Starting phenix.real_space_refine on Mon Mar 25 10:13:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rer_24437/03_2024/7rer_24437_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rer_24437/03_2024/7rer_24437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rer_24437/03_2024/7rer_24437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rer_24437/03_2024/7rer_24437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rer_24437/03_2024/7rer_24437_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rer_24437/03_2024/7rer_24437_trim_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.294 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 168 5.16 5 C 15088 2.51 5 N 4112 2.21 5 O 4648 1.98 5 H 23697 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 404": "OD1" <-> "OD2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D GLU 500": "OE1" <-> "OE2" Residue "D ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "C ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 470": "OD1" <-> "OD2" Residue "B ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 470": "OD1" <-> "OD2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "E ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 28": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H ASP 77": "OD1" <-> "OD2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 404": "OD1" <-> "OD2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 470": "OD1" <-> "OD2" Residue "H GLU 500": "OE1" <-> "OE2" Residue "H ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 404": "OD1" <-> "OD2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 470": "OD1" <-> "OD2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 470": "OD1" <-> "OD2" Residue "F GLU 487": "OE1" <-> "OE2" Residue "F ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47737 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5887 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5887 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5916 Chain: "D" Number of atoms: 5900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5915 Chain: "C" Number of atoms: 5900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5915 Chain: "B" Number of atoms: 5900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5915 Chain: "E" Number of atoms: 5900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5915 Chain: "H" Number of atoms: 5900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5915 Chain: "G" Number of atoms: 5900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5915 Chain: "F" Number of atoms: 5900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 389, 5886 Classifications: {'peptide': 389} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 376} Chain breaks: 2 bond proxies already assigned to first conformer: 5915 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 34.73, per 1000 atoms: 0.73 Number of scatterers: 47737 At special positions: 0 Unit cell: (122.85, 122.85, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 P 24 15.00 O 4648 8.00 N 4112 7.00 C 15088 6.00 H 23697 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: 38.08 Conformation dependent library (CDL) restraints added in 8.7 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 32 sheets defined 36.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.72 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.867A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.864A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.548A pdb=" N THR C 264 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.636A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.841A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.547A pdb=" N SER B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 7' Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.830A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.798A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 421 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'H' and resid 3 through 7 Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.804A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 421 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 501 Processing helix chain 'G' and resid 3 through 7 Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.584A pdb=" N THR G 264 " --> pdb=" O ASP G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.679A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 3.804A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 417 through 421 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.581A pdb=" N SER F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3 through 7' Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.811A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.479A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.587A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 400 through 403 Processing sheet with id= E, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.455A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.607A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 400 through 403 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.489A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.582A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 400 through 403 Processing sheet