 340 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP P 340 " -0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP P 340 " -0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP P 340 " -0.082 2.00e-02 2.50e+03 pdb=" CE3 TRP P 340 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 340 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 340 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP P 340 " 0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP P 340 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 TRP P 340 " -0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP P 340 " -0.152 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 340 " 0.060 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 340 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP P 340 " 0.155 2.00e-02 2.50e+03 ... (remaining 7845 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 1315 1.97 - 2.62: 57699 2.62 - 3.28: 164098 3.28 - 3.94: 219553 3.94 - 4.60: 331813 Nonbonded interactions: 774478 Sorted by model distance: nonbonded pdb=" H GLY R 302 " pdb=" O2A ADP R 401 " model vdw 1.308 1.850 nonbonded pdb=" H GLY J 302 " pdb=" O2A ADP J 401 " model vdw 1.322 1.850 nonbonded pdb=" H GLY K 302 " pdb=" O2A ADP K 401 " model vdw 1.372 1.850 nonbonded pdb=" H GLY P 302 " pdb=" O2A ADP P 401 " model vdw 1.416 1.850 nonbonded pdb=" H GLY O 302 " pdb=" O2A ADP O 401 " model vdw 1.452 1.850 ... (remaining 774473 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.740 Extract box with map and model: 6.530 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 157.840 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.320 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 0.091 27009 Z= 0.776 Angle : 1.890 9.531 36657 Z= 1.253 Chirality : 0.112 0.805 4068 Planarity : 0.017 0.187 4689 Dihedral : 15.935 168.186 10053 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 3.11 % Allowed : 5.17 % Favored : 91.72 % Cbeta Deviations : 1.29 % 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: -1.29 (0.13), residues: 3303 helix: -1.72 (0.12), residues: 1305 sheet: 0.40 (0.23), residues: 360 loop : -0.22 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.206 0.034 TRP J 340 HIS 0.014 0.004 HIS L 275 PHE 0.067 0.013 PHE Q 262 TYR 0.132 0.019 TYR N 69 ARG 0.021 0.002 ARG P 210 *********************** 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 616 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 528 time to evaluate : 3.907 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: J 82 MET cc_start: 0.7861 (tpt) cc_final: 0.7603 (tpt) REVERT: J 195 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: J 244 ASP cc_start: 0.4099 (OUTLIER) cc_final: 0.2269 (m-30) REVERT: J 283 MET cc_start: 0.9226 (mmm) cc_final: 0.8840 (mmm) REVERT: J 326 LYS cc_start: 0.8230 (pttt) cc_final: 0.7980 (ptmt) REVERT: J 330 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8102 (mt) REVERT: K 227 MET cc_start: 0.8943 (mmm) cc_final: 0.8620 (mmm) REVERT: K 269 MET cc_start: 0.8857 (ptp) cc_final: 0.8586 (ptp) REVERT: L 17 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8296 (p) REVERT: L 82 MET cc_start: 0.8743 (tpt) cc_final: 0.8531 (tpp) REVERT: L 277 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (m) REVERT: M 54 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8841 (t) REVERT: M 111 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8836 (t0) REVERT: M 326 LYS cc_start: 0.7655 (pttt) cc_final: 0.7223 (mmtm) REVERT: M 361 GLU cc_start: 0.8250 (tt0) cc_final: 0.7993 (tt0) REVERT: N 50 LYS cc_start: 0.8165 (tttt) cc_final: 0.7962 (ttmt) REVERT: N 119 MET cc_start: 0.8852 (ttm) cc_final: 0.8565 (ttp) REVERT: N 132 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9252 (ppp) REVERT: N 176 MET cc_start: 0.9081 (mmm) cc_final: 0.8849 (mmm) REVERT: N 225 ASN cc_start: 0.8314 (t0) cc_final: 0.7900 (t0) REVERT: N 227 MET cc_start: 0.8379 (mmm) cc_final: 0.8098 (mmm) REVERT: N 269 MET cc_start: 0.8948 (ptp) cc_final: 0.8452 (ptm) REVERT: N 328 LYS cc_start: 0.8419 (ttpm) cc_final: 0.8210 (tttt) REVERT: O 17 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8154 (p) REVERT: O 47 MET cc_start: 0.7254 (ttp) cc_final: 0.6985 (ttp) REVERT: O 82 MET cc_start: 0.9254 (tpt) cc_final: 0.8962 (tpt) REVERT: O 123 MET cc_start: 0.9015 (tpp) cc_final: 0.8785 (tpp) REVERT: O 190 MET cc_start: 0.9218 (mtm) cc_final: 0.9016 (mtp) REVERT: O 227 MET cc_start: 0.9070 (mmm) cc_final: 0.8689 (mmm) REVERT: O 283 MET cc_start: 0.9135 (mmt) cc_final: 0.8731 (mmm) REVERT: P 17 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8272 (p) REVERT: P 41 GLN cc_start: 0.7851 (tt0) cc_final: 0.7365 (tp-100) REVERT: P 225 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7823 (m110) REVERT: P 227 MET cc_start: 0.8964 (mmm) cc_final: 0.8647 (mmm) REVERT: P 269 MET cc_start: 0.9058 (ptp) cc_final: 0.8846 (ptm) REVERT: P 313 MET cc_start: 0.8501 (ttp) cc_final: 0.8273 (mtp) REVERT: Q 80 ASP cc_start: 0.8308 (m-30) cc_final: 0.8080 (m-30) REVERT: R 180 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8929 (tt) REVERT: R 191 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8176 (ttmm) REVERT: R 291 LYS cc_start: 