Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 17:55:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bqt_30155/08_2023/7bqt_30155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bqt_30155/08_2023/7bqt_30155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bqt_30155/08_2023/7bqt_30155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bqt_30155/08_2023/7bqt_30155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bqt_30155/08_2023/7bqt_30155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bqt_30155/08_2023/7bqt_30155.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 25116 2.51 5 N 6660 2.21 5 O 7248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 517": "OD1" <-> "OD2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 537": "OE1" <-> "OE2" Residue "C ASP 567": "OD1" <-> "OD2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D GLU 490": "OE1" <-> "OE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 517": "OD1" <-> "OD2" Residue "D TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 537": "OE1" <-> "OE2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 140": "NH1" <-> "NH2" Residue "E ASP 143": "OD1" <-> "OD2" Residue "E GLU 161": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 480": "OE1" <-> "OE2" Residue "E GLU 492": "OE1" <-> "OE2" Residue "E ARG 509": "NH1" <-> "NH2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 517": "OD1" <-> "OD2" Residue "E GLU 532": "OE1" <-> "OE2" Residue "E GLU 537": "OE1" <-> "OE2" Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 140": "NH1" <-> "NH2" Residue "G ASP 143": "OD1" <-> "OD2" Residue "G ARG 176": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "G ASP 222": "OD1" <-> "OD2" Residue "G TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 458": "NH1" <-> "NH2" Residue "G PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 480": "OE1" <-> "OE2" Residue "G GLU 492": "OE1" <-> "OE2" Residue "G ARG 509": "NH1" <-> "NH2" Residue "G TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 517": "OD1" <-> "OD2" Residue "G TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 537": "OE1" <-> "OE2" Residue "G GLU 550": "OE1" <-> "OE2" Residue "G ASP 567": "OD1" <-> "OD2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 120": "OD1" <-> "OD2" Residue "I TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I ARG 140": "NH1" <-> "NH2" Residue "I ASP 143": "OD1" <-> "OD2" Residue "I GLU 161": "OE1" <-> "OE2" Residue "I ARG 176": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 445": "OE1" <-> "OE2" Residue "I ARG 458": "NH1" <-> "NH2" Residue "I GLU 480": "OE1" <-> "OE2" Residue "I ARG 509": "NH1" <-> "NH2" Residue "I TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 517": "OD1" <-> "OD2" Residue "I GLU 537": "OE1" <-> "OE2" Residue "K TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 140": "NH1" <-> "NH2" Residue "K ASP 143": "OD1" <-> "OD2" Residue "K GLU 161": "OE1" <-> "OE2" Residue "K ARG 176": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K GLU 197": "OE1" <-> "OE2" Residue "K GLU 200": "OE1" <-> "OE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K ASP 222": "OD1" <-> "OD2" Residue "K GLU 223": "OE1" <-> "OE2" Residue "K TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 458": "NH1" <-> "NH2" Residue "K PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 492": "OE1" <-> "OE2" Residue "K ARG 509": "NH1" <-> "NH2" Residue "K TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 517": "OD1" <-> "OD2" Residue "K GLU 532": "OE1" <-> "OE2" Residue "K GLU 537": "OE1" <-> "OE2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 140": "NH1" <-> "NH2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F ARG 176": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 458": "NH1" <-> "NH2" Residue "F GLU 490": "OE1" <-> "OE2" Residue "F ASP 504": "OD1" <-> "OD2" Residue "F ARG 509": "NH1" <-> "NH2" Residue "F TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 537": "OE1" <-> "OE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 133": "NH1" <-> "NH2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 140": "NH1" <-> "NH2" Residue "H ASP 143": "OD1" <-> "OD2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H ARG 176": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H ASP 222": "OD1" <-> "OD2" Residue "H TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 458": "NH1" <-> "NH2" Residue "H PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 480": "OE1" <-> "OE2" Residue "H GLU 490": "OE1" <-> "OE2" Residue "H GLU 492": "OE1" <-> "OE2" Residue "H ARG 509": "NH1" <-> "NH2" Residue "H TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 537": "OE1" <-> "OE2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J ARG 140": "NH1" <-> "NH2" Residue "J ASP 143": "OD1" <-> "OD2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J ARG 176": "NH1" <-> "NH2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J GLU 200": "OE1" <-> "OE2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 458": "NH1" <-> "NH2" Residue "J PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 490": "OE1" <-> "OE2" Residue "J ASP 504": "OD1" <-> "OD2" Residue "J ARG 509": "NH1" <-> "NH2" Residue "J TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 537": "OE1" <-> "OE2" Residue "J TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L ASP 120": "OD1" <-> "OD2" Residue "L TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 133": "NH1" <-> "NH2" Residue "L ARG 140": "NH1" <-> "NH2" Residue "L ASP 143": "OD1" <-> "OD2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L ARG 176": "NH1" <-> "NH2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "L GLU 216": "OE1" <-> "OE2" Residue "L TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 458": "NH1" <-> "NH2" Residue "L PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 504": "OD1" <-> "OD2" Residue "L ARG 509": "NH1" <-> "NH2" Residue "L TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 532": "OE1" <-> "OE2" Residue "L GLU 537": "OE1" <-> "OE2" Residue "L TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 39180 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3265 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 17.55, per 1000 atoms: 0.45 Number of scatterers: 39180 At special positions: 0 Unit cell: (151.96, 151.96, 138.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 7248 8.00 N 6660 7.00 C 25116 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: 15.64 Conformation dependent library (CDL) restraints added in 5.6 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 64 sheets defined 55.