with id= M, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.484A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.584A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 400 through 403 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.483A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.610A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 400 through 403 Processing sheet with id= U, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.459A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.594A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'H' and resid 400 through 403 Processing sheet with id= Y, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.476A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.600A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 400 through 403 Processing sheet with id= AC, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.476A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.594A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'F' and resid 400 through 403 725 hydrogen bonds defined for protein. 1998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.15 Time building geometry restraints manager: 39.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 23649 1.13 - 1.31: 4461 1.31 - 1.50: 9734 1.50 - 1.68: 10029 1.68 - 1.86: 288 Bond restraints: 48161 Sorted by residual: bond pdb=" C HIS G 296 " pdb=" CA BHIS G 296 " ideal model delta sigma weight residual 1.522 1.339 0.184 1.37e-02 5.33e+03 1.80e+02 bond pdb=" N HIS C 296 " pdb=" H BHIS C 296 " ideal model delta sigma weight residual 0.860 1.083 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C HIS C 296 " pdb=" CA BHIS C 296 " ideal model delta sigma weight residual 1.522 1.383 0.139 1.40e-02 5.10e+03 9.86e+01 bond pdb=" C HIS E 296 " pdb=" CA BHIS E 296 " ideal model delta sigma weight residual 1.522 1.408 0.114 1.40e-02 5.10e+03 6.67e+01 bond pdb=" N HIS H 296 " pdb=" H BHIS H 296 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 48156 not shown) Histogram of bond angle deviations from ideal: 94.39 - 102.50: 243 102.50 - 110.61: 47757 110.61 - 118.72: 18993 118.72 - 126.84: 19598 126.84 - 134.95: 315 Bond angle restraints: 86906 Sorted by residual: angle pdb=" N HIS G 296 " pdb=" CA BHIS G 296 " pdb=" C HIS G 296 " ideal model delta sigma weight residual 113.18 130.13 -16.95 1.21e+00 6.83e-01 1.96e+02 angle pdb=" N HIS C 296 " pdb=" CA BHIS C 296 " pdb=" C HIS C 296 " ideal model delta sigma weight residual 112.54 128.73 -16.19 1.22e+00 6.72e-01 1.76e+02 angle pdb=" N HIS E 296 " pdb=" CA BHIS E 296 " pdb=" C HIS E 296 " ideal model delta sigma weight residual 112.54 122.05 -9.51 1.22e+00 6.72e-01 6.07e+01 angle pdb=" N HIS D 296 " pdb=" CA BHIS D 296 " pdb=" C HIS D 296 " ideal model delta sigma weight residual 112.89 121.92 -9.03 1.24e+00 6.50e-01 5.31e+01 angle pdb=" N HIS B 296 " pdb=" CA BHIS B 296 " pdb=" C HIS B 296 " ideal model delta sigma weight residual 112.89 121.84 -8.95 1.24e+00 6.50e-01 5.20e+01 ... (remaining 86901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 21165 24.65 - 49.31: 993 49.31 - 73.96: 608 73.96 - 98.62: 31 98.62 - 123.27: 4 Dihedral angle restraints: 22801 sinusoidal: 12768 harmonic: 10033 Sorted by residual: dihedral pdb=" C5' IMP E 602 " pdb=" O5' IMP E 602 " pdb=" P IMP E 602 " pdb=" O2P IMP E 602 " ideal model delta sinusoidal sigma weight residual -168.07 -44.80 -123.27 1 2.00e+01 2.50e-03 3.72e+01 dihedral pdb=" C5' IMP G 602 " pdb=" O5' IMP G 602 " pdb=" P IMP G 602 " pdb=" O2P IMP G 602 " ideal model delta sinusoidal sigma weight residual -168.07 -46.02 -122.05 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" C5' IMP F 602 " pdb=" O5' IMP F 602 " pdb=" P IMP F 602 " pdb=" O2P IMP F 602 " ideal model delta sinusoidal sigma weight residual -168.07 -46.23 -121.84 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 22798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 3481 0.173 - 0.347: 244 0.347 - 0.520: 14 0.520 - 0.693: 4 0.693 - 0.867: 1 Chirality restraints: 3744 Sorted by residual: chirality pdb=" CA BHIS C 296 " pdb=" N HIS C 296 " pdb=" C HIS C 296 " pdb=" CB BHIS C 296 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CA BHIS G 296 " pdb=" N HIS G 296 " pdb=" C HIS G 296 " pdb=" CB BHIS G 296 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" CA CYS A 327 " pdb=" N CYS A 327 " pdb=" C CYS A 327 " pdb=" CB CYS A 327 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.09e+00 ... (remaining 3741 not shown) Planarity restraints: 7192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 282 " -0.163 2.00e-02 2.50e+03 6.71e-02 1.35e+02 pdb=" CG TYR G 282 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR G 282 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR G 282 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR G 282 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR G 282 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR G 282 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 282 " -0.126 2.00e-02 2.50e+03 pdb=" HD1 TYR G 282 " 0.045 2.00e-02 2.50e+03 pdb=" HD2 TYR G 282 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR G 282 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR G 282 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 282 " 0.155 2.00e-02 2.50e+03 6.37e-02 