Starting phenix.real_space_refine (version: dev) on Mon Dec 19 07:14:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/12_2022/7jy5_22521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/12_2022/7jy5_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_22521/12_2022/7jy5_22521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/12_2022/7jy5_22521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/12_2022/7jy5_22521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy5_22521/12_2022/7jy5_22521_updated.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 18.54, per 1000 atoms: 0.53 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: 15.07 Conformation dependent library (CDL) restraints added in 5.3 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: 5.01 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: 13.74 Time building geometry restraints manager: 16.30 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: 21310 30.71 - 61.41: 518 61.41 - 92.12: 54 92.12 - 122.82: 6 122.82 - 153.53: 6 Dihedral angle restraints: 21894 sinusoidal: 9210 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 21891 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 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. 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: 1.040 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: 0.020 Extract box with map and model: 6.700 Check model and map are aligned: 0.590 Convert atoms to be neutral: 0.300 Process input model: 91.260 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 13.957 153.525 13638 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 4.872 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 1.6876 time to fit residues: 419.3271 Evaluate side-chains 140 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 4.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1210 ------------------------------------------------------------------------------- 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: ** 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: 0.8050 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 35274 Z= 0.197 Angle : 0.546 8.327 47700 Z= 0.273 Chirality : 0.044 0.191 5436 Planarity : 0.004 0.046 6222 Dihedral : 9.009 149.771 4872 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.94 % 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: 0.46 (0.13), residues: 4338 helix: 0.33 (0.12), residues: 2028 sheet: 0.24 (0.22), residues: 636 loop : 0.59 (0.16), residues: 1674 *********************** 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 192 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 4.413 Fit side-chains outliers start: 35 outliers final: 3 residues processed: 172 average time/residue: 1.5355 time to fit residues: 318.6041 Evaluate side-chains 143 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 4.078 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.2471 time to fit residues: 8.4829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 398 optimal weight: 2.9990 chunk 430 optimal weight: 6.9990 chunk 354 optimal weight: 2.9990 chunk 395 optimal weight: 0.7980 chunk 135 optimal weight: 0.0770 chunk 319 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.1398 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= 0.201 Angle : 0.506 8.391 47700 Z= 0.252 Chirality : 0.044 0.148 5436 Planarity : 0.004 0.045 6222 Dihedral : 8.819 149.041 4872 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.75 % 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: 0.90 (0.13), residues: 4338 helix: 0.86 (0.12), residues: 2022 sheet: 0.36 (0.22), residues: 636 loop : 0.61 (0.16), residues: 1680 *********************** 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 174 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 4.535 Fit side-chains outliers start: 28 outliers final: 3 residues processed: 154 average time/residue: 1.5396 time to fit residues: 286.3685 Evaluate side-chains 137 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 4.510 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.3562 time to fit residues: 11.0050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 399 optimal weight: 4.9990 chunk 423 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 379 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 35274 Z= 0.419 Angle : 0.594 10.313 47700 Z= 0.288 Chirality : 0.047 0.188 5436 Planarity : 0.004 0.058 6222 Dihedral : 8.697 146.043 4872 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.99 % 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: 1.14 (0.13), residues: 4338 helix: 1.09 (0.12), residues: 2028 sheet: 0.65 (0.23), residues: 606 loop : 0.60 (0.16), residues: 1704 *********************** 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 182 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 4.733 Fit side-chains outliers start: 37 outliers final: 7 residues processed: 155 average time/residue: 1.5596 time to fit residues: 291.9238 Evaluate side-chains 142 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 4.611 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 6 average time/residue: 1.4652 time to fit residues: 16.8015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 6 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 380 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN B 660 ASN D 660 ASN E 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1765 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= 0.268 Angle : 0.516 9.629 47700 Z= 0.255 Chirality : 0.044 0.164 5436 Planarity : 0.004 0.046 6222 Dihedral : 8.612 146.299 4872 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.91 % 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: 1.33 (0.13), residues: 4338 helix: 1.32 (0.12), residues: 2028 sheet: 0.70 (0.23), residues: 606 loop : 0.61 (0.16), residues: 1704 *********************** 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 177 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 7 residues processed: 157 average time/residue: 1.5564 time to fit residues: 295.2790 Evaluate side-chains 141 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 4.525 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.3209 time to fit residues: 9.1090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 83 optimal weight: 30.0000 chunk 248 