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 44 through 50 removed outlier: 4.011A pdb=" N ALA A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 50' Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.753A pdb=" N HIS A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.970A pdb=" N VAL A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 131 removed outlier: 4.498A pdb=" N ARG A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.160A pdb=" N ASP A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 removed outlier: 4.113A pdb=" N SER A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 204 removed outlier: 4.768A pdb=" N THR A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.790A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 496 removed outlier: 3.773A pdb=" N LEU A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 removed outlier: 3.780A pdb=" N GLY A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.840A pdb=" N TYR A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.760A pdb=" N ALA A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.591A pdb=" N SER A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'B' and resid 24 through 33 removed outlier: 3.722A pdb=" N ILE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.927A pdb=" N ASN B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 71 removed outlier: 4.128A pdb=" N HIS B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.910A pdb=" N VAL B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 131 removed outlier: 4.239A pdb=" N LEU B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.843A pdb=" N ASP B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TRP B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 4.174A pdb=" N SER B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 204 removed outlier: 4.961A pdb=" N THR B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 Processing helix chain 'B' and resid 439 through 449 removed outlier: 3.621A pdb=" N GLU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 496 removed outlier: 3.705A pdb=" N LEU B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 530 removed outlier: 3.958A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.530A pdb=" N TYR B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 3.660A pdb=" N ALA B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.954A pdb=" N ASN C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 50 " --> pdb=" O ILE C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 71 removed outlier: 3.539A pdb=" N GLN C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 4.069A pdb=" N VAL C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS C 79 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 131 removed outlier: 3.774A pdb=" N LEU C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 4.110A pdb=" N ASP C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 145 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 166 removed outlier: 4.153A pdb=" N SER C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 204 removed outlier: 4.757A pdb=" N THR C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 196 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 278 Processing helix chain 'C' and resid 439 through 449 removed outlier: 3.524A pdb=" N GLU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 496 removed outlier: 3.741A pdb=" N LEU C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 487 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 529 removed outlier: 3.844A pdb=" N ILE C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 520 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 524 " --> pdb=" O SER C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.628A pdb=" N TYR C 528 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.978A pdb=" N LEU D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.987A pdb=" N HIS D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.838A pdb=" N VAL D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 131 removed outlier: 3.992A pdb=" N LEU D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.778A pdb=" N ASP D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 181 through 204 removed outlier: 4.959A pdb=" N THR D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 196 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 278 Processing helix chain 'D' and resid 439 through 449 removed outlier: 3.573A pdb=" N GLU D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 496 removed outlier: 3.722A pdb=" N LEU D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 487 " --> pdb=" O LYS D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 529 removed outlier: 4.006A pdb=" N GLY D 524 " --> pdb=" O SER D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.529A pdb=" N TYR D 528 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 3.511A pdb=" N ALA D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.892A pdb=" N ILE E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 44 through 50 removed outlier: 3.613A pdb=" N ALA E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 71 removed outlier: 3.705A pdb=" N HIS E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 90 removed outlier: 4.216A pdb=" N VAL E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 131 removed outlier: 3.846A pdb=" N LEU E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.957A pdb=" N ASP E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 removed outlier: 3.747A pdb=" N SER E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 204 removed outlier: 4.008A pdb=" N THR E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 278 Processing helix chain 'E' and resid 439 through 449 removed outlier: 3.737A pdb=" N LEU E 447 " --> pdb=" O ALA E 443 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 496 removed outlier: 3.803A pdb=" N LEU E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU E 487 " --> pdb=" O LYS E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 529 removed outlier: 4.042A pdb=" N ILE E 519 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER E 520 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY E 524 " --> pdb=" O SER E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.555A pdb=" N TYR E 528 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 546 removed outlier: 3.745A pdb=" N ALA E 544 " --> pdb=" O THR E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 558 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.955A pdb=" N ILE G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 51 removed outlier: 3.905A pdb=" N ALA G 48 " --> pdb=" O GLN G 44 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN G 49 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 71 removed outlier: 3.715A pdb=" N HIS G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 90 removed outlier: 4.105A pdb=" N VAL