Starting phenix.real_space_refine on Thu Feb 22 16:43:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/02_2024/7jy5_22521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/02_2024/7jy5_22521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/02_2024/7jy5_22521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/02_2024/7jy5_22521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/02_2024/7jy5_22521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/02_2024/7jy5_22521_updated.pdb" } resolution = 2.89 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= 0.003 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 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21732 2.51 5 N 6156 2.21 5 O 6600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ASP 669": "OD1" <-> "OD2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B ASP 395": "OD1" <-> "OD2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ASP 669": "OD1" <-> "OD2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ASP 395": "OD1" <-> "OD2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C ASP 438": "OD1" <-> "OD2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ASP 564": "OD1" <-> "OD2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C ARG 662": "NH1" <-> "NH2" Residue "C ASP 669": "OD1" <-> "OD2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 710": "OE1" <-> "OE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 393": "OD1" <-> "OD2" Residue "D ASP 395": "OD1" <-> "OD2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D ASP 438": "OD1" <-> "OD2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ASP 564": "OD1" <-> "OD2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D ARG 662": "NH1" <-> "NH2" Residue "D ASP 669": "OD1" <-> "OD2" Residue "D PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E ASP 395": "OD1" <-> "OD2" Residue "E ASP 410": "OD1" <-> "OD2" Residue "E ASP 438": "OD1" <-> "OD2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 561": "OE1" <-> "OE2" Residue "E ASP 564": "OD1" <-> "OD2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 586": "NH1" <-> "NH2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E ARG 662": "NH1" <-> "NH2" Residue "E ASP 669": "OD1" <-> "OD2" Residue "E PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "E GLU 710": "OE1" <-> "OE2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "E GLU 756": "OE1" <-> "OE2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "F ARG 25": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F ASP 395": "OD1" <-> "OD2" Residue "F ASP 410": "OD1" <-> "OD2" Residue "F ASP 438": "OD1" <-> "OD2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F ARG 662": "NH1" <-> "NH2" Residue "F ASP 669": "OD1" <-> "OD2" Residue "F PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 693": "NH1" <-> "NH2" Residue "F GLU 704": "OE1" <-> "OE2" Residue "F GLU 710": "OE1" <-> "OE2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F GLU 730": "OE1" <-> "OE2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "F GLU 756": "OE1" <-> "OE2" Residue "F ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34728 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5724 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 17.64, per 1000 atoms: 0.51 Number of scatterers: 34728 At special positions: 0 Unit cell: (175.56, 170.28, 114.84, 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 192 16.00 P 36 15.00 Mg 12 11.99 O 6600 8.00 N 6156 7.00 C 21732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.13 Conformation dependent library (CDL) restraints added in 5.7 seconds 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 30 sheets defined 43.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.70 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.017A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 429 removed outlier: 3.609A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.578A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 613 removed outlier: 3.807A pdb=" N SER A 612 " --> pdb=" O MET A 608 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 713 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.851A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.017A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 429 removed outlier: 3.608A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.578A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 613 removed outlier: 3.807A pdb=" N SER B 612 " --> pdb=" O MET B 608 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 713 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.852A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.016A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 429 removed outlier: 3.609A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 