1.22e+02 pdb=" CG TYR A 282 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 282 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 282 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A 282 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR A 282 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 282 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 282 " 0.120 2.00e-02 2.50e+03 pdb=" HD1 TYR A 282 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 TYR A 282 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 282 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 282 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 282 " 0.154 2.00e-02 2.50e+03 6.29e-02 1.19e+02 pdb=" CG TYR D 282 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 282 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR D 282 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 282 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR D 282 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR D 282 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 282 " 0.118 2.00e-02 2.50e+03 pdb=" HD1 TYR D 282 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR D 282 " -0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR D 282 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR D 282 " -0.019 2.00e-02 2.50e+03 ... (remaining 7189 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 4215 2.20 - 2.80: 92744 2.80 - 3.40: 146353 3.40 - 4.00: 202880 4.00 - 4.60: 295517 Nonbonded interactions: 741709 Sorted by model distance: nonbonded pdb=" OD1 ASP A 50 " pdb=" HG1 THR A 52 " model vdw 1.597 1.850 nonbonded pdb=" OD1 ASP D 50 " pdb=" HG1 THR D 52 " model vdw 1.599 1.850 nonbonded pdb=" OD1 ASP B 50 " pdb=" HG1 THR B 52 " model vdw 1.602 1.850 nonbonded pdb=" OD1 ASP C 50 " pdb=" HG1 THR C 52 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASP G 261 " pdb=" HH TYR G 294 " model vdw 1.610 1.850 ... (remaining 741704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 295 or resid 297 through 503 or (resid 504 and ( \ name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1 or name HE2)) or resid 505 through 514 or resid 601 through 602 \ )) selection = (chain 'B' and (resid 1 through 295 or resid 297 through 514 or resid 601 throug \ h 602)) selection = (chain 'C' and (resid 1 through 295 or resid 297 through 514 or resid 601 throug \ h 602)) selection = (chain 'D' and (resid 1 through 295 or resid 297 through 514 or resid 601 throug \ h 602)) selection = (chain 'E' and (resid 1 through 295 or resid 297 through 514 or resid 601 throug \ h 602)) selection = (chain 'F' and (resid 1 through 295 or resid 297 through 514 or resid 601 throug \ h 602)) selection = (chain 'G' and (resid 1 through 295 or resid 297 through 514 or resid 601 throug \ h 602)) selection = (chain 'H' and (resid 1 through 295 or resid 297 through 514 or resid 601 throug \ h 602)) } 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=0.50 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: 1.470 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: 0.730 Extract box with map and model: 9.170 Check model and map are aligned: 0.650 Set scattering table: 0.410 Process input model: 165.360 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.330 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 0.184 24464 Z= 0.795 Angle : 1.733 16.953 33072 Z= 1.122 Chirality : 0.097 0.867 3744 Planarity : 0.013 0.089 4184 Dihedral : 14.329 123.274 9304 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.98 % Favored : 95.69 % Rotamer: Outliers : 1.09 % Allowed : 2.33 % Favored : 96.58 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.64 (0.14), residues: 3072 helix: -0.12 (0.14), residues: 1248 sheet: -0.88 (0.30), residues: 176 loop : -0.51 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS A 92 PHE 0.080 0.011 PHE C 357 TYR 0.140 0.017 TYR G 282 ARG 0.013 0.002 ARG D 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 480 time to evaluate : 3.651 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: A 261 ASP cc_start: 0.7347 (m-30) cc_final: 0.7033 (m-30) REVERT: A 293 LYS cc_start: 0.8590 (tttp) cc_final: 0.8350 (tttm) REVERT: A 294 TYR cc_start: 0.8693 (m-80) cc_final: 0.8429 (m-80) REVERT: A 325 MET cc_start: 0.8772 (ttt) cc_final: 0.8420 (ttt) REVERT: D 325 MET cc_start: 0.8889 (ttt) cc_final: 0.8599 (ttt) REVERT: D 337 MET cc_start: 0.8506 (mmt) cc_final: 0.8295 (mmt) REVERT: C 325 MET cc_start: 0.9023 (ttt) cc_final: 0.8774 (ttt) REVERT: C 337 MET cc_start: 0.8522 (mmt) cc_final: 0.8288 (mmt) REVERT: B 48 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7494 (mt-10) REVERT: B 325 MET cc_start: 0.8751 (ttt) cc_final: 0.8419 (ttt) REVERT: B 483 MET cc_start: 0.9356 (tmm) cc_final: 0.9148 (tmm) REVERT: E 70 MET cc_start: 0.9173 (mtp) cc_final: 0.8946 (mtp) REVERT: E 293 LYS cc_start: 0.8592 (tttp) cc_final: 0.8346 (tttm) REVERT: E 325 MET cc_start: 0.8826 (ttt) cc_final: 0.8525 (ttt) REVERT: E 337 MET cc_start: 0.8510 (mmt) cc_final: 0.8280 (mmt) REVERT: E 368 GLN cc_start: 0.8044 (mt0) cc_final: 0.7840 (mt0) REVERT: E 395 GLU cc_start: 0.8401 (mp0) cc_final: 0.8155 (mp0) REVERT: E 482 MET cc_start: 0.9076 (mtp) cc_final: 0.8853 (mtp) REVERT: H 325 MET cc_start: 0.8840 (ttt) cc_final: 0.8545 (ttt) REVERT: H 337 MET