G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS G 79 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 131 removed outlier: 4.501A pdb=" N LEU G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.800A pdb=" N ASP G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP G 144 " --> pdb=" O ARG G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 removed outlier: 3.966A pdb=" N SER G 164 " --> pdb=" O GLN G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 204 removed outlier: 4.479A pdb=" N THR G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU G 200 " --> pdb=" O LYS G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 278 Processing helix chain 'G' and resid 439 through 449 removed outlier: 3.525A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 496 removed outlier: 3.690A pdb=" N LEU G 485 " --> pdb=" O MET G 481 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU G 487 " --> pdb=" O LYS G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 529 removed outlier: 4.137A pdb=" N ILE G 519 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER G 520 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY G 524 " --> pdb=" O SER G 520 " (cutoff:3.500A) Proline residue: G 525 - end of helix Processing helix chain 'G' and resid 540 through 546 removed outlier: 3.782A pdb=" N ALA G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 558 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'I' and resid 24 through 33 removed outlier: 3.888A pdb=" N ILE I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 51 removed outlier: 3.968A pdb=" N ALA I 48 " --> pdb=" O GLN I 44 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 50 " --> pdb=" O ILE I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 71 removed outlier: 3.824A pdb=" N HIS I 71 " --> pdb=" O ARG I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 90 removed outlier: 4.110A pdb=" N VAL I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 78 " --> pdb=" O TYR I 74 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS I 79 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 131 removed outlier: 4.311A pdb=" N LEU I 121 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR I 127 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.858A pdb=" N ASP I 143 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP I 144 " --> pdb=" O ARG I 140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR I 148 " --> pdb=" O TRP I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 166 removed outlier: 3.705A pdb=" N SER I 164 " --> pdb=" O GLN I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 204 removed outlier: 4.010A pdb=" N THR I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 278 Processing helix chain 'I' and resid 439 through 449 removed outlier: 3.717A pdb=" N LEU I 447 " --> pdb=" O ALA I 443 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN I 449 " --> pdb=" O GLU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 496 removed outlier: 3.738A pdb=" N LEU I 485 " --> pdb=" O MET I 481 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU I 487 " --> pdb=" O LYS I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 530 removed outlier: 4.127A pdb=" N ILE I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER I 520 " --> pdb=" O SER I 516 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY I 524 " --> pdb=" O SER I 520 " (cutoff:3.500A) Proline residue: I 525 - end of helix removed outlier: 3.584A pdb=" N VAL I 530 " --> pdb=" O PHE I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 546 removed outlier: 3.642A pdb=" N ALA I 544 " --> pdb=" O THR I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 549 through 558 removed outlier: 4.077A pdb=" N ASP I 553 " --> pdb=" O VAL I 549 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 554 " --> pdb=" O GLU I 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER I 558 " --> pdb=" O GLU I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 570 removed outlier: 3.615A pdb=" N ARG I 570 " --> pdb=" O GLU I 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 33 removed outlier: 3.931A pdb=" N ILE K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 50 removed outlier: 4.018A pdb=" N TYR K 47 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU K 50 " --> pdb=" O ILE K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.725A pdb=" N HIS K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 90 removed outlier: 4.143A pdb=" N VAL K 77 " --> pdb=" O THR K 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU K 78 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 131 removed outlier: 4.483A pdb=" N LEU K 121 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 149 removed outlier: 3.795A pdb=" N ASP K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP K 144 " --> pdb=" O ARG K 140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 166 removed outlier: 3.908A pdb=" N SER K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 204 removed outlier: 4.365A pdb=" N THR K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS K 196 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU K 200 " --> pdb=" O LYS K 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 278 Processing helix chain 'K' and resid 439 through 449 removed outlier: 3.873A pdb=" N LEU K 447 " --> pdb=" O ALA K 443 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN K 449 " --> pdb=" O GLU K 445 " (cutoff:3.500A) Processing helix chain 'K' and resid 477 through 496 removed outlier: 3.660A pdb=" N LEU K 485 " --> pdb=" O MET K 481 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU K 487 " --> pdb=" O LYS K 483 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 530 removed outlier: 4.083A pdb=" N ILE K 519 " --> pdb=" O SER K 515 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER K 520 " --> pdb=" O SER K 516 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY K 524 " --> pdb=" O SER K 520 " (cutoff:3.500A) Proline residue: K 525 - end of helix removed outlier: 3.648A pdb=" N TYR K 528 " --> pdb=" O GLY K 524 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 530 " --> pdb=" O PHE K 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 546 removed outlier: 3.596A pdb=" N ALA K 544 " --> pdb=" O THR K 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 551 through 558 Processing helix chain 'K' and resid 559 through 570 Processing helix chain 'F' and resid 24 through 33 removed outlier: 3.942A pdb=" N ILE F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 44 through 50 removed outlier: 3.851A pdb=" N ALA F 48 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 44 through 50' Processing helix chain 'F' and resid 54 through 71 removed outlier: 3.880A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 90 removed