0.7115 (mmtt) cc_final: 0.5954 (mptt) outliers start: 88 outliers final: 18 residues processed: 587 average time/residue: 3.0453 time to fit residues: 2075.5864 Evaluate side-chains 341 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 310 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 211 ASP Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 191 LYS Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 302 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 162 ASN ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN K 225 ASN L 121 GLN L 162 ASN O 41 GLN O 137 GLN O 161 HIS P 40 HIS Q 137 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27009 Z= 0.198 Angle : 0.676 6.444 36657 Z= 0.340 Chirality : 0.045 0.160 4068 Planarity : 0.005 0.051 4689 Dihedral : 12.864 179.921 3818 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.04 % Allowed : 11.78 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.10 (0.15), residues: 3303 helix: -0.40 (0.14), residues: 1305 sheet: -0.03 (0.21), residues: 567 loop : 0.53 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 356 HIS 0.004 0.001 HIS J 87 PHE 0.014 0.001 PHE J 127 TYR 0.015 0.001 TYR M 294 ARG 0.005 0.001 ARG J 372 *********************** 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 422 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 336 time to evaluate : 4.080 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: J 82 MET cc_start: 0.7958 (tpt) cc_final: 0.7673 (tpt) REVERT: J 227 MET cc_start: 0.8463 (mmm) cc_final: 0.7852 (tpp) REVERT: J 283 MET cc_start: 0.9064 (mmm) cc_final: 0.8815 (mmm) REVERT: J 326 LYS cc_start: 0.8094 (pttt) cc_final: 0.7718 (pttt) REVERT: J 330 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8021 (mt) REVERT: J 355 MET cc_start: 0.8324 (mtm) cc_final: 0.8119 (mtt) REVERT: K 190 MET cc_start: 0.8818 (mtm) cc_final: 0.8549 (mtm) REVERT: K 227 MET cc_start: 0.8712 (mmm) cc_final: 0.8430 (mmm) REVERT: L 17 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8258 (p) REVERT: M 54 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8820 (t) REVERT: M 61 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8207 (mttt) REVERT: M 72 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: M 118 LYS cc_start: 0.8732 (tptm) cc_final: 0.8424 (mtmt) REVERT: M 361 GLU cc_start: 0.8197 (tt0) cc_final: 0.7915 (tt0) REVERT: N 132 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9219 (ppp) REVERT: N 225 ASN cc_start: 0.8141 (t0) cc_final: 0.7780 (t0) REVERT: N 227 MET cc_start: 0.8384 (mmm) cc_final: 0.8180 (mmm) REVERT: N 328 LYS cc_start: 0.8485 (ttpm) cc_final: 0.8148 (tttt) REVERT: N 336 LYS cc_start: 0.8205 (tptm) cc_final: 0.7847 (ttpt) REVERT: O 17 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8124 (p) REVERT: O 82 MET cc_start: 0.9268 (tpt) cc_final: 0.8964 (tpt) REVERT: O 137 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: O 225 ASN cc_start: 0.8119 (t0) cc_final: 0.7915 (t160) REVERT: O 227 MET cc_start: 0.8684 (mmm) cc_final: 0.8379 (mmm) REVERT: O 234 SER cc_start: 0.8103 (m) cc_final: 0.7395 (t) REVERT: O 283 MET cc_start: 0.8986 (mmt) cc_final: 0.8641 (mmm) REVERT: O 326 LYS cc_start: 0.8080 (pttt) cc_final: 0.7861 (pttp) REVERT: O 355 MET cc_start: 0.9096 (mtt) cc_final: 0.8711 (mtt) REVERT: O 363 ASP cc_start: 0.7981 (p0) cc_final: 0.7545 (p0) REVERT: P 17 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8192 (p) REVERT: P 57 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: P 225 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7743 (m110) REVERT: P 227 MET cc_start: 0.8679 (mmm) cc_final: 0.8299 (mmm) REVERT: P 269 MET cc_start: 0.9009 (ptp) cc_final: 0.8786 (ptm) REVERT: P 329 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8863 (mp) REVERT: P 360 GLN cc_start: 0.8507 (tp40) cc_final: 0.8217 (tp-100) REVERT: Q 137 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: Q 360 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8179 (tm130) REVERT: R 72 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7951 (mp0) REVERT: R 180 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8973 (tt) REVERT: R 227 MET cc_start: 0.8813 (mmm) cc_final: 0.8267 (mmt) REVERT: R 291 LYS cc_start: 0.6717 (mmtt) cc_final: 0.5767 (mptt) outliers start: 86 outliers final: 34 residues processed: 395 average time/residue: 2.8546 time to fit residues: 1321.4840 Evaluate side-chains 341 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 293 time to evaluate : 4.