579 through 585 removed outlier: 3.578A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 613 removed outlier: 3.808A pdb=" N SER C 612 " --> pdb=" O MET C 608 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 713 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 761 removed outlier: 3.850A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.017A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 429 removed outlier: 3.608A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.578A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 613 removed outlier: 3.808A pdb=" N SER D 612 " --> pdb=" O MET D 608 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR D 613 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 713 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 749 through 761 removed outlier: 3.851A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.016A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 429 removed outlier: 3.609A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 548 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 579 through 585 removed outlier: 3.578A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 613 removed outlier: 3.808A pdb=" N SER E 612 " --> pdb=" O MET E 608 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR E 613 " --> pdb=" O ASP E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 749 through 761 removed outlier: 3.851A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.016A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'F' and resid 355 through 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 429 removed outlier: 3.608A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 493 Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 548 Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 585 removed outlier: 3.577A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 613 removed outlier: 3.808A pdb=" N SER F 612 " --> pdb=" O MET F 608 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 713 Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 749 through 761 removed outlier: 3.851A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 6.989A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.880A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 113 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.515A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 644 removed outlier: 3.571A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.989A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.881A pdb=" N HIS B 183 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 113 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.516A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.572A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 84 removed outlier: 6.989A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.880A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 113 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.515A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 644 removed outlier: 3.571A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 81 through 84 removed outlier: 6.989A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.880A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 113 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.516A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 644 removed outlier: 3.571A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 84 removed outlier: 6.988A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.880A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG E 113 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.515A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 644 removed outlier: 3.572A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 84 removed outlier: 6.989A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.879A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG F 113 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.517A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 644 removed outlier: 3.573A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3492 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: 13.56 Time building geometry restraints manager: 13.