outlier: 3.902A pdb=" N VAL F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS F 79 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 131 removed outlier: 4.097A pdb=" N LEU F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 146 removed outlier: 4.202A pdb=" N ASP F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP F 144 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 145 " --> pdb=" O TYR F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 166 Processing helix chain 'F' and resid 181 through 204 removed outlier: 3.514A pdb=" N ARG F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS F 196 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 278 Processing helix chain 'F' and resid 439 through 449 removed outlier: 3.824A pdb=" N LEU F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 496 removed outlier: 3.729A pdb=" N LEU F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 487 " --> pdb=" O LYS F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 529 removed outlier: 3.970A pdb=" N ILE F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY F 524 " --> pdb=" O SER F 520 " (cutoff:3.500A) Proline residue: F 525 - end of helix removed outlier: 3.551A pdb=" N TYR F 528 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 546 removed outlier: 3.737A pdb=" N ALA F 544 " --> pdb=" O THR F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 557 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.023A pdb=" N ILE H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 44 through 51 removed outlier: 4.019A pdb=" N ALA H 48 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 71 removed outlier: 3.924A pdb=" N HIS H 71 " --> pdb=" O ARG H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 90 removed outlier: 3.970A pdb=" N HIS H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 131 removed outlier: 4.171A pdb=" N LEU H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 148 removed outlier: 4.065A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP H 144 " --> pdb=" O ARG H 140 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 145 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 166 Processing helix chain 'H' and resid 181 through 204 removed outlier: 4.756A pdb=" N THR H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 196 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER H 201 " --> pdb=" O GLU H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 278 Processing helix chain 'H' and resid 439 through 449 removed outlier: 3.847A pdb=" N LEU H 447 " --> pdb=" O ALA H 443 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN H 449 " --> pdb=" O GLU H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 496 removed outlier: 3.515A pdb=" N ASP H 484 " --> pdb=" O GLU H 480 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU H 485 " --> pdb=" O MET H 481 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU H 487 " --> pdb=" O LYS H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 529 removed outlier: 4.066A pdb=" N ILE H 519 " --> pdb=" O SER H 515 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER H 520 " --> pdb=" O SER H 516 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY H 524 " --> pdb=" O SER H 520 " (cutoff:3.500A) Proline residue: H 525 - end of helix removed outlier: 3.739A pdb=" N TYR H 528 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 546 removed outlier: 3.718A pdb=" N ALA H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 557 Processing helix chain 'H' and resid 559 through 568 Processing helix chain 'J' and resid 24 through 33 removed outlier: 3.955A pdb=" N ILE J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 50 removed outlier: 4.178A pdb=" N TYR J 47 " --> pdb=" O GLY J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 71 removed outlier: 3.742A pdb=" N HIS J 71 " --> pdb=" O ARG J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 90 removed outlier: 3.876A pdb=" N VAL J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 131 removed outlier: 4.275A pdb=" N LEU J 121 " --> pdb=" O THR J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 148 removed outlier: 3.865A pdb=" N ASP J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TRP J 144 " --> pdb=" O ARG J 140 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE J 145 " --> pdb=" O TYR J 141 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS J 146 " --> pdb=" O VAL J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 166 Processing helix chain 'J' and resid 181 through 204 removed outlier: 4.592A pdb=" N THR J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS J 196 " --> pdb=" O TYR J 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU J 200 " --> pdb=" O LYS J 196 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 256 No H-bonds generated for 'chain 'J' and resid 254 through 256' Processing helix chain 'J' and resid 257 through 278 Processing helix chain 'J' and resid 439 through 449 removed outlier: 3.810A pdb=" N LEU J 447 " --> pdb=" O ALA J 443 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN J 449 " --> pdb=" O GLU J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 477 through 496 removed outlier: 3.780A pdb=" N LEU J 485 " --> pdb=" O MET J 481 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU J 487 " --> pdb=" O LYS J 483 " (cutoff:3.500A) Processing helix chain 'J' and resid 515 through 529 removed outlier: 3.890A pdb=" N ILE J 519 " --> pdb=" O SER J 515 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER J 520 " --> pdb=" O SER J 516 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY J 524 " --> pdb=" O SER J 520 " (cutoff:3.500A) Proline residue: J 525 - end of helix removed outlier: 3.743A pdb=" N TYR J 528 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 546 removed outlier: 3.657A pdb=" N ALA J 544 " --> pdb=" O THR J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 557 Processing helix chain 'J' and resid 559 through 568 Processing helix chain 'L' and resid 24 through 33 removed outlier: 3.905A pdb=" N ILE L 33 " --> pdb=" O ARG L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' Processing helix chain 'L' and resid 44 through 50 removed outlier: 3.666A pdb=" N ALA L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 71 removed outlier: 3.706A pdb=" N HIS L 71 " --> pdb=" O ARG L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 90 removed outlier: 3.869A pdb=" N VAL L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 131 removed outlier: 4.067A pdb=" N LEU L 121 " --> pdb=" O THR L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 removed outlier: 3.700A pdb=" N ASP L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP L 144 " --> pdb=" O ARG L 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE L 