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 95 ARG Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 329 ILE Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 0.0060 chunk 93 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 205 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 225 ASN K 297 ASN L 225 ASN M 162 ASN O 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27009 Z= 0.216 Angle : 0.622 6.573 36657 Z= 0.303 Chirality : 0.044 0.151 4068 Planarity : 0.004 0.050 4689 Dihedral : 11.200 176.182 3796 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.18 % Allowed : 13.13 % Favored : 83.69 % 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: 0.21 (0.15), residues: 3303 helix: 0.05 (0.14), residues: 1323 sheet: -0.04 (0.21), residues: 585 loop : 0.60 (0.18), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 356 HIS 0.004 0.001 HIS R 161 PHE 0.013 0.001 PHE J 90 TYR 0.011 0.001 TYR O 294 ARG 0.003 0.000 ARG M 210 *********************** 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 412 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 322 time to evaluate : 4.181 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: J 82 MET cc_start: 0.7931 (tpt) cc_final: 0.7624 (tpt) REVERT: J 227 MET cc_start: 0.8456 (mmm) cc_final: 0.7872 (tpp) REVERT: J 283 MET cc_start: 0.8998 (mmm) cc_final: 0.8731 (mmm) REVERT: J 314 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: J 326 LYS cc_start: 0.8144 (pttt) cc_final: 0.7734 (pttt) REVERT: J 330 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7946 (mt) REVERT: K 227 MET cc_start: 0.8695 (mmm) cc_final: 0.8482 (mmm) REVERT: L 17 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8283 (p) REVERT: L 57 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: L 72 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: L 119 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8451 (ttp) REVERT: M 61 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8228 (mttt) REVERT: M 72 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: M 95 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7746 (ptp90) REVERT: M 118 LYS cc_start: 0.8744 (tptm) cc_final: 0.8375 (mtmt) REVERT: M 326 LYS cc_start: 0.7831 (pptt) cc_final: 0.6766 (mmtm) REVERT: M 361 GLU cc_start: 0.8341 (tt0) cc_final: 0.7983 (tt0) REVERT: N 17 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8238 (p) REVERT: N 137 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8606 (mt0) REVERT: N 225 ASN cc_start: 0.8166 (t0) cc_final: 0.7829 (t0) REVERT: N 336 LYS cc_start: 0.8311 (tptm) cc_final: 0.8036 (ttpt) REVERT: O 17 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8145 (p) REVERT: O 82 MET cc_start: 0.9222 (tpt) cc_final: 0.8909 (tpt) REVERT: O 106 THR cc_start: 0.8983 (m) cc_final: 0.8756 (m) REVERT: O 225 ASN cc_start: 0.8464 (t0) cc_final: 0.7816 (m110) REVERT: O 227 MET cc_start: 0.8673 (mmm) cc_final: 0.8443 (mmm) REVERT: O 283 MET cc_start: 0.9021 (mmt) cc_final: 0.8680 (mmm) REVERT: O 328 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8414 (tttm) REVERT: O 355 MET cc_start: 0.9090 (mtt) cc_final: 0.8696 (mtt) REVERT: O 363 ASP cc_start: 0.7708 (p0) cc_final: 0.7292 (p0) REVERT: P 17 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8138 (p) REVERT: P 57 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: P 123 MET cc_start: 0.8779 (mmp) cc_final: 0.8522 (mmp) REVERT: P 211 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8473 (t70) REVERT: P 225 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7826 (m110) REVERT: P 227 MET cc_start: 0.8656 (mmm) cc_final: 0.8304 (mmm) REVERT: P 269 MET cc_start: 0.8847 (ptp) cc_final: 0.8631 (ptm) REVERT: P 360 GLN cc_start: 0.8438 (tp40) cc_final: 0.8197 (tp-100) REVERT: Q 72 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: Q 360 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8165 (tm130) REVERT: R 41 GLN cc_start: 0.7671 (tt0) cc_final: 0.7441 (tt0) REVERT: R 72 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7786 (mp0) REVERT: R 227 MET cc_start: 0.8749 (mmm) cc_final: 0.8206 (mmt) REVERT: R 291 LYS cc_start: 0.6460 (mmtt) cc_final: 0.5811 (mptt) outliers start: 90 outliers final: 36 residues processed: 378 average time/residue: 2.8899 time to fit residues: 1280.2126 Evaluate side-chains 349 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 295 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 314 GLN Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 269 MET Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 338 SER 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: 1.9990 chunk 157 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 288 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 297 ASN M 314 GLN P 162 ASN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27009 Z= 0.269 Angle : 0.626 6.462 36657 Z= 0.302 Chirality : 0.045 0.170 4068 Planarity : 0.004 0.050 4689 Dihedral : 9.972 174.347 3786 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 14.33 % Favored : 82.80 % 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: 0.43 (0.15), residues: 3303 helix: 0.26 (0.15), residues: 1305 sheet: -0.01 (0.21), residues: 585 loop : 0.72 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 356 HIS 0.004 0.001 HIS M 161 PHE 0.011 0.001 PHE O 31 TYR 0.012 0.001 TYR P 69 ARG 0.003 0.000 ARG P 37 *********************** 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 385 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 304 time to evaluate : 4.152 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: J 44 MET cc_start: 0.2640 (mmm) cc_final: 0.2314 (mmm) REVERT: J 82 MET cc_start: 0.7931 (tpt) cc_final: 0.7627 (tpt) REVERT: J 227 MET cc_start: 0.8442 (mmm) cc_final: 0.7911 (tpp) REVERT: J 283 MET cc_start: 0.9001 (mmm) cc_final: 0.8750 (mmm) REVERT: J 314 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: J 326 LYS cc_start: 0.8246 (pttt) cc_final: 0.7813 (pttt) REVERT: J 330 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7866 (mt) REVERT: K 227 MET cc_start: 0.8685 (mmm) cc_final: 0.8457 (mmm) REVERT: L 17 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8333 (p) REVERT: L 57 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: L 119 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8467 (ttp) REVERT: L 241 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: M 61 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8289 (mttt) REVERT: M 72 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: M 95 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7721 (ptp90) REVERT: M 283 MET cc_start: 0.8801 (mmp) cc_final: 0.8546 (mmm) REVERT: M 326 LYS cc_start: 0.7985 (pptt) cc_final: 0.6836 (mmtm) REVERT: M 361 GLU cc_start: 0.8390 (tt0) cc_final: 0.8137 (tt0) REVERT: N 137 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8637 (mt0) REVERT: N 225 ASN cc_start: 0.8178 (t0) cc_final: 0.7873 (t0) REVERT: N 336 LYS cc_start: 0.8565 (tptm) cc_final: 0.8165 (ttpt) REVERT: O 17 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8173 (p) REVERT: O 47 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7120 (ttp) REVERT: O 225 ASN cc_start: 0.8508 (t0) cc_final: 0.7854 (m110) REVERT: O 227 MET cc_start: 0.8680 (mmm) cc_final: 0.8423 (mmm) REVERT: O 244 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7453 (p0) REVERT: O 283 MET cc_start: 0.9021 (mmt) cc_final: 0.8707 (mmm) REVERT: O 328 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8377 (tttm) REVERT: O 363 ASP cc_start: 0.7597 (p0) cc_final: 0.7222 (p0) REVERT: P 17 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8197 (p) REVERT: P 57 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: P 211 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8539 (t70) REVERT: P 227 MET cc_start: 0.8662 (mmm) cc_final: 0.8318 (mmm) REVERT: P 269 MET cc_start: 0.8831 (ptp) cc_final: 0.8601 (ptm) REVERT: P 360 GLN cc_start: 0.8524 (tp40) cc_final: 0.8287 (tp-100) REVERT: Q 72 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: Q 360 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8202 (tm130) REVERT: R 72 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8025 (mp0) REVERT: R 227 MET cc_start: 0.8737 (mmm) cc_final: 0.8489 (mmt) REVERT: R 291 LYS cc_start: 0.6294 (mmtt) cc_final: 0.5777 (mptt) REVERT: R 325 MET cc_start: 0.7008 (ptm) cc_final: 0.6717 (ptm) outliers start: 81 outliers final: 44 residues processed: 363 average time/residue: 2.8896 time to fit residues: 1247.9760 Evaluate side-chains 354 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 292 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 314 GLN Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 360 GLN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 27009 Z= 0.376 Angle : 0.662 7.130 36657 Z= 0.324 Chirality : 0.047 0.209 4068 Planarity : 0.005 0.052 4689 Dihedral : 9.802 169.124 3784 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.36 % Allowed : 14.83 % Favored : 81.81 % 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: 0.22 (0.15), residues: 1296 sheet: -0.04 (0.21), residues: 585 loop : 0.55 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 340 HIS 0.005 0.001 HIS P 88 PHE 0.012 0.002 PHE R 31 TYR 0.015 0.001 TYR P 69 ARG 0.005 0.001 ARG M 290 *********************** 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 392 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 297 time to evaluate : 3.687 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: J 44 MET cc_start: 0.2767 (mmm) cc_final: 0.2416 (mmm) REVERT: J 82 MET cc_start: 0.7938 (tpt) cc_final: 0.7671 (tpt) REVERT: J 227 MET cc_start: 0.8408 (mmm) cc_final: 0.7929 (tpp) REVERT: J 314 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: J 330 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7895 (mt) REVERT: K 227 MET cc_start: 0.8651 (mmm) cc_final: 0.8398 (mmm) REVERT: L 17 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8438 (p) REVERT: L 57 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8073 (mm-30) REVERT: L 119 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8492 (ttp) REVERT: L 241 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: L 244 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7252 (p0) REVERT: M 72 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: M 283 MET cc_start: 0.8799 (mmp) cc_final: 0.8486 (mmm) REVERT: M 326 LYS cc_start: 0.8103 (pptt) cc_final: 0.7013 (mmtm) REVERT: M 361 GLU cc_start: 0.8406 (tt0) cc_final: 0.8135 (tt0) REVERT: N 225 ASN cc_start: 0.8206 (t0) cc_final: 0.7929 (t0) REVERT: N 257 CYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8844 (t) REVERT: N 336 LYS cc_start: 0.8720 (tptm) cc_final: 0.8417 (tttt) REVERT: O 47 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6997 (ttp) REVERT: O 154 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8722 (t0) REVERT: O 225 ASN cc_start: 0.8532 (t0) cc_final: 0.7905 (m110) REVERT: O 227 MET cc_start: 0.8717 (mmm) cc_final: 0.8419 (mmm) REVERT: O 234 SER cc_start: 0.8267 (m) cc_final: 0.7453 (t) REVERT: O 244 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7790 (p0) REVERT: O 283 MET cc_start: 0.9025 (mmt) cc_final: 0.8765 (mmm) REVERT: O 328 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8380 (tttm) REVERT: O 355 MET cc_start: 0.9141 (mtt) cc_final: 0.8929 (mtt) REVERT: O 363 ASP cc_start: 0.7956 (p0) cc_final: 0.7586 (p0) REVERT: P 17 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8251 (p) REVERT: P 57 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: P 72 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: P 211 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8567 (t70) REVERT: P 225 ASN cc_start: 0.8400 (m-40) cc_final: 0.7905 (m110) REVERT: P 227 MET cc_start: 0.8685 (mmm) cc_final: 0.8253 (mmm) REVERT: P 244 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7629 (p0) REVERT: P 246 GLN cc_start: 0.8920 (mt0) cc_final: 0.8676 (mt0) REVERT: P 269 MET cc_start: 0.8787 (ptp) cc_final: 0.8584 (ptm) REVERT: Q 360 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8194 (tm130) REVERT: R 72 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8063 (mp0) REVERT: R 291 LYS cc_start: 0.6233 (mmtt) cc_final: 0.5679 (mptt) REVERT: R 325 MET cc_start: 0.6939 (ptm) cc_final: 0.6515 (ptm) outliers start: 95 outliers final: 47 residues processed: 364 average time/residue: 2.5826 time to fit residues: 1106.3771 Evaluate side-chains 347 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 282 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 314 GLN Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 322 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 314 GLN N 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27009 Z= 0.304 Angle : 0.627 7.320 36657 Z= 0.303 Chirality : 0.045 0.178 4068 Planarity : 0.004 0.050 4689 Dihedral : 9.469 165.796 3782 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.22 % Allowed : 15.43 % Favored : 81.35 % 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: 0.39 (0.15), residues: 3303 helix: 0.31 (0.15), residues: 1296 sheet: -0.01 (0.22), residues: 585 loop : 0.58 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 340 HIS 0.004 0.001 HIS P 88 PHE 0.012 0.001 PHE O 31 TYR 0.011 0.001 TYR P 69 ARG 0.004 0.000 ARG M 290 *********************** 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 381 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 290 time to evaluate : 3.558 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: J 44 MET cc_start: 0.2744 (mmm) cc_final: 0.2437 (mmm) REVERT: J 227 MET cc_start: 0.8337 (mmm) cc_final: 0.7851 (tpp) REVERT: J 330 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7871 (mt) REVERT: K 227 MET cc_start: 0.8643 (mmm) cc_final: 0.8388 (mmm) REVERT: L 17 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8435 (p) REVERT: L 119 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8476 (ttp) REVERT: L 241 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: M 72 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: M 283 MET cc_start: 0.8802 (mmp) cc_final: 0.8501 (mmm) REVERT: M 326 LYS cc_start: 0.8071 (pptt) cc_final: 0.7011 (mmtm) REVERT: M 361 GLU cc_start: 0.8403 (tt0) cc_final: 0.8127 (tt0) REVERT: N 225 ASN cc_start: 0.8247 (t0) cc_final: 0.7985 (t0) REVERT: N 257 CYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8842 (t) REVERT: N 336 LYS cc_start: 0.8647 (tptm) cc_final: 0.8422 (ttmt) REVERT: O 33 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8749 (t) REVERT: O 47 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6960 (ttp) REVERT: O 225 ASN cc_start: 0.8531 (t0) cc_final: 0.7920 (m110) REVERT: O 227 MET cc_start: 0.8698 (mmm) cc_final: 0.8399 (mmm) REVERT: O 244 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7557 (p0) REVERT: O 283 MET cc_start: 0.9010 (mmt) cc_final: 0.8756 (mmm) REVERT: O 328 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8357 (tttm) REVERT: O 355 MET cc_start: 0.9110 (mtt) cc_final: 0.8825 (mtt) REVERT: O 363 ASP cc_start: 0.7944 (p0) cc_final: 0.7579 (p0) REVERT: P 17 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8247 (p) REVERT: P 47 MET cc_start: 0.7076 (ttm) cc_final: 0.6850 (ttm) REVERT: P 57 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: P 72 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: P 211 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8558 (t70) REVERT: P 225 ASN cc_start: 0.8403 (m-40) cc_final: 0.7916 (m110) REVERT: P 227 MET cc_start: 0.8663 (mmm) cc_final: 0.8270 (mmm) REVERT: P 244 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7974 (p0) REVERT: P 246 GLN cc_start: 0.8942 (mt0) cc_final: 0.8703 (mt0) REVERT: P 313 MET cc_start: 0.8954 (mmm) cc_final: 0.8613 (mmm) REVERT: Q 360 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8109 (tm130) REVERT: R 291 LYS cc_start: 0.6226 (mmtt) cc_final: 0.5675 (mptt) REVERT: R 325 MET cc_start: 0.7136 (ptm) cc_final: 0.6601 (ptm) outliers start: 91 outliers final: 46 residues processed: 358 average time/residue: 2.4976 time to fit residues: 1048.0206 Evaluate side-chains 345 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 284 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 271 optimal weight: 0.4980 chunk 179 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 314 GLN N 