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 12217 1.36 - 1.51: 10109 1.51 - 1.65: 12648 1.65 - 1.79: 184 1.79 - 1.94: 116 Bond restraints: 35274 Sorted by residual: bond pdb=" CB ARG E 377 " pdb=" CG ARG E 377 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.17e+00 bond pdb=" CG1 ILE F 645 " pdb=" CD1 ILE F 645 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.16e+00 bond pdb=" CB ARG F 377 " pdb=" CG ARG F 377 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CG1 ILE B 645 " pdb=" CD1 ILE B 645 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.14e+00 bond pdb=" CG1 ILE A 645 " pdb=" CD1 ILE A 645 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.13e+00 ... (remaining 35269 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.87: 982 105.87 - 112.94: 19335 112.94 - 120.01: 12415 120.01 - 127.08: 14614 127.08 - 134.15: 354 Bond angle restraints: 47700 Sorted by residual: angle pdb=" NE ARG E 465 " pdb=" CZ ARG E 465 " pdb=" NH1 ARG E 465 " ideal model delta sigma weight residual 121.50 119.20 2.30 1.00e+00 1.00e+00 5.31e+00 angle pdb=" NE ARG B 465 " pdb=" CZ ARG B 465 " pdb=" NH1 ARG B 465 " ideal model delta sigma weight residual 121.50 119.21 2.29 1.00e+00 1.00e+00 5.24e+00 angle pdb=" NE ARG A 465 " pdb=" CZ ARG A 465 " pdb=" NH1 ARG A 465 " ideal model delta sigma weight residual 121.50 119.24 2.26 1.00e+00 1.00e+00 5.12e+00 angle pdb=" NE ARG F 465 " pdb=" CZ ARG F 465 " pdb=" NH1 ARG F 465 " ideal model delta sigma weight residual 121.50 119.24 2.26 1.00e+00 1.00e+00 5.10e+00 angle pdb=" NE ARG C 465 " pdb=" CZ ARG C 465 " pdb=" NH1 ARG C 465 " ideal model delta sigma weight residual 121.50 119.25 2.25 1.00e+00 1.00e+00 5.05e+00 ... (remaining 47695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.71: 21409 30.71 - 61.41: 551 61.41 - 92.12: 54 92.12 - 122.82: 6 122.82 - 153.53: 6 Dihedral angle restraints: 22026 sinusoidal: 9342 harmonic: 12684 Sorted by residual: dihedral pdb=" O1A AGS C 903 " pdb=" O3A AGS C 903 " pdb=" PA AGS C 903 " pdb=" PB AGS C 903 " ideal model delta sinusoidal sigma weight residual -67.73 85.80 -153.53 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O1A AGS F 903 " pdb=" O3A AGS F 903 " pdb=" PA AGS F 903 " pdb=" PB AGS F 903 " ideal model delta sinusoidal sigma weight residual -67.73 85.46 -153.19 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA ASN F 296 " pdb=" C ASN F 296 " pdb=" N ALA F 297 " pdb=" CA ALA F 297 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 22023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3490 0.046 - 0.093: 1489 0.093 - 0.139: 434 0.139 - 0.185: 17 0.185 - 0.232: 6 Chirality restraints: 5436 Sorted by residual: chirality pdb=" PA AGS A 904 " pdb=" O2A AGS A 904 " pdb=" O3A AGS A 904 " pdb=" O5' AGS A 904 " both_signs ideal model delta sigma weight residual True 3.18 2.95 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" PA AGS D 904 " pdb=" O2A AGS D 904 " pdb=" O3A AGS D 904 " pdb=" O5' AGS D 904 " both_signs ideal model delta sigma weight residual True 3.18 2.95 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" PA AGS E 904 " pdb=" O2A AGS E 904 " pdb=" O3A AGS E 904 " pdb=" O5' AGS E 904 " both_signs ideal model delta sigma weight residual True 3.18 2.96 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 5433 not shown) Planarity restraints: 6222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 544 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO E 545 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 545 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 545 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 544 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 545 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 544 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO F 545 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 545 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 545 " 0.028 5.00e-02 4.00e+02 ... (remaining 6219 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 161 2.49 - 3.09: 24650 3.09 - 3.69: 53683 3.69 - 4.30: 81657 4.30 - 4.90: 133412 Nonbonded interactions: 293563 Sorted by model distance: nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 901 " model vdw 1.883 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 901 " model vdw 1.884 2.170 nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 901 " model vdw 1.884 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 901 " model vdw 1.890 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 901 " model vdw 1.897 2.170 ... (remaining 293558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.030 Extract box with map and model: 5.460 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 87.640 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.009 0.069 35274 Z= 0.567 Angle : 0.672 6.859 47700 Z= 0.366 Chirality : 0.052 0.232 5436 Planarity : 0.004 0.050 6222 Dihedral : 14.156 153.525 13770 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4338 helix: -0.55 (0.11), residues: 2046 sheet: 0.53 (0.22), residues: 576 loop : 0.30 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 454 HIS 0.004 0.001 HIS F 384 PHE 0.010 0.002 PHE D 758 TYR 0.016 0.002 TYR A 203 ARG 0.010 0.001 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.762 Fit