145 " --> pdb=" O TYR L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 166 Processing helix chain 'L' and resid 181 through 204 removed outlier: 4.219A pdb=" N THR L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU L 190 " --> pdb=" O SER L 186 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS L 196 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU L 200 " --> pdb=" O LYS L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 278 Processing helix chain 'L' and resid 439 through 449 removed outlier: 3.818A pdb=" N LEU L 447 " --> pdb=" O ALA L 443 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN L 449 " --> pdb=" O GLU L 445 " (cutoff:3.500A) Processing helix chain 'L' and resid 477 through 496 removed outlier: 3.682A pdb=" N LEU L 485 " --> pdb=" O MET L 481 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU L 487 " --> pdb=" O LYS L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 515 through 529 removed outlier: 4.034A pdb=" N ILE L 519 " --> pdb=" O SER L 515 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER L 520 " --> pdb=" O SER L 516 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY L 524 " --> pdb=" O SER L 520 " (cutoff:3.500A) Proline residue: L 525 - end of helix removed outlier: 3.598A pdb=" N TYR L 528 " --> pdb=" O GLY L 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 546 removed outlier: 3.754A pdb=" N ALA L 544 " --> pdb=" O THR L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 557 Processing helix chain 'L' and resid 559 through 568 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.517A pdb=" N THR A 214 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 223 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.727A pdb=" N VAL A 151 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 236 " --> pdb=" O VAL A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.591A pdb=" N VAL A 154 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 457 removed outlier: 7.724A pdb=" N ALA A 457 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 284 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN F 468 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY A 287 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE F 466 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 465 through 469 removed outlier: 7.086A pdb=" N ILE K 285 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.507A pdb=" N THR A 500 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 513 " --> pdb=" O THR A 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.624A pdb=" N GLU B 223 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 205 through 206 removed outlier: 3.622A pdb=" N VAL B 151 " --> pdb=" O HIS B 236 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AB2, first strand: chain 'B' and resid 456 through 457 removed outlier: 7.671A pdb=" N ALA B 457 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 284 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 285 " --> pdb=" O ASN H 468 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN H 468 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 287 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE H 466 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 465 through 469 removed outlier: 3.854A pdb=" N SER B 465 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 285 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA E 284 " --> pdb=" O ALA E 457 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 499 through 502 removed outlier: 3.766A pdb=" N ARG B 513 " --> pdb=" O THR B 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.679A pdb=" N GLU C 223 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 226 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 228 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 231 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 150 through 152 removed outlier: 3.627A pdb=" N VAL C 151 " --> pdb=" O HIS C 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB9, first strand: chain 'C' and resid 456 through 457 removed outlier: 4.569A pdb=" N ASN J 468 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY C 287 " --> pdb=" O ILE J 466 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE J 466 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 465 through 469 removed outlier: 3.503A pdb=" N SER C 465 " --> pdb=" O GLY G 287 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE G 285 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA G 284 " --> pdb=" O ALA G 457 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 499 through 502 removed outlier: 3.570A pdb=" N THR C 500 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 513 " --> pdb=" O THR C 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.849A pdb=" N GLU D 223 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 226 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR D 228 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D 231 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.612A pdb=" N VAL D 151 " --> pdb=" O HIS D 236 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC7, first strand: chain 'D' and resid 456 through 457 removed outlier: 7.037A pdb=" N ALA D 284 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE D 285 " --> pdb=" O LEU L 467 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER L 465 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 465 through 469 removed outlier: 7.063A pdb=" N ILE I 285 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA I 284 " --> pdb=" O ALA I 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 499 through 502 removed outlier: 3.858A pdb=" N ARG D 513 " --> pdb=" O THR D 500 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.893A pdb=" N GLU E 223 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA E 226 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E 228 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG E 231 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.537A pdb=" N VAL E 154 " --> pdb=" O PHE E 206 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 242 through 243 Processing sheet with id=AD4, first strand: chain 'E' and resid 465 through 471 removed outlier: 6.140A pdb=" N ILE E 466 " --> pdb=" O GLY F 287 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY F 287 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN E 468 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 285 " --> pdb=" O ASN E 468 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA F 457 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 284 " --> pdb=" O ALA F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 499 through 502 removed outlier: 3.711A pdb=" N ARG E 513 " --> pdb=" O THR E 500 