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 423 optimal weight: 5.9990 chunk 351 optimal weight: 0.9980 chunk 196 optimal weight: 0.0020 chunk 35 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.1899 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= 0.254 Angle : 0.515 8.417 47700 Z= 0.253 Chirality : 0.044 0.187 5436 Planarity : 0.004 0.045 6222 Dihedral : 8.544 145.703 4872 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.70 % 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: 1.44 (0.13), residues: 4338 helix: 1.44 (0.12), residues: 2028 sheet: 0.75 (0.23), residues: 606 loop : 0.62 (0.16), residues: 1704 *********************** 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 170 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 160 average time/residue: 1.5722 time to fit residues: 304.8440 Evaluate side-chains 145 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 4.229 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.3627 time to fit residues: 7.0170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 239 optimal weight: 0.4980 chunk 356 optimal weight: 0.6980 chunk 236 optimal weight: 9.9990 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: 1.7784 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 35274 Z= 0.233 Angle : 0.506 7.669 47700 Z= 0.249 Chirality : 0.044 0.179 5436 Planarity : 0.004 0.059 6222 Dihedral : 8.486 145.325 4872 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.05 % 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: 1.50 (0.14), residues: 4338 helix: 1.51 (0.12), residues: 2028 sheet: 0.77 (0.23), residues: 606 loop : 0.63 (0.16), residues: 1704 *********************** 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 183 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 4.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 172 average time/residue: 1.4095 time to fit residues: 297.3625 Evaluate side-chains 150 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 4.350 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 3 average time/residue: 1.0142 time to fit residues: 9.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 0.0980 chunk 168 optimal weight: 5.9990 chunk 252 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 331 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 35274 Z= 0.200 Angle : 0.504 7.511 47700 Z= 0.248 Chirality : 0.044 0.178 5436 Planarity : 0.003 0.045 6222 Dihedral : 8.429 145.179 4872 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.72 % 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: 1.53 (0.14), residues: 4338 helix: 1.53 (0.12), residues: 2028 sheet: 0.81 (0.23), residues: 606 loop : 0.65 (0.16), residues: 1704 *********************** 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 168 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 4.553 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 159 average time/residue: 1.4367 time to fit residues: 280.5709 Evaluate side-chains 152 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 4.339 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.3478 time to fit residues: 9.1850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.0030 chunk 404 optimal weight: 2.9990 chunk 368 optimal weight: 20.0000 chunk 393 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 120 optimal weight: 0.3980 chunk 355 optimal weight: 2.9990 chunk 372 optimal weight: 6.9990 chunk 392 optimal weight: 1.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 35274 Z= 0.187 Angle : 0.508 10.392 47700 Z= 0.249 Chirality : 0.044 0.182 5436 Planarity : 0.003 0.045 6222 Dihedral : 8.375 144.925 4872 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.51 % 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: 1.57 (0.14), residues: 4338 helix: 1.56 (0.12), residues: 2028 sheet: 0.85 (0.23), residues: 606 loop : 0.66 (0.16), residues: 1704 *********************** 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 164 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 4.283 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 160 average time/residue: 1.4828 time to fit residues: 290.1838 Evaluate side-chains 150 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 4.308 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.4179 time to fit residues: 9.2096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 253 optimal weight: 0.0040 chunk 197 optimal weight: 0.7980 chunk 289 optimal weight: 9.9990 chunk 436 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.033 35274 Z= 0.173 Angle : 0.510 14.407 47700 Z= 0.250 Chirality : 0.044 0.224 5436 Planarity : 0.003 0.045 6222 Dihedral : 8.330 144.774 4872 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.40 % 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: 1.59 (0.14), residues: 4338 helix: 1.56 (0.12), residues: 2034 sheet: 0.89 (0.23), residues: 606 loop : 0.67 (0.16), residues: 1698 ********************** 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: 15 poor density : 143 time to evaluate : 4.384 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 156 average time/residue: 1.4781 time to fit residues: 282.5679 Evaluate side-chains 148 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 4.223 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 5.7236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 106 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 348 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN B 660 ASN E 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.091995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055717 restraints weight = 83884.778| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.25 r_work: 0.2693 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2411 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= 0.149 Angle : 0.500 13.140 47700 Z= 0.247 Chirality : 0.043 0.212 5436 Planarity : 0.003 0.046 6222 Dihedral : 8.251 144.737 4872 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.51 % 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: 1.63 (0.14), residues: 4338 helix: 1.59 (0.12), residues: 2034 sheet: 0.70 (0.22), residues: 648 loop : 0.80 (0.16), residues: 1656 =============================================================================== Job complete usr+sys time: 6974.71 seconds wall clock time: 126 minutes 30.75 seconds (7590.75 seconds total)