side-chains REVERT: B 449 MET cc_start: 0.7990 (tpt) cc_final: 0.7762 (tpt) REVERT: E 449 MET cc_start: 0.7936 (tpt) cc_final: 0.7678 (tpt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 1.7681 time to fit residues: 436.8955 Evaluate side-chains 140 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 10.0000 chunk 331 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 255 optimal weight: 0.9980 chunk 397 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35274 Z= 0.195 Angle : 0.547 8.418 47700 Z= 0.274 Chirality : 0.045 0.223 5436 Planarity : 0.004 0.046 6222 Dihedral : 9.780 154.730 5004 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.94 % Allowed : 4.75 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4338 helix: 0.35 (0.12), residues: 2028 sheet: 0.26 (0.22), residues: 636 loop : 0.59 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 454 HIS 0.004 0.001 HIS B 183 PHE 0.009 0.001 PHE D 302 TYR 0.007 0.001 TYR A 203 ARG 0.004 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 4.120 Fit side-chains REVERT: A 158 MET cc_start: 0.3316 (OUTLIER) cc_final: 0.2805 (pp-130) REVERT: B 158 MET cc_start: 0.3031 (OUTLIER) cc_final: 0.2779 (pp-130) REVERT: B 449 MET cc_start: 0.7954 (tpt) cc_final: 0.7592 (tpt) REVERT: D 158 MET cc_start: 0.3392 (OUTLIER) cc_final: 0.2857 (pp-130) REVERT: E 449 MET cc_start: 0.7916 (tpt) cc_final: 0.7627 (tpt) outliers start: 35 outliers final: 2 residues processed: 173 average time/residue: 1.5842 time to fit residues: 328.2169 Evaluate side-chains 143 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 757 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 398 optimal weight: 0.9980 chunk 430 optimal weight: 4.9990 chunk 354 optimal weight: 0.0270 chunk 395 optimal weight: 0.0670 chunk 135 optimal weight: 0.6980 chunk 319 optimal weight: 6.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 215 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN E 215 GLN ** E 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35274 Z= 0.147 Angle : 0.483 10.338 47700 Z= 0.241 Chirality : 0.043 0.196 5436 Planarity : 0.004 0.044 6222 Dihedral : 9.542 156.731 5004 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.81 % Allowed : 6.60 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.13), residues: 4338 helix: 0.91 (0.12), residues: 2028 sheet: 0.40 (0.22), residues: 636 loop : 0.61 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 476 HIS 0.003 0.000 HIS E 183 PHE 0.010 0.001 PHE D 302 TYR 0.007 0.001 TYR E 244 ARG 0.005 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 4.436 Fit side-chains revert: symmetry clash REVERT: B 158 MET cc_start: 0.2836 (OUTLIER) cc_final: 0.2612 (pp-130) REVERT: B 449 MET cc_start: 0.8014 (tpt) cc_final: 0.7475 (tpp) REVERT: E 158 MET cc_start: 0.3461 (OUTLIER) cc_final: 0.3067 (pp-130) outliers start: 30 outliers final: 0 residues processed: 155 average time/residue: 1.6067 time to fit residues: 299.6529 Evaluate side-chains 132 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain E residue 158 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 267 optimal weight: 0.0010 chunk 399 optimal weight: 4.9990 chunk 423 optimal weight: 7.9990 chunk 208 optimal weight: 0.0570 chunk 379 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS F 384 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 35274 Z= 0.301 Angle : 0.528 8.906 47700 Z= 0.259 Chirality : 0.045 0.187 5436 Planarity : 0.004 0.058 6222 Dihedral : 9.453 157.143 5004 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.05 % Allowed : 8.53 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4338 helix: 1.21 (0.12), residues: 2028 sheet: 0.49 (0.22), residues: 636 loop : 0.67 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 476 HIS 0.002 0.001 HIS D 499 PHE 0.011 0.001 PHE A 302 TYR 0.005 0.001 TYR A 517 ARG 0.005 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 4.245 Fit side-chains REVERT: A 158 MET cc_start: 0.2355 (OUTLIER) cc_final: 0.2101 (pp-130) REVERT: B 449 MET cc_start: 0.8061 (tpt) cc_final: 0.7674 (tpt) REVERT: C 158 MET cc_start: 0.3628 (OUTLIER) cc_final: 0.3417 (pp-130) REVERT: C 305 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: D 158 MET cc_start: 0.2381 (OUTLIER) cc_final: 0.2113 (pp-130) REVERT: E 158 MET cc_start: 0.3319 (OUTLIER) cc_final: 0.3012 (pp-130) REVERT: E 449 MET cc_start: 0.8041 (tpt) cc_final: 0.7731 (tpt) REVERT: F 158 MET cc_start: 0.3633 (OUTLIER) cc_final: 0.3426 (pp-130) REVERT: F 305 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6758 (mt-10) outliers start: 39 outliers final: 6 residues processed: 150 average time/residue: 1.6197 time to fit residues: 290.4151 Evaluate side-chains 146 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 315 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 