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.720A pdb=" N GLU G 223 " --> pdb=" O LEU G 218 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 150 through 152 removed outlier: 3.897A pdb=" N VAL G 151 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS G 236 " --> pdb=" O VAL G 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AD9, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE1, first strand: chain 'G' and resid 465 through 471 removed outlier: 6.193A pdb=" N ILE G 466 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY H 287 " --> pdb=" O ILE G 466 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN G 468 " --> pdb=" O ILE H 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 499 through 502 removed outlier: 3.792A pdb=" N ARG G 513 " --> pdb=" O THR G 500 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.801A pdb=" N GLU I 223 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA I 226 " --> pdb=" O ILE I 233 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR I 228 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG I 231 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 150 through 152 removed outlier: 3.681A pdb=" N VAL I 151 " --> pdb=" O HIS I 236 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AE6, first strand: chain 'I' and resid 242 through 243 Processing sheet with id=AE7, first strand: chain 'I' and resid 465 through 469 removed outlier: 4.249A pdb=" N SER I 465 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE J 285 " --> pdb=" O LEU I 467 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 499 through 502 removed outlier: 3.732A pdb=" N ARG I 513 " --> pdb=" O THR I 500 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.554A pdb=" N TYR K 217 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU K 223 " --> pdb=" O LEU K 218 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 150 through 152 removed outlier: 3.717A pdb=" N VAL K 151 " --> pdb=" O HIS K 236 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 154 through 155 Processing sheet with id=AF3, first strand: chain 'K' and resid 242 through 243 Processing sheet with id=AF4, first strand: chain 'K' and resid 465 through 471 removed outlier: 6.051A pdb=" N ILE K 466 " --> pdb=" O GLY L 287 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY L 287 " --> pdb=" O ILE K 466 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN K 468 " --> pdb=" O ILE L 285 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA L 457 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA L 284 " --> pdb=" O ALA L 457 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 499 through 502 removed outlier: 3.718A pdb=" N ARG K 513 " --> pdb=" O THR K 500 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.657A pdb=" N TYR F 217 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU F 223 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR F 224 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU F 235 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 226 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR F 228 " --> pdb=" O ARG F 231 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG F 231 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N ARG F 232 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS F 155 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 151 " --> pdb=" O HIS F 236 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AF8, first strand: chain 'F' and resid 499 through 502 removed outlier: 3.701A pdb=" N ARG F 513 " --> pdb=" O THR F 500 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 19 through 20 removed outlier: 8.434A pdb=" N TYR H 224 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU H 235 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA H 226 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR H 228 " --> pdb=" O ARG H 231 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG H 231 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N ARG H 232 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N LYS H 155 " --> pdb=" O ARG H 232 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS H 236 " --> pdb=" O VAL H 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 151 " --> pdb=" O HIS H 236 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AG2, first strand: chain 'H' and resid 499 through 502 removed outlier: 3.683A pdb=" N ARG H 513 " --> pdb=" O THR H 500 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 19 through 20 removed outlier: 3.703A pdb=" N TYR J 217 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU J 223 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N TYR J 224 " --> pdb=" O LEU J 235 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU J 235 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG J 231 " --> pdb=" O TYR J 228 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ARG J 232 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS J 155 " --> pdb=" O ARG J 232 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS J 236 " --> pdb=" O VAL J 151 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL J 151 " --> pdb=" O HIS J 236 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 242 through 243 Processing sheet with id=AG5, first strand: chain 'J' and resid 499 through 502 removed outlier: 3.689A pdb=" N ARG J 513 " --> pdb=" O THR J 500 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.643A pdb=" N TYR L 217 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU L 223 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA L 226 " --> pdb=" O ILE L 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR L 228 " --> pdb=" O ARG L 231 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG L 231 " --> pdb=" O TYR L 228 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 150 through 152 removed outlier: 3.582A pdb=" N VAL L 151 " --> pdb=" O HIS L 236 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AG9, first strand: chain 'L' and resid 242 through 243 Processing sheet with id=AH1, first strand: chain 'L' and resid 499 through 502 removed outlier: 3.839A pdb=" N ARG L 513 " --> pdb=" O THR L 500 " (cutoff:3.500A) 1822 hydrogen bonds defined for protein. 5286 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: 14.84 Time building geometry restraints manager: 16.