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27009 Z= 0.166 Angle : 0.578 6.589 36657 Z= 0.274 Chirality : 0.043 0.146 4068 Planarity : 0.004 0.049 4689 Dihedral : 8.796 154.229 3782 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.76 % Allowed : 16.31 % Favored : 80.93 % 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: 0.68 (0.15), residues: 3303 helix: 0.62 (0.15), residues: 1296 sheet: 0.07 (0.21), residues: 585 loop : 0.71 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 340 HIS 0.004 0.001 HIS P 88 PHE 0.015 0.001 PHE O 31 TYR 0.007 0.001 TYR P 69 ARG 0.002 0.000 ARG N 254 *********************** 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 386 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 308 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 44 MET cc_start: 0.2560 (mmm) cc_final: 0.2291 (mmm) REVERT: J 227 MET cc_start: 0.8322 (mmm) cc_final: 0.7842 (tpp) REVERT: J 283 MET cc_start: 0.9021 (mmm) cc_final: 0.8798 (mmm) REVERT: J 330 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7817 (mt) REVERT: K 227 MET cc_start: 0.8663 (mmm) cc_final: 0.8461 (mmm) REVERT: L 17 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8347 (p) REVERT: M 118 LYS cc_start: 0.8635 (tptm) cc_final: 0.8390 (mtmt) REVERT: M 283 MET cc_start: 0.8762 (mmp) cc_final: 0.8469 (mmm) REVERT: M 326 LYS cc_start: 0.8010 (pptt) cc_final: 0.6928 (mmtm) REVERT: M 361 GLU cc_start: 0.8354 (tt0) cc_final: 0.8110 (tt0) REVERT: N 137 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8592 (mt0) REVERT: N 225 ASN cc_start: 0.8234 (t0) cc_final: 0.7987 (t0) REVERT: N 257 CYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8932 (t) REVERT: O 33 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8766 (t) REVERT: O 47 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6900 (ttp) REVERT: O 95 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7931 (ptp-110) REVERT: O 225 ASN cc_start: 0.8319 (t0) cc_final: 0.7792 (m110) REVERT: O 227 MET cc_start: 0.8654 (mmm) cc_final: 0.8358 (mmm) REVERT: O 244 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7676 (p0) REVERT: O 283 MET cc_start: 0.8964 (mmt) cc_final: 0.8690 (mmm) REVERT: O 355 MET cc_start: 0.9083 (mtt) cc_final: 0.8863 (mtt) REVERT: O 363 ASP cc_start: 0.7847 (p0) cc_final: 0.7460 (p0) REVERT: P 17 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8162 (p) REVERT: P 57 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: P 211 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8543 (t70) REVERT: P 225 ASN cc_start: 0.8366 (m-40) cc_final: 0.7849 (m-40) REVERT: P 227 MET cc_start: 0.8612 (mmm) cc_final: 0.8250 (mmm) REVERT: P 244 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7700 (p0) REVERT: P 246 GLN cc_start: 0.8927 (mt0) cc_final: 0.8699 (mt0) REVERT: P 372 ARG cc_start: 0.8568 (ttm170) cc_final: 0.8271 (mtm110) REVERT: Q 360 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7976 (tm130) REVERT: R 283 MET cc_start: 0.8305 (mmt) cc_final: 0.7965 (tpp) REVERT: R 286 ASP cc_start: 0.7549 (t70) cc_final: 0.7205 (m-30) REVERT: R 291 LYS cc_start: 0.6189 (mmtt) cc_final: 0.5711 (mptt) outliers start: 78 outliers final: 44 residues processed: 364 average time/residue: 2.3434 time to fit residues: 998.9794 Evaluate side-chains 350 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 294 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 12 ASN N 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27009 Z= 0.302 Angle : 0.618 6.958 36657 Z= 0.296 Chirality : 0.045 0.185 4068 Planarity : 0.004 0.058 4689 Dihedral : 8.710 144.897 3779 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.48 % Allowed : 17.09 % Favored : 80.43 % 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: 0.62 (0.15), residues: 3303 helix: 0.55 (0.15), residues: 1296 sheet: 0.09 (0.22), residues: 585 loop : 0.66 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 340 HIS 0.004 0.001 HIS P 88 PHE 0.014 0.001 PHE O 31 TYR 0.011 0.001 TYR P 69 ARG 0.010 0.000 ARG J 372 *********************** 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 366 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 296 time to evaluate : 3.068 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: J 44 MET cc_start: 0.2544 (mmm) cc_final: 0.2308 (mmm) REVERT: J 227 MET cc_start: 0.8327 (mmm) cc_final: 0.7862 (tpp) REVERT: J 283 MET cc_start: 0.9027 (mmm) cc_final: 0.8720 (mmm) REVERT: J 330 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7826 (mt) REVERT: K 227 MET cc_start: 0.8681 (mmm) cc_final: 0.8462 (mmm) REVERT: L 17 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8382 (p) REVERT: M 72 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: M 95 ARG cc_start: 0.8298 (ptp90) cc_final: 0.7949 (mtp85) REVERT: M 283 MET cc_start: 0.8768 (mmp) cc_final: 0.8495 (mmm) REVERT: M 326 LYS cc_start: 0.7885 (pptt) cc_final: 0.6851 (mmtm) REVERT: M 361 GLU cc_start: 0.8416 (tt0) cc_final: 0.8026 (tt0) REVERT: N 225 ASN cc_start: 0.8243 (t0) cc_final: 0.7994 (t0) REVERT: N 257 CYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8889 (t) REVERT: O 33 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8755 (t) REVERT: O 47 