cc_start: 0.8614 (mmt) cc_final: 0.8235 (mmt) REVERT: H 368 GLN cc_start: 0.8167 (mt0) cc_final: 0.7945 (mt0) REVERT: G 70 MET cc_start: 0.9171 (mtp) cc_final: 0.8951 (mtp) REVERT: G 325 MET cc_start: 0.8824 (ttt) cc_final: 0.8537 (ttt) REVERT: G 337 MET cc_start: 0.8651 (mmt) cc_final: 0.8451 (mmt) REVERT: G 510 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6395 (mm-30) REVERT: F 293 LYS cc_start: 0.8640 (tttp) cc_final: 0.8388 (tttm) REVERT: F 325 MET cc_start: 0.8740 (ttt) cc_final: 0.8416 (ttt) REVERT: F 337 MET cc_start: 0.8565 (mmt) cc_final: 0.8353 (mmt) REVERT: F 368 GLN cc_start: 0.8163 (mt0) cc_final: 0.7958 (mt0) REVERT: F 482 MET cc_start: 0.9087 (mtp) cc_final: 0.8858 (mtp) outliers start: 27 outliers final: 8 residues processed: 504 average time/residue: 2.6000 time to fit residues: 1539.3980 Evaluate side-chains 424 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 416 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 498 GLN D 94 ASN D 112 GLN D 243 GLN C 94 ASN C 368 GLN C 498 GLN B 94 ASN B 498 GLN E 94 ASN E 243 GLN H 94 ASN H 243 GLN H 441 GLN G 94 ASN G 498 GLN F 94 ASN F 498 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24464 Z= 0.193 Angle : 0.573 6.284 33072 Z= 0.304 Chirality : 0.042 0.165 3744 Planarity : 0.004 0.047 4184 Dihedral : 9.448 86.372 3896 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % Rotamer: Outliers : 0.96 % Allowed : 6.75 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.11 (0.14), residues: 3072 helix: 0.50 (0.14), residues: 1280 sheet: 0.07 (0.28), residues: 272 loop : -0.52 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 92 PHE 0.012 0.002 PHE F 357 TYR 0.014 0.001 TYR G 282 ARG 0.005 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 450 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8808 (ttt) cc_final: 0.8578 (ttt) REVERT: A 330 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9013 (pp) REVERT: A 407 ARG cc_start: 0.8011 (ttt90) cc_final: 0.7695 (ttt-90) REVERT: D 21 GLN cc_start: 0.7911 (tt0) cc_final: 0.7666 (tt0) REVERT: D 407 ARG cc_start: 0.8026 (ttt90) cc_final: 0.7665 (ttt-90) REVERT: C 58 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8203 (mttp) REVERT: C 325 MET cc_start: 0.9032 (ttt) cc_final: 0.8813 (ttt) REVERT: C 407 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7602 (ttt-90) REVERT: B 7 SER cc_start: 0.7575 (p) cc_final: 0.7326 (t) REVERT: B 58 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8162 (mttp) REVERT: B 325 MET cc_start: 0.8775 (ttt) cc_final: 0.8543 (ttt) REVERT: B 330 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8979 (pp) REVERT: B 394 THR cc_start: 0.9070 (m) cc_final: 0.8856 (m) REVERT: B 407 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7768 (ttt-90) REVERT: B 483 MET cc_start: 0.9347 (tmm) cc_final: 0.9111 (tmm) REVERT: E 70 MET cc_start: 0.9195 (mtp) cc_final: 0.8981 (mtp) REVERT: E 319 ASP cc_start: 0.8374 (m-30) cc_final: 0.8151 (m-30) REVERT: E 368 GLN cc_start: 0.8164 (mt0) cc_final: 0.7898 (mt0) REVERT: E 407 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7670 (ttt-90) REVERT: E 454 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: H 368 GLN cc_start: 0.8240 (mt0) cc_final: 0.7958 (mt0) REVERT: H 454 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: H 514 TYR cc_start: 0.8430 (p90) cc_final: 0.8228 (p90) REVERT: G 407 ARG cc_start: 0.8111 (ttt90) cc_final: 0.7748 (ttt-90) REVERT: G 510 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6390 (mm-30) REVERT: F 319 ASP cc_start: 0.8384 (m-30) cc_final: 0.8169 (m-30) REVERT: F 325 MET cc_start: 0.8800 (ttt) cc_final: 0.8567 (ttt) REVERT: F 330 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8979 (pp) REVERT: F 407 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7735 (ttt-90) REVERT: F 438 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7940 (mtpt) outliers start: 24 outliers final: 8 residues processed: 466 average time/residue: 2.7504 time to fit residues: 1498.4701 Evaluate side-chains 447 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 431 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 454 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.0870 chunk 187 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN D 498 GLN B 94 ASN B 243 GLN E 498 GLN H 498 GLN G 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24464 Z= 0.326 Angle : 0.597 6.107 33072 Z= 0.317 Chirality : 0.044 0.176 3744 Planarity : 0.004 0.056 4184 Dihedral : 9.709 85.302 3896 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 1.13 % Allowed : 8.84 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -0.09 (0.14), residues: 3072 helix: 0.55 (0.14), residues: 1272 sheet: 0.05 (0.28), residues: 272 loop : -0.53 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 92 PHE 0.015 0.002 PHE H 44 TYR 0.017 0.002 TYR A 282 ARG 0.006 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 433 time to evaluate : 3.