380 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35274 Z= 0.182 Angle : 0.480 8.516 47700 Z= 0.239 Chirality : 0.043 0.170 5436 Planarity : 0.003 0.045 6222 Dihedral : 9.420 158.021 5004 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.81 % Allowed : 9.42 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.13), residues: 4338 helix: 1.43 (0.12), residues: 2022 sheet: 1.11 (0.25), residues: 546 loop : 0.59 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 454 HIS 0.002 0.000 HIS B 183 PHE 0.018 0.001 PHE A 674 TYR 0.007 0.001 TYR B 244 ARG 0.003 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 449 MET cc_start: 0.8044 (tpt) cc_final: 0.7746 (tpt) REVERT: E 158 MET cc_start: 0.3126 (OUTLIER) cc_final: 0.2870 (pp-130) outliers start: 30 outliers final: 9 residues processed: 156 average time/residue: 1.6176 time to fit residues: 301.0784 Evaluate side-chains 143 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 757 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 6.9990 chunk 381 optimal weight: 0.0020 chunk 83 optimal weight: 40.0000 chunk 248 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 423 optimal weight: 0.4980 chunk 351 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35274 Z= 0.187 Angle : 0.481 8.272 47700 Z= 0.238 Chirality : 0.043 0.232 5436 Planarity : 0.003 0.044 6222 Dihedral : 9.405 158.007 5004 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.72 % Allowed : 10.14 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.13), residues: 4338 helix: 1.54 (0.12), residues: 2022 sheet: 1.16 (0.25), residues: 546 loop : 0.63 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.002 0.000 HIS B 183 PHE 0.022 0.001 PHE B 674 TYR 0.006 0.001 TYR B 244 ARG 0.004 0.000 ARG B 653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 4.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.3562 (pp-130) cc_final: 0.3307 (pp-130) REVERT: E 158 MET cc_start: 0.3019 (OUTLIER) cc_final: 0.2788 (pp-130) outliers start: 27 outliers final: 7 residues processed: 163 average time/residue: 1.4869 time to fit residues: 294.1720 Evaluate side-chains 141 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 241 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 356 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 422 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 35274 Z= 0.317 Angle : 0.536 9.104 47700 Z= 0.261 Chirality : 0.045 0.181 5436 Planarity : 0.004 0.043 6222 Dihedral : 9.435 157.580 5004 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.64 % Allowed : 10.47 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.13), residues: 4338 helix: 1.52 (0.12), residues: 2028 sheet: 1.15 (0.25), residues: 546 loop : 0.70 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 476 HIS 0.003 0.001 HIS E 406 PHE 0.032 0.001 PHE B 674 TYR 0.007 0.001 TYR A 517 ARG 0.004 0.000 ARG E 653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.6221 (ppp) cc_final: 0.5910 (ttp) REVERT: B 158 MET cc_start: 0.3649 (OUTLIER) cc_final: 0.3248 (pp-130) REVERT: C 305 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: E 84 MET cc_start: 0.6170 (ppp) cc_final: 0.5855 (ttp) REVERT: E 158 MET cc_start: 0.3035 (OUTLIER) cc_final: 0.2622 (pp-130) REVERT: E 427 MET cc_start: 0.6586 (ttm) cc_final: 0.6375 (mtm) REVERT: F 305 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6800 (mt-10) outliers start: 24 outliers final: 10 residues processed: 157 average time/residue: 1.5845 time to fit residues: 298.6830 Evaluate side-chains 152 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 331 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35274 Z= 0.232 Angle : 0.503 7.904 47700 Z= 0.248 Chirality : 0.044 0.177 5436 Planarity : 0.003 0.045 6222 Dihedral : 9.451 157.724 5004 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.83 % Allowed : 10.41 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 4338 helix: 1.55 (0.12), residues: 2028 sheet: 0.87 (0.24), residues: 588 loop : 0.82 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.002 0.001 HIS D 404 PHE 0.016 0.001 PHE D 674 TYR 0.006 0.001 TYR A 517 ARG 0.004 0.000 ARG E 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.3591 (OUTLIER) cc_final: 0.3197 (pp-130) REVERT: B 427 MET cc_start: 0.6585 (ttm) cc_final: 0.6339 (mtm) REVERT: C 305 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: E 158 MET cc_start: 0.2971 (OUTLIER) cc_final: 0.2573 (pp-130) REVERT: E 427 MET cc_start: 0.6535 (ttm) cc_final: 0.6276 (mtm) REVERT: F 305 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6780 (mt-10) outliers start: 31 outliers final: 10 residues processed: 165 average time/residue: 1.4256 time to fit residues: 285.4133 Evaluate side-chains 153 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.4980 chunk 404 optimal weight: 4.9990 chunk 368 optimal weight: 20.0000 chunk 393 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 171 optimal weight: 0.0030 chunk 308 optimal weight: 0.0030 chunk 120 optimal weight: 0.6980 chunk 355 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 chunk 392 optimal weight: 0.