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6925 (ttp) REVERT: O 95 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7964 (ptp-110) REVERT: O 224 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8167 (tp30) REVERT: O 225 ASN cc_start: 0.8543 (t0) cc_final: 0.7957 (m110) REVERT: O 227 MET cc_start: 0.8658 (mmm) cc_final: 0.8360 (mmm) REVERT: O 244 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7635 (p0) REVERT: O 283 MET cc_start: 0.8979 (mmt) cc_final: 0.8720 (mmm) REVERT: O 328 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8342 (tttm) REVERT: O 355 MET cc_start: 0.9098 (mtt) cc_final: 0.8817 (mtt) REVERT: O 363 ASP cc_start: 0.7929 (p0) cc_final: 0.7559 (p0) REVERT: P 17 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8203 (p) REVERT: P 57 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: P 72 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: P 157 ASP cc_start: 0.8394 (t0) cc_final: 0.8183 (t0) REVERT: P 211 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8565 (t70) REVERT: P 225 ASN cc_start: 0.8376 (m-40) cc_final: 0.7879 (m-40) REVERT: P 227 MET cc_start: 0.8631 (mmm) cc_final: 0.8239 (mmm) REVERT: P 244 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7775 (p0) REVERT: P 246 GLN cc_start: 0.8970 (mt0) cc_final: 0.8717 (mt0) REVERT: Q 355 MET cc_start: 0.9108 (mtp) cc_final: 0.8867 (mpp) REVERT: Q 360 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8070 (tm130) REVERT: R 283 MET cc_start: 0.8327 (mmt) cc_final: 0.7990 (tpp) REVERT: R 286 ASP cc_start: 0.7621 (t70) cc_final: 0.7270 (m-30) REVERT: R 291 LYS cc_start: 0.6194 (mmtt) cc_final: 0.5705 (mptt) REVERT: R 325 MET cc_start: 0.7060 (ptm) cc_final: 0.6820 (ptm) outliers start: 70 outliers final: 45 residues processed: 347 average time/residue: 2.2922 time to fit residues: 936.6641 Evaluate side-chains 347 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 288 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.7980 chunk 307 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 270 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 12 ASN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27009 Z= 0.164 Angle : 0.577 6.517 36657 Z= 0.273 Chirality : 0.043 0.147 4068 Planarity : 0.004 0.056 4689 Dihedral : 8.260 142.597 3779 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.19 % Allowed : 17.59 % Favored : 80.22 % 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: 0.56 (0.15), residues: 3303 helix: 0.62 (0.15), residues: 1350 sheet: 0.13 (0.21), residues: 585 loop : 0.46 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 340 HIS 0.004 0.001 HIS P 88 PHE 0.013 0.001 PHE O 31 TYR 0.008 0.001 TYR N 294 ARG 0.011 0.000 ARG J 372 *********************** 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 365 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 303 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 196 ARG cc_start: 0.6556 (mtt-85) cc_final: 0.6290 (mtt180) REVERT: J 227 MET cc_start: 0.8320 (mmm) cc_final: 0.7853 (tpp) REVERT: J 283 MET cc_start: 0.9043 (mmm) cc_final: 0.8728 (mmm) REVERT: J 330 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7804 (mt) REVERT: K 227 MET cc_start: 0.8650 (mmm) cc_final: 0.8443 (mmm) REVERT: L 17 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8336 (p) REVERT: M 95 ARG cc_start: 0.8296 (ptp90) cc_final: 0.7962 (mtp85) REVERT: M 118 LYS cc_start: 0.8636 (tptm) cc_final: 0.8391 (mtmt) REVERT: M 283 MET cc_start: 0.8741 (mmp) cc_final: 0.8366 (mmm) REVERT: M 326 LYS cc_start: 0.7841 (pptt) cc_final: 0.6786 (mmtm) REVERT: M 361 GLU cc_start: 0.8402 (tt0) cc_final: 0.8165 (tt0) REVERT: N 17 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8235 (p) REVERT: N 137 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8667 (mt0) REVERT: N 225 ASN cc_start: 0.8229 (t0) cc_final: 0.7992 (t0) REVERT: N 257 CYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8905 (t) REVERT: O 95 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7892 (ptp-110) REVERT: O 225 ASN cc_start: 0.8326 (t0) cc_final: 0.7830 (m110) REVERT: O 227 MET cc_start: 0.8627 (mmm) cc_final: 0.8331 (mmm) REVERT: O 238 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8516 (mmtp) REVERT: O 244 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7718 (p0) REVERT: O 283 MET cc_start: 0.8957 (mmt) cc_final: 0.8689 (mmm) REVERT: O 328 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8371 (tttm) REVERT: O 355 MET cc_start: 0.9079 (mtt) cc_final: 0.8873 (mtt) REVERT: O 363 ASP cc_start: 0.7849 (p0) cc_final: 0.7459 (p0) REVERT: P 17 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8163 (p) REVERT: P 57 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: P 211 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8546 (t70) REVERT: P 225 ASN cc_start: 0.8376 (m-40) cc_final: 0.7870 (m-40) REVERT: P 227 MET cc_start: 0.8598 (mmm) cc_final: 0.8231 (mmm) REVERT: P 246 GLN cc_start: 0.8944 (mt0) cc_final: 0.8700 (mt0) REVERT: P 313 MET cc_start: 0.8962 (mmm) cc_final: 0.8643 (mmm) REVERT: Q 355 MET cc_start: 0.9083 (mtp) cc_final: 0.8854 (mpp) REVERT: Q 360 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8070 (tm-30) REVERT: R 283 MET cc_start: 0.8280 (mmt) cc_final: 