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12028 1.34 - 1.46: 8228 1.46 - 1.58: 19608 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 40068 Sorted by residual: bond pdb=" C HIS C 22 " pdb=" N PRO C 23 " ideal model delta sigma weight residual 1.334 1.367 -0.034 8.40e-03 1.42e+04 1.61e+01 bond pdb=" C HIS B 22 " pdb=" N PRO B 23 " ideal model delta sigma weight residual 1.334 1.362 -0.029 8.40e-03 1.42e+04 1.17e+01 bond pdb=" C HIS E 22 " pdb=" N PRO E 23 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.13e+01 bond pdb=" CA LEU C 218 " pdb=" CB LEU C 218 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.55e-02 4.16e+03 4.52e+00 bond pdb=" CB THR K 279 " pdb=" CG2 THR K 279 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.60e+00 ... (remaining 40063 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.29: 737 105.29 - 112.50: 20126 112.50 - 119.70: 14655 119.70 - 126.91: 18444 126.91 - 134.11: 470 Bond angle restraints: 54432 Sorted by residual: angle pdb=" C VAL K 60 " pdb=" N PHE K 61 " pdb=" CA PHE K 61 " ideal model delta sigma weight residual 120.65 126.20 -5.55 1.32e+00 5.74e-01 1.77e+01 angle pdb=" C SER L 168 " pdb=" N LEU L 169 " pdb=" CA LEU L 169 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C SER G 168 " pdb=" N LEU G 169 " pdb=" CA LEU G 169 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER E 168 " pdb=" N LEU E 169 " pdb=" CA LEU E 169 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C VAL A 60 " pdb=" N PHE A 61 " pdb=" CA PHE A 61 " ideal model delta sigma weight residual 120.65 125.71 -5.06 1.32e+00 5.74e-01 1.47e+01 ... (remaining 54427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 21051 17.95 - 35.90: 2446 35.90 - 53.86: 422 53.86 - 71.81: 65 71.81 - 89.76: 64 Dihedral angle restraints: 24048 sinusoidal: 9636 harmonic: 14412 Sorted by residual: dihedral pdb=" CA LEU I 257 " pdb=" C LEU I 257 " pdb=" N TYR I 258 " pdb=" CA TYR I 258 " ideal model delta harmonic sigma weight residual 180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU G 257 " pdb=" C LEU G 257 " pdb=" N TYR G 258 " pdb=" CA TYR G 258 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU A 257 " pdb=" C LEU A 257 " pdb=" N TYR A 258 " pdb=" CA TYR A 258 " ideal model delta harmonic sigma weight residual 180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 24045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5275 0.082 - 0.164: 889 0.164 - 0.246: 79 0.246 - 0.328: 19 0.328 - 0.410: 2 Chirality restraints: 6264 Sorted by residual: chirality pdb=" CG LEU F 122 " pdb=" CB LEU F 122 " pdb=" CD1 LEU F 122 " pdb=" CD2 LEU F 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE E 166 " pdb=" CA ILE E 166 " pdb=" CG1 ILE E 166 " pdb=" CG2 ILE E 166 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE G 215 " pdb=" CA ILE G 215 " pdb=" CG1 ILE G 215 " pdb=" CG2 ILE G 215 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 6261 not shown) Planarity restraints: 6840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 118 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C VAL G 118 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL G 118 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG G 119 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 63 " 0.019 2.00e-02 2.50e+03 2.45e-02 8.97e+00 pdb=" CG HIS K 63 " -0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS K 63 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS K 63 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS K 63 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS K 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 63 " 0.019 2.00e-02 2.50e+03 2.40e-02 8.61e+00 pdb=" CG HIS B 63 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS B 63 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS B 63 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS B 63 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 63 " 0.002 2.00e-02 2.50e+03 ... (remaining 6837 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7804 2.76 - 3.30: 40238 3.30 - 3.83: 69666 3.83 - 4.37: 78009 4.37 - 4.90: 125205 Nonbonded interactions: 320922 Sorted by model distance: nonbonded pdb=" OH TYR J 528 " pdb=" O VAL J 536 " model vdw 2.230 2.440 nonbonded pdb=" O LYS B 483 " pdb=" OG1 THR B 486 " model vdw 2.232 2.440 nonbonded pdb=" O LYS G 483 " pdb=" OG1 THR G 486 " model vdw 2.239 2.440 nonbonded pdb=" O LYS L 483 " pdb=" OG1 THR L 486 " model vdw 2.242 2.440 nonbonded pdb=" O ARG B 119 " pdb=" OG1 THR B 123 " model vdw 2.246 2.440 ... (remaining 320917 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.810 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 91.900 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.006 0.063 40068 Z= 0.377 Angle : 1.070 13.311 54432 Z= 0.580 Chirality : 0.061 0.410 6264 Planarity : 0.007 0.064 6840 Dihedral : 15.962 89.761 14712 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.10), residues: 4788 helix: -2.82 (0.08), residues: 2280 sheet: -2.28 (0.31), residues: 264 loop : -2.67 (0.12), residues: 2244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.1831 time to fit residues: 40.9654 Evaluate side-chains 167 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0332 time to fit residues: 0.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 0.0010 chunk 363 optimal weight: 5.9990 chunk 201 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 435 optimal weight: 9.9990 overall best weight: 3.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.036 1.618 40068 Z= 2.361 Angle : 0.999 26.742 54432 Z= 0.513 Chirality : 0.048 0.214 6264 Planarity : 0.006 0.062 6840 Dihedral : 6.251 22.694 5412 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 33.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.11), residues: 4788 helix: -1.70 (0.09), residues: 2532 sheet: -2.20 (0.27), residues: 384 loop : -2.50 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.1734 time to fit residues: 37.1431 Evaluate side-chains 154 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.0870 chunk 135 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 chunk 296 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 chunk 471 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 433 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 350 optimal weight: 20.0000 overall best weight: 5.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN K 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.036 1.608 40068 Z= 2.347 Angle : 0.963 25.268 54432 Z= 0.508 Chirality : 0.047 0.247 6264 Planarity : 0.005 0.037 6840 Dihedral : 6.084 23.234 5412 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 34.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.12), residues: 4788 helix: -1.34 (0.09), residues: 2496 sheet: -2.32 (0.25), residues: 408 loop : -2.23 (0.15), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1667 time to fit residues: 36.7800 Evaluate side-chains 154 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.0980 chunk 328 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 5.9990 chunk 463 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 415 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.035 1.656 40068 Z= 2.326 Angle : 0.959 20.721 54432 Z= 0.484 Chirality : 0.049 0.242 6264 Planarity : 0.006 0.059 6840 Dihedral : 5.869 22.177 5412 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 33.