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8788 (ttt) cc_final: 0.8535 (ttt) REVERT: A 330 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9002 (pp) REVERT: A 407 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7554 (ttt-90) REVERT: D 330 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8847 (pp) REVERT: C 43 ASP cc_start: 0.8291 (p0) cc_final: 0.8060 (p0) REVERT: B 325 MET cc_start: 0.8840 (ttt) cc_final: 0.8590 (ttt) REVERT: B 330 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8997 (pp) REVERT: B 394 THR cc_start: 0.9074 (m) cc_final: 0.8847 (m) REVERT: E 70 MET cc_start: 0.9223 (mtp) cc_final: 0.9009 (mtp) REVERT: E 319 ASP cc_start: 0.8339 (m-30) cc_final: 0.8135 (m-30) REVERT: E 368 GLN cc_start: 0.8243 (mt0) cc_final: 0.7947 (mt0) REVERT: E 394 THR cc_start: 0.9006 (m) cc_final: 0.8782 (m) REVERT: E 454 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: H 454 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: G 335 GLU cc_start: 0.7732 (pt0) cc_final: 0.7473 (mm-30) REVERT: F 319 ASP cc_start: 0.8275 (m-30) cc_final: 0.8065 (m-30) REVERT: F 325 MET cc_start: 0.8787 (ttt) cc_final: 0.8535 (ttt) REVERT: F 330 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8990 (pp) REVERT: F 407 ARG cc_start: 0.8073 (ttt90) cc_final: 0.7584 (ttt-90) REVERT: F 438 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (mtpt) outliers start: 28 outliers final: 13 residues processed: 452 average time/residue: 2.6666 time to fit residues: 1409.6033 Evaluate side-chains 445 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 425 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 454 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN H 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24464 Z= 0.245 Angle : 0.536 6.343 33072 Z= 0.282 Chirality : 0.041 0.169 3744 Planarity : 0.004 0.037 4184 Dihedral : 9.083 73.724 3896 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.33 % Favored : 96.54 % Rotamer: Outliers : 1.13 % Allowed : 8.84 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.08 (0.15), residues: 3072 helix: 0.70 (0.15), residues: 1280 sheet: 0.23 (0.28), residues: 272 loop : -0.47 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 92 PHE 0.010 0.002 PHE F 357 TYR 0.013 0.001 TYR A 282 ARG 0.004 0.001 ARG D 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 452 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9183 (t0) cc_final: 0.8820 (t0) REVERT: A 252 THR cc_start: 0.8862 (p) cc_final: 0.8625 (p) REVERT: A 325 MET cc_start: 0.8760 (ttt) cc_final: 0.8533 (ttt) REVERT: A 330 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8978 (pp) REVERT: A 407 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7590 (ttt-90) REVERT: D 102 ASN cc_start: 0.9211 (t0) cc_final: 0.8853 (t0) REVERT: D 330 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8876 (pp) REVERT: D 394 THR cc_start: 0.9037 (m) cc_final: 0.8792 (m) REVERT: C 102 ASN cc_start: 0.9168 (t0) cc_final: 0.8844 (t0) REVERT: B 325 MET cc_start: 0.8768 (ttt) cc_final: 0.8489 (ttt) REVERT: B 330 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8980 (pp) REVERT: B 394 THR cc_start: 0.9036 (m) cc_final: 0.8786 (m) REVERT: B 407 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7815 (ttt-90) REVERT: E 70 MET cc_start: 0.9229 (mtp) cc_final: 0.9016 (mtp) REVERT: E 102 ASN cc_start: 0.9176 (t0) cc_final: 0.8826 (t0) REVERT: E 319 ASP cc_start: 0.8313 (m-30) cc_final: 0.8065 (m-30) REVERT: E 394 THR cc_start: 0.8978 (m) cc_final: 0.8757 (m) REVERT: G 102 ASN cc_start: 0.9187 (t0) cc_final: 0.8838 (t0) REVERT: F 102 ASN cc_start: 0.9170 (t0) cc_final: 0.8820 (t0) REVERT: F 319 ASP cc_start: 0.8316 (m-30) cc_final: 0.8072 (m-30) REVERT: F 325 MET cc_start: 0.8756 (ttt) cc_final: 0.8526 (ttt) REVERT: F 407 ARG cc_start: 0.8150 (ttt90) cc_final: 0.7649 (ttt-90) REVERT: F 438 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7922 (mtpt) outliers start: 28 outliers final: 15 residues processed: 472 average time/residue: 2.6661 time to fit residues: 1473.6768 Evaluate side-chains 457 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 438 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 438 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 250 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN E 93 HIS G 441 GLN F 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24464 Z= 0.257 Angle : 0.544 6.600 33072 Z= 0.286 Chirality : 0.042 0.168 3744 Planarity : 0.004 0.040 4184 Dihedral : 8.983 64.163 3896 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 1.29 % Allowed : 9.41 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.06 (0.15), residues: 3072 helix: 0.67 (0.15), residues: 1280 sheet: 0.40 (0.29), residues: 272 loop : -0.50 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 92 PHE 0.011 0.002 PHE F 357 TYR 0.013 0.001 TYR D 348 ARG 0.004 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 450 time to evaluate : 3.615 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: A 102 ASN cc_start: 0.9191 (t0) cc_final: 0.8836 (t0) REVERT: A 325 MET cc_start: 0.8774 (ttt) cc_final: 0.8536 (ttt) REVERT: A 330 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9005 (pp) REVERT: A 407 ARG cc_start: 0.8123 (ttt90) cc_final: 0.7608 (ttt-90) REVERT: D 102 ASN cc_start: 0.9214 (t0) cc_final: 0.8846 (t0) REVERT: D 330 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8889 (pp) REVERT: D 394 THR cc_start: 0.9045 (m) cc_final: 0.8820 (m) REVERT: C 102 ASN cc_start: 0.9167 (t0) cc_final: 0.8837 (t0) REVERT: B 325 MET cc_start: 0.8786 (ttt) cc_final: 0.8536 (ttt) REVERT: B 330 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8966 (pp) REVERT: B 394 THR cc_start: 0.9051 (m) cc_final: 