0.7956 (tpp) REVERT: R 286 ASP cc_start: 0.7624 (t70) cc_final: 0.7276 (m-30) REVERT: R 291 LYS cc_start: 0.6153 (mmtt) cc_final: 0.5652 (mptt) REVERT: R 325 MET cc_start: 0.6937 (ptm) cc_final: 0.6686 (ptm) outliers start: 62 outliers final: 41 residues processed: 349 average time/residue: 2.1298 time to fit residues: 867.5749 Evaluate side-chains 346 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 294 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER 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: 4.9990 chunk 193 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 12 ASN P 354 GLN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27009 Z= 0.304 Angle : 0.622 7.365 36657 Z= 0.297 Chirality : 0.045 0.190 4068 Planarity : 0.004 0.060 4689 Dihedral : 8.352 136.279 3779 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.12 % Allowed : 17.83 % Favored : 80.04 % 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: 0.66 (0.15), residues: 3303 helix: 0.67 (0.15), residues: 1296 sheet: 0.12 (0.22), residues: 585 loop : 0.60 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 340 HIS 0.005 0.001 HIS P 88 PHE 0.013 0.001 PHE O 31 TYR 0.012 0.001 TYR P 69 ARG 0.011 0.000 ARG J 372 ********************** 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 359 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 299 time to evaluate : 2.802 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: J 196 ARG cc_start: 0.6701 (mtt-85) cc_final: 0.6398 (mtt180) REVERT: J 227 MET cc_start: 0.8323 (mmm) cc_final: 0.7871 (tpp) REVERT: J 283 MET cc_start: 0.9084 (mmm) cc_final: 0.8775 (mmm) REVERT: J 330 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7777 (mt) REVERT: L 17 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8375 (p) REVERT: M 72 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: M 95 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7934 (mtt-85) REVERT: M 118 LYS cc_start: 0.8650 (tptm) cc_final: 0.8379 (mtmt) REVERT: M 283 MET cc_start: 0.8756 (mmp) cc_final: 0.8479 (mmm) REVERT: M 326 LYS cc_start: 0.7803 (pptt) cc_final: 0.6805 (mmtm) REVERT: M 361 GLU cc_start: 0.8454 (tt0) cc_final: 0.8073 (tt0) REVERT: N 17 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8319 (p) REVERT: N 225 ASN cc_start: 0.8232 (t0) cc_final: 0.8000 (t0) REVERT: N 257 CYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8861 (t) REVERT: O 47 MET cc_start: 0.7365 (ttp) cc_final: 0.7110 (tmt) REVERT: O 95 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8020 (ptp-110) REVERT: O 225 ASN cc_start: 0.8490 (t0) cc_final: 0.7965 (m110) REVERT: O 227 MET cc_start: 0.8652 (mmm) cc_final: 0.8359 (mmm) REVERT: O 238 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8409 (mmtp) REVERT: O 244 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7718 (p0) REVERT: O 283 MET cc_start: 0.8992 (mmt) cc_final: 0.8737 (mmm) REVERT: O 328 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8334 (tttm) REVERT: O 355 MET cc_start: 0.9093 (mtt) cc_final: 0.8795 (mtt) REVERT: O 363 ASP cc_start: 0.7948 (p0) cc_final: 0.7560 (p0) REVERT: P 17 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8224 (p) REVERT: P 57 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: P 72 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: P 157 ASP cc_start: 0.8312 (t0) cc_final: 0.8090 (t0) REVERT: P 211 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8563 (t70) REVERT: P 225 ASN cc_start: 0.8386 (m-40) cc_final: 0.7923 (m110) REVERT: P 227 MET cc_start: 0.8634 (mmm) cc_final: 0.8232 (mmm) REVERT: P 246 GLN cc_start: 0.8964 (mt0) cc_final: 0.8679 (mt0) REVERT: Q 355 MET cc_start: 0.9096 (mtp) cc_final: 0.8861 (mpp) REVERT: Q 360 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8168 (tm-30) REVERT: R 286 ASP cc_start: 0.7631 (t70) cc_final: 0.7272 (m-30) REVERT: R 291 LYS cc_start: 0.6260 (mmtt) cc_final: 0.5714 (mptt) REVERT: R 325 MET cc_start: 0.6967 (ptm) cc_final: 0.6735 (ptm) outliers start: 60 outliers final: 40 residues processed: 345 average time/residue: 2.0905 time to fit residues: 843.7117 Evaluate side-chains 347 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 295 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 271 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 12 ASN M 314 GLN P 354 GLN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.092687 restraints weight = 92928.784| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.63 r_work: 0.3006 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27009 Z= 0.169 Angle : 0.577 6.656 36657 Z= 0.272 Chirality : 0.043 0.148 4068 Planarity : 0.004 0.056 4689 Dihedral : 8.083 139.305 3779 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 17.98 % Favored : 80.08 % 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: 0.63 (0.15), residues: 3303 helix: 0.67 (0.15), residues: 1350 sheet: 0.18 (0.22), residues: 585 loop : 0.51 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 340 HIS 0.004 0.001 HIS P 88 PHE 0.018 0.001 PHE L 31 TYR 0.011 0.001 TYR J 53 ARG 0.011 0.000 ARG J 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16873.56 seconds wall clock time: 293 minutes 2.75 seconds (17582.75 seconds total)