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35274 Z= 0.128 Angle : 0.478 9.169 47700 Z= 0.237 Chirality : 0.043 0.173 5436 Planarity : 0.003 0.045 6222 Dihedral : 9.427 157.993 5004 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.56 % Allowed : 10.68 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.14), residues: 4338 helix: 1.60 (0.12), residues: 2028 sheet: 0.92 (0.24), residues: 588 loop : 0.81 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 476 HIS 0.002 0.000 HIS B 404 PHE 0.015 0.001 PHE D 674 TYR 0.008 0.001 TYR B 244 ARG 0.004 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 3.997 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.6068 (ppp) cc_final: 0.5806 (ttp) REVERT: B 158 MET cc_start: 0.3603 (OUTLIER) cc_final: 0.3229 (pp-130) REVERT: C 305 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: E 84 MET cc_start: 0.6006 (ppp) cc_final: 0.5751 (ttp) REVERT: E 158 MET cc_start: 0.3682 (OUTLIER) cc_final: 0.3278 (pp-130) REVERT: E 427 MET cc_start: 0.6425 (ttm) cc_final: 0.6165 (mtm) REVERT: F 305 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6661 (mt-10) outliers start: 21 outliers final: 8 residues processed: 162 average time/residue: 1.5574 time to fit residues: 303.3941 Evaluate side-chains 154 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 3.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 8.9990 chunk 415 optimal weight: 0.0870 chunk 253 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 289 optimal weight: 7.9990 chunk 436 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 347 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 268 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35274 Z= 0.147 Angle : 0.496 8.553 47700 Z= 0.244 Chirality : 0.043 0.183 5436 Planarity : 0.003 0.045 6222 Dihedral : 9.419 158.064 5004 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.38 % Allowed : 10.90 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.14), residues: 4338 helix: 1.64 (0.12), residues: 2028 sheet: 0.95 (0.24), residues: 588 loop : 0.82 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.002 0.000 HIS F 183 PHE 0.028 0.001 PHE B 674 TYR 0.006 0.001 TYR C 244 ARG 0.003 0.000 ARG A 693 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 4.395 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.6047 (ppp) cc_final: 0.5808 (ttp) REVERT: B 158 MET cc_start: 0.3500 (OUTLIER) cc_final: 0.3057 (pp-130) REVERT: C 84 MET cc_start: 0.5655 (pp-130) cc_final: 0.5445 (pp-130) REVERT: C 305 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: D 51 LEU cc_start: 0.5703 (mm) cc_final: 0.5302 (mm) REVERT: E 84 MET cc_start: 0.5994 (ppp) cc_final: 0.5758 (ttp) REVERT: E 158 MET cc_start: 0.3635 (OUTLIER) cc_final: 0.3207 (pp-130) REVERT: E 427 MET cc_start: 0.6414 (ttm) cc_final: 0.6155 (mtm) REVERT: E 449 MET cc_start: 0.7915 (tpt) cc_final: 0.7642 (tpt) REVERT: F 84 MET cc_start: 0.5596 (pp-130) cc_final: 0.5393 (pp-130) REVERT: F 305 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6666 (mt-10) outliers start: 14 outliers final: 6 residues processed: 154 average time/residue: 1.4923 time to fit residues: 278.7283 Evaluate side-chains 151 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 3.9990 chunk 370 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 320 optimal weight: 0.0970 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 348 optimal weight: 0.3980 chunk 145 optimal weight: 6.9990 chunk 357 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 602 ASN F 602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.092814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056496 restraints weight = 83726.346| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.27 r_work: 0.2717 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35274 Z= 0.128 Angle : 0.488 11.857 47700 Z= 0.239 Chirality : 0.043 0.195 5436 Planarity : 0.003 0.045 6222 Dihedral : 9.396 157.762 5004 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.43 % Allowed : 10.84 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.14), residues: 4338 helix: 1.67 (0.12), residues: 2028 sheet: 0.98 (0.24), residues: 588 loop : 0.82 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.002 0.000 HIS C 183 PHE 0.026 0.001 PHE E 674 TYR 0.006 0.001 TYR F 244 ARG 0.003 0.000 ARG E 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7402.76 seconds wall clock time: 134 minutes 58.35 seconds (8098.35 seconds total)