0.8812 (m) REVERT: B 407 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7824 (ttt-90) REVERT: E 1 MET cc_start: 0.4735 (tpt) cc_final: 0.4497 (tpt) REVERT: E 102 ASN cc_start: 0.9176 (t0) cc_final: 0.8815 (t0) REVERT: E 319 ASP cc_start: 0.8287 (m-30) cc_final: 0.8080 (m-30) REVERT: E 394 THR cc_start: 0.8978 (m) cc_final: 0.8775 (m) REVERT: E 410 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8165 (mmtp) REVERT: H 102 ASN cc_start: 0.9177 (t0) cc_final: 0.8778 (t0) REVERT: G 102 ASN cc_start: 0.9189 (t0) cc_final: 0.8831 (t0) REVERT: G 394 THR cc_start: 0.9034 (m) cc_final: 0.8826 (m) REVERT: F 102 ASN cc_start: 0.9171 (t0) cc_final: 0.8812 (t0) REVERT: F 319 ASP cc_start: 0.8288 (m-30) cc_final: 0.8079 (m-30) REVERT: F 325 MET cc_start: 0.8775 (ttt) cc_final: 0.8513 (ttt) REVERT: F 330 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8948 (pp) REVERT: F 407 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7662 (ttt-90) REVERT: F 438 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7886 (mtpt) REVERT: F 454 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7814 (mp10) outliers start: 32 outliers final: 20 residues processed: 470 average time/residue: 2.7452 time to fit residues: 1539.2405 Evaluate side-chains 466 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 440 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 454 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN F 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24464 Z= 0.251 Angle : 0.538 6.636 33072 Z= 0.281 Chirality : 0.041 0.165 3744 Planarity : 0.004 0.039 4184 Dihedral : 8.814 61.943 3896 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 1.05 % Allowed : 9.65 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.18 (0.15), residues: 3072 helix: 0.84 (0.15), residues: 1248 sheet: 0.48 (0.29), residues: 272 loop : -0.49 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 92 PHE 0.010 0.002 PHE F 357 TYR 0.012 0.001 TYR D 348 ARG 0.004 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 445 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9192 (t0) cc_final: 0.8860 (t0) REVERT: A 325 MET cc_start: 0.8757 (ttt) cc_final: 0.8503 (ttt) REVERT: A 330 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8975 (pp) REVERT: A 407 ARG cc_start: 0.8131 (ttt90) cc_final: 0.7626 (ttt-90) REVERT: D 102 ASN cc_start: 0.9214 (t0) cc_final: 0.8843 (t0) REVERT: D 330 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8925 (pp) REVERT: D 394 THR cc_start: 0.9040 (m) cc_final: 0.8833 (m) REVERT: C 102 ASN cc_start: 0.9165 (t0) cc_final: 0.8830 (t0) REVERT: B 325 MET cc_start: 0.8781 (ttt) cc_final: 0.8522 (ttt) REVERT: B 330 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8968 (pp) REVERT: B 394 THR cc_start: 0.9036 (m) cc_final: 0.8783 (m) REVERT: B 407 ARG cc_start: 0.8166 (ttt90) cc_final: 0.7842 (ttt-90) REVERT: E 102 ASN cc_start: 0.9174 (t0) cc_final: 0.8818 (t0) REVERT: E 319 ASP cc_start: 0.8307 (m-30) cc_final: 0.8085 (m-30) REVERT: E 394 THR cc_start: 0.8990 (m) cc_final: 0.8775 (m) REVERT: H 102 ASN cc_start: 0.9176 (t0) cc_final: 0.8807 (t0) REVERT: G 102 ASN cc_start: 0.9181 (t0) cc_final: 0.8827 (t0) REVERT: G 394 THR cc_start: 0.9053 (m) cc_final: 0.8829 (m) REVERT: F 102 ASN cc_start: 0.9171 (t0) cc_final: 0.8809 (t0) REVERT: F 319 ASP cc_start: 0.8281 (m-30) cc_final: 0.8076 (m-30) REVERT: F 325 MET cc_start: 0.8759 (ttt) cc_final: 0.8521 (ttt) REVERT: F 330 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8946 (pp) REVERT: F 407 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7673 (ttt-90) REVERT: F 438 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7907 (mtpt) REVERT: F 454 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7822 (mp10) outliers start: 26 outliers final: 19 residues processed: 464 average time/residue: 2.6302 time to fit residues: 1431.9865 Evaluate side-chains 466 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 441 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 454 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 214 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN B 243 GLN E 292 GLN H 243 GLN G 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24464 Z= 0.306 Angle : 0.568 6.510 33072 Z= 0.298 Chirality : 0.043 0.165 3744 Planarity : 0.004 0.043 4184 Dihedral : 9.117 70.941 3896 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 1.29 % Allowed : 9.28 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.11 (0.15), residues: 3072 helix: 0.76 (0.15), residues: 1248 sheet: 0.55 (0.30), residues: 272 loop : -0.53 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 92 PHE 0.012 0.002 PHE F 357 TYR 0.014 0.002 TYR D 348 ARG 0.004 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 444 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9219 (t0) cc_final: 0.8874 (t0) REVERT: A 325 MET cc_start: 0.8782 (ttt) cc_final: 0.8554 (ttt) REVERT: A 330 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 407 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7646 (ttt-90) REVERT: D 102 ASN cc_start: 0.9217 (t0) cc_final: 0.8857 (t0) REVERT: D 330 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8919 (pp) REVERT: D 394 THR cc_start: 0.9060 (m) cc_final: 0.8834 (m) REVERT: D 410 LYS cc_start: 0.8397 (mmtm) cc_final: 0.8169 (mmtp) REVERT: C 102 ASN cc_start: 0.9164 (t0) cc_final: 0.8825 (t0) REVERT: C 454 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: B 325 MET cc_start: 0.8803 (ttt) cc_final: 0.8578 (ttt) REVERT: B 330 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8976 (pp) REVERT: B 394 THR cc_start: 0.9058 (m) cc_final: 0.8815 (m) REVERT: B 407 ARG cc_start: 0.8186 (ttt90) cc_final: 0.7844 (ttt-90) REVERT: B 420 MET cc_start: 0.8811 (mtm) cc_final: 0.8218 (mtp) REVERT: E 102 ASN cc_start: 0.9179 (t0) cc_final: 0.8825 (t0) REVERT: E 319 ASP cc_start: 0.8247 (m-30) cc_final: 0.8022 (m-30) REVERT: E 394 THR cc_start: 0.8993 (m) cc_final: 0.8782 (m) REVERT: E 410 LYS cc_start: 0.8389 (mmtm) cc_final: 0.8154 (mmtp) REVERT: H 102 ASN cc_start: 0.9206 (t0) cc_final: 0.8815 (t0) REVERT: G 102 ASN cc_start: 0.9190 (t0) cc_final: 0.8838 (t0) REVERT: G 420 MET cc_start: 0.8863 (mtm) cc_final: 0.8483 (mtp) REVERT: G 454 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: F 102 ASN cc_start: 0.9173 (t0) cc_final: 0.8821 (t0) REVERT: F 319 ASP cc_start: 0.8250 (m-30) cc_final: 0.8046 (m-30) REVERT: F 325 MET cc_start: 0.8787 (ttt) cc_final: 0.8552 (ttt) REVERT: F 330 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8953 (pp) REVERT: F 407 ARG cc_start: 0.8152 (ttt90) cc_final: 0.7679 (ttt-90) REVERT: F 420 MET cc_start: 0.8825 (mtm) cc_final: 0.8208 (mtp) REVERT: F 438 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7917 (mtpt) REVERT: F 454 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7831 (mp10) outliers start: 32 outliers final: 20 residues processed: 464 average time/residue: 2.6386 time to fit residues: 1435.8630 Evaluate side-chains 468 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 440 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 454 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24464 Z= 0.345 Angle : 0.587 7.369 33072 Z= 0.308 Chirality : 0.043 0.164 3744 Planarity : 0.004 0.044 4184 Dihedral : 9.310 74.855 3896 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 1.21 % Allowed : 9.57 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.05 (0.15), residues: 3072 helix: 0.72 (0.15), residues: 1248 sheet: 0.51 (0.30), residues: 272 loop : -0.57 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 92 PHE 0.013 0.002 PHE F 357 TYR 0.014 0.002 TYR D 348 ARG 0.005 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 442 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9220 (t0) cc_final: 0.8878 (t0) REVERT: A 325 MET cc_start: 0.8779 (ttt) cc_final: 0.8549 (ttt) REVERT: A 330 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 407 ARG cc_start: 0.8122 (ttt90) cc_final: 0.7642 (ttt-90) REVERT: D 102 ASN cc_start: 0.9220 (t0) cc_final: 0.8864 (t0) REVERT: D 330 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8907 (pp) REVERT: C 102 ASN cc_start: 0.9166 (t0) cc_final: 0.8829 (t0) REVERT: C 454 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: B 58 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8163 (mttp) REVERT: B 325 MET cc_start: 0.8797 (ttt) cc_final: 0.8560 (ttt) REVERT: B 330 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8995 (pp) REVERT: B 394 THR cc_start: 0.9057 (m) cc_final: 0.8815 (m) REVERT: B 407 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7846 (ttt-90) REVERT: E 102 ASN cc_start: 0.9175 (t0) cc_final: 0.8823 (t0) REVERT: E 394 THR cc_start: 0.8991 (m) cc_final: 0.8788 (m) REVERT: H 102 ASN cc_start: 0.9206 (t0) cc_final: 0.8819 (t0) REVERT: G 102 ASN cc_start: 0.9215 (t0) cc_final: 0.8855 (t0) REVERT: G 454 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: F 102 ASN cc_start: 0.9173 (t0) cc_final: 0.8823 (t0) REVERT: F 319 ASP cc_start: 0.8247 (m-30) cc_final: 0.8042 (m-30) REVERT: F 325 MET cc_start: 0.8786 (ttt) cc_final: 0.8543 (ttt) REVERT: F 330 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8973 (pp) REVERT: F 407 ARG cc_start: 0.8168 (ttt90) cc_final: 0.7692 (ttt-90) REVERT: F 438 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7948 (mtpt) REVERT: F 454 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7837 (mp10) outliers start: 30 outliers final: 21 residues processed: 463 average time/residue: 2.6522 time to fit residues: 1437.8388 Evaluate side-chains 468 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 438 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 454 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 258 optimal weight: 0.0970 chunk 272 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN H 441 GLN G 441 GLN F 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24464 Z= 0.163 Angle : 0.496 6.844 33072 Z= 0.257 Chirality : 0.040 0.162 3744 Planarity : 0.003 0.036 4184 Dihedral : 8.292 63.821 3896 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 0.64 % Allowed : 10.13 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3072 helix: 1.04 (0.15), residues: 1248 sheet: 0.70 (0.30), residues: 272 loop : -0.45 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 92 PHE 0.012 0.001 PHE D 401 TYR 0.010 0.001 TYR B 353 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 461 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9197 (t0) cc_final: 0.8842 (t0) REVERT: A 325 MET cc_start: 0.8728 (ttt) cc_final: 0.8468 (ttt) REVERT: A 330 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8991 (pp) REVERT: A 407 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7630 (ttt-90) REVERT: D 102 ASN cc_start: 0.9186 (t0) cc_final: 0.8788 (t0) REVERT: D 330 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8902 (pp) REVERT: D 394 THR cc_start: 0.9024 (m) cc_final: 0.8791 (m) REVERT: C 102 ASN cc_start: 0.9160 (t0) cc_final: 0.8785 (t0) REVERT: C 252 THR cc_start: 0.8760 (p) cc_final: 0.8529 (p) REVERT: C 394 THR cc_start: 0.9000 (m) cc_final: 0.8772 (m) REVERT: B 102 ASN cc_start: 0.9171 (t0) cc_final: 0.8753 (t0) REVERT: B 319 ASP cc_start: 0.8257 (m-30) cc_final: 0.8027 (m-30) REVERT: B 325 MET cc_start: 0.8740 (ttt) cc_final: 0.8474 (ttt) REVERT: B 330 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8941 (pp) REVERT: B 394 THR cc_start: 0.8993 (m) cc_final: 0.8740 (m) REVERT: B 420 MET cc_start: 0.8787 (mtm) cc_final: 0.8462 (mtp) REVERT: E 102 ASN cc_start: 0.9167 (t0) cc_final: 0.8779 (t0) REVERT: E 394 THR cc_start: 0.8960 (m) cc_final: 0.8758 (m) REVERT: H 102 ASN cc_start: 0.9169 (t0) cc_final: 0.8771 (t0) REVERT: H 420 MET cc_start: 0.8748 (mtm) cc_final: 0.8314 (mtp) REVERT: G 102 ASN cc_start: 0.9172 (t0) cc_final: 0.8777 (t0) REVERT: G 394 THR cc_start: 0.9006 (m) cc_final: 0.8782 (m) REVERT: F 102 ASN cc_start: 0.9168 (t0) cc_final: 0.8773 (t0) REVERT: F 319 ASP cc_start: 0.8294 (m-30) cc_final: 0.8074 (m-30) REVERT: F 325 MET cc_start: 0.8723 (ttt) cc_final: 0.8446 (ttt) REVERT: F 330 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8922 (pp) REVERT: F 407 ARG cc_start: 0.8158 (ttt90) cc_final: 0.7683 (ttt-90) outliers start: 16 outliers final: 9 residues processed: 473 average time/residue: 2.7765 time to fit residues: 1534.6718 Evaluate side-chains 456 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 443 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 200 optimal weight: 0.5980 chunk 302 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 498 GLN D 243 GLN B 93 HIS H 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24464 Z= 0.309 Angle : 0.571 11.284 33072 Z= 0.298 Chirality : 0.043 0.164 3744 Planarity : 0.004 0.037 4184 Dihedral : 8.925 64.313 3896 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 0.60 % Allowed : 10.41 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 3072 helix: 0.90 (0.15), residues: 1248 sheet: 0.64 (0.30), residues: 272 loop : -0.53 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 92 PHE 0.012 0.002 PHE F 357 TYR 0.014 0.002 TYR G 282 ARG 0.004 0.001 ARG A 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 436 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9200 (t0) cc_final: 0.8860 (t0) REVERT: A 325 MET cc_start: 0.8783 (ttt) cc_final: 0.8554 (ttt) REVERT: A 330 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8985 (pp) REVERT: A 407 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7648 (ttt-90) REVERT: D 102 ASN cc_start: 0.9213 (t0) cc_final: 0.8834 (t0) REVERT: D 330 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8915 (pp) REVERT: D 394 THR cc_start: 0.9055 (m) cc_final: 0.8825 (m) REVERT: C 102 ASN cc_start: 0.9164 (t0) cc_final: 0.8816 (t0) REVERT: B 319 ASP cc_start: 0.8272 (m-30) cc_final: 0.8065 (m-30) REVERT: B 325 MET cc_start: 0.8810 (ttt) cc_final: 0.8578 (ttt) REVERT: B 330 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8978 (pp) REVERT: B 394 THR cc_start: 0.9037 (m) cc_final: 0.8799 (m) REVERT: E 102 ASN cc_start: 0.9177 (t0) cc_final: 0.8822 (t0) REVERT: E 394 THR cc_start: 0.8999 (m) cc_final: 0.8799 (m) REVERT: H 102 ASN cc_start: 0.9175 (t0) cc_final: 0.8798 (t0) REVERT: G 102 ASN cc_start: 0.9186 (t0) cc_final: 0.8817 (t0) REVERT: F 102 ASN cc_start: 0.9174 (t0) cc_final: 0.8808 (t0) REVERT: F 319 ASP cc_start: 0.8247 (m-30) cc_final: 0.8045 (m-30) REVERT: F 325 MET cc_start: 0.8785 (ttt) cc_final: 0.8541 (ttt) REVERT: F 330 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8948 (pp) REVERT: F 407 ARG cc_start: 0.8163 (ttt90) cc_final: 0.7689 (ttt-90) REVERT: F 438 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7941 (mtpt) outliers start: 15 outliers final: 9 residues processed: 449 average time/residue: 2.7457 time to fit residues: 1444.0041 Evaluate side-chains 449 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 435 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.0670 chunk 256 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 222 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN D 243 GLN F 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.088244 restraints weight = 97254.607| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.54 r_work: 0.2674 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24464 Z= 0.160 Angle : 0.498 9.847 33072 Z= 0.257 Chirality : 0.040 0.161 3744 Planarity : 0.003 0.036 4184 Dihedral : 8.222 63.610 3896 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.33 % Favored : 96.54 % Rotamer: Outliers : 0.60 % Allowed : 10.21 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3072 helix: 1.10 (0.15), residues: 1248 sheet: 0.73 (0.31), residues: 272 loop : -0.45 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 92 PHE 0.011 0.001 PHE E 401 TYR 0.009 0.001 TYR B 353 ARG 0.003 0.000 ARG D 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20703.86 seconds wall clock time: 361 minutes 0.43 seconds (21660.43 seconds total)