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.11), residues: 4788 helix: -1.21 (0.09), residues: 2544 sheet: -2.31 (0.25), residues: 384 loop : -2.36 (0.14), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.1550 time to fit residues: 33.1546 Evaluate side-chains 150 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0400 time to fit residues: 0.5849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 191 optimal weight: 0.0010 chunk 395 optimal weight: 0.5980 chunk 320 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 416 optimal weight: 0.9980 chunk 117 optimal weight: 0.0570 overall best weight: 0.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 40068 Z= 0.238 Angle : 0.804 7.772 54432 Z= 0.421 Chirality : 0.050 0.192 6264 Planarity : 0.005 0.047 6840 Dihedral : 5.625 21.347 5412 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.11), residues: 4788 helix: -1.17 (0.09), residues: 2592 sheet: -2.15 (0.25), residues: 384 loop : -2.92 (0.13), residues: 1812 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1374 time to fit residues: 28.6451 Evaluate side-chains 150 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 5.9990 chunk 417 optimal weight: 6.9990 chunk 91 optimal weight: 0.0070 chunk 272 optimal weight: 0.3980 chunk 114 optimal weight: 40.0000 chunk 464 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 chunk 215 optimal weight: 0.1980 chunk 38 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 ASN ** F 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 40068 Z= 0.239 Angle : 0.797 7.562 54432 Z= 0.416 Chirality : 0.048 0.168 6264 Planarity : 0.005 0.043 6840 Dihedral : 5.477 25.104 5412 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.11), residues: 4788 helix: -0.86 (0.10), residues: 2580 sheet: -2.13 (0.24), residues: 384 loop : -2.67 (0.14), residues: 1824 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1431 time to fit residues: 28.9914 Evaluate side-chains 150 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 chunk 262 optimal weight: 0.6980 chunk 390 optimal weight: 20.0000 chunk 259 optimal weight: 0.0670 chunk 462 optimal weight: 0.2980 chunk 289 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 213 optimal weight: 0.0070 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 ASN J 163 HIS ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.8261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 40068 Z= 0.216 Angle : 0.803 11.622 54432 Z= 0.414 Chirality : 0.050 0.209 6264 Planarity : 0.005 0.041 6840 Dihedral : 5.362 28.439 5412 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.11), residues: 4788 helix: -1.12 (0.09), residues: 2568 sheet: -1.64 (0.23), residues: 264 loop : -2.99 (0.13), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1420 time to fit residues: 28.4112 Evaluate side-chains 141 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 294 optimal weight: 7.9990 chunk 315 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 363 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 ASN F 163 HIS ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.8476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 40068 Z= 0.216 Angle : 0.781 8.832 54432 Z= 0.403 Chirality : 0.048 0.202 6264 Planarity : 0.005 0.043 6840 Dihedral : 5.247 26.692 5412 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.11), residues: 4788 helix: -1.03 (0.09), residues: 2592 sheet: -2.16 (0.22), residues: 384 loop : -2.87 (0.13), residues: 1812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1529 time to fit residues: 30.4995 Evaluate side-chains 143 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 30.0000 chunk 443 optimal weight: 6.9990 chunk 404 optimal weight: 7.9990 chunk 431 optimal weight: 0.3980 chunk 259 optimal weight: 0.0020 chunk 187 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 389 optimal weight: 0.9980 chunk 407 optimal weight: 0.0470 chunk 429 optimal weight: 0.0670 overall best weight: 0.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 ASN ** F 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 HIS ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.8721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 40068 Z= 0.234 Angle : 0.793 8.151 54432 Z= 0.414 Chirality : 0.049 0.196 6264 Planarity : 0.005 0.046 6840 Dihedral : 5.170 23.918 5412 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.11), residues: 4788 helix: -1.10 (0.09), residues: 2580 sheet: -1.88 (0.22), residues: 384 loop : -3.14 (0.12), residues: 1824 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1541 time to fit residues: 31.3752 Evaluate side-chains 139 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 0.8980 chunk 455 optimal weight: 0.5980 chunk 278 optimal weight: 0.0370 chunk 216 optimal weight: 0.0170 chunk 316 optimal weight: 0.5980 chunk 478 optimal weight: 0.5980 chunk 440 optimal weight: 10.0000 chunk 380 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.8905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 40068 Z= 0.233 Angle : 0.813 8.205 54432 Z= 0.421 Chirality : 0.049 0.199 6264 Planarity : 0.005 0.048 6840 Dihedral : 5.103 23.059 5412 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 4788 helix: -1.08 (0.10), residues: 2532 sheet: -1.69 (0.23), residues: 384 loop : -2.92 (0.13), residues: 1872 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7182 Ramachandran restraints generated. 3591 Oldfield, 0 Emsley, 3591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1496 time to fit residues: 28.9438 Evaluate side-chains 141 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 116 optimal weight: 0.0870 chunk 351 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 381 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 391 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 82 ASN ** F 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113906 restraints weight = 8569.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117072 restraints weight = 5542.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119387 restraints weight = 3987.290| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.8942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 40068 Z= 0.237 Angle : 0.811 9.120 54432 Z= 0.420 Chirality : 0.050 0.198 6264 Planarity : 0.005 0.049 6840 Dihedral : 5.130 20.666 5412 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.11), residues: 4788 helix: -1.01 (0.09), residues: 2568 sheet: -1.85 (0.23), residues: 408 loop : -2.77 (0.13), residues: 1812 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.32 seconds wall clock time: 73 minutes 35.53 seconds (4415.53 seconds total)