Starting phenix.real_space_refine on Mon Mar 25 23:18:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5w_23191/03_2024/7l5w_23191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5w_23191/03_2024/7l5w_23191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5w_23191/03_2024/7l5w_23191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5w_23191/03_2024/7l5w_23191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5w_23191/03_2024/7l5w_23191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5w_23191/03_2024/7l5w_23191.pdb" } resolution = 3.34 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= 0.006 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 264 5.16 5 C 32616 2.51 5 N 9252 2.21 5 O 9696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B ASP 669": "OD1" <-> "OD2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B ASP 734": "OD1" <-> "OD2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B ARG 772": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "C ASP 734": "OD1" <-> "OD2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 772": "NH1" <-> "NH2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 649": "OD1" <-> "OD2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D ASP 669": "OD1" <-> "OD2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "D GLU 737": "OE1" <-> "OE2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 772": "NH1" <-> "NH2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E ARG 358": "NH1" <-> "NH2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E ASP 501": "OD1" <-> "OD2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 599": "NH1" <-> "NH2" Residue "E PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 706": "OE1" <-> "OE2" Residue "E ARG 708": "NH1" <-> "NH2" Residue "E GLU 712": "OE1" <-> "OE2" Residue "E ASP 734": "OD1" <-> "OD2" Residue "E ARG 741": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "E GLU 756": "OE1" <-> "OE2" Residue "E ARG 772": "NH1" <-> "NH2" Residue "E PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 501": "OD1" <-> "OD2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 546": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F ARG 708": "NH1" <-> "NH2" Residue "F GLU 712": "OE1" <-> "OE2" Residue "F ASP 734": "OD1" <-> "OD2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 737": "OE1" <-> "OE2" Residue "F ARG 741": "NH1" <-> "NH2" Residue "F ASP 749": "OD1" <-> "OD2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "F GLU 756": "OE1" <-> "OE2" Residue "F PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 772": "NH1" <-> "NH2" Residue "G ARG 239": "NH1" <-> "NH2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 354": "OD1" <-> "OD2" Residue "G ARG 358": "NH1" <-> "NH2" Residue "G GLU 366": "OE1" <-> "OE2" Residue "G GLU 440": "OE1" <-> "OE2" Residue "G GLU 466": "OE1" <-> "OE2" Residue "G GLU 488": "OE1" <-> "OE2" Residue "G GLU 498": "OE1" <-> "OE2" Residue "G ASP 501": "OD1" <-> "OD2" Residue "G PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 546": "OE1" <-> "OE2" Residue "G PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 578": "OE1" <-> "OE2" Residue "G ARG 599": "NH1" <-> "NH2" Residue "G GLU 607": "OE1" <-> "OE2" Residue "G PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 649": "OD1" <-> "OD2" Residue "G GLU 650": "OE1" <-> "OE2" Residue "G ASP 669": "OD1" <-> "OD2" Residue "G GLU 673": "OE1" <-> "OE2" Residue "G PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 701": "OE1" <-> "OE2" Residue "G GLU 706": "OE1" <-> "OE2" Residue "G ARG 708": "NH1" <-> "NH2" Residue "G GLU 730": "OE1" <-> "OE2" Residue "G GLU 737": "OE1" <-> "OE2" Residue "G ARG 741": "NH1" <-> "NH2" Residue "G ARG 753": "NH1" <-> "NH2" Residue "G GLU 756": "OE1" <-> "OE2" Residue "G PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 772": "NH1" <-> "NH2" Residue "G PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 239": "NH1" <-> "NH2" Residue "H TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 273": "OE1" <-> "OE2" Residue "H GLU 281": "OE1" <-> "OE2" Residue "H PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 354": "OD1" <-> "OD2" Residue "H ARG 358": "NH1" <-> "NH2" Residue "H GLU 366": "OE1" <-> "OE2" Residue "H ASP 392": "OD1" <-> "OD2" Residue "H GLU 417": "OE1" <-> "OE2" Residue "H GLU 440": "OE1" <-> "OE2" Residue "H GLU 466": "OE1" <-> "OE2" Residue "H GLU 477": "OE1" <-> "OE2" Residue "H GLU 488": "OE1" <-> "OE2" Residue "H GLU 491": "OE1" <-> "OE2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H ASP 501": "OD1" <-> "OD2" Residue "H TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 546": "OE1" <-> "OE2" Residue "H PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 599": "NH1" <-> "NH2" Residue "H PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 650": "OE1" <-> "OE2" Residue "H GLU 701": "OE1" <-> "OE2" Residue "H GLU 706": "OE1" <-> "OE2" Residue "H ARG 708": "NH1" <-> "NH2" Residue "H ASP 734": "OD1" <-> "OD2" Residue "H ARG 741": "NH1" <-> "NH2" Residue "H ARG 753": "NH1" <-> "NH2" Residue "H GLU 756": "OE1" <-> "OE2" Residue "H ARG 772": "NH1" <-> "NH2" Residue "I ARG 239": "NH1" <-> "NH2" Residue "I TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 281": "OE1" <-> "OE2" Residue "I PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 354": "OD1" <-> "OD2" Residue "I ARG 358": "NH1" <-> "NH2" Residue "I ASP 368": "OD1" <-> "OD2" Residue "I GLU 397": "OE1" <-> "OE2" Residue "I GLU 440": "OE1" <-> "OE2" Residue "I GLU 466": "OE1" <-> "OE2" Residue "I ASP 478": "OD1" <-> "OD2" Residue "I GLU 488": "OE1" <-> "OE2" Residue "I GLU 498": "OE1" <-> "OE2" Residue "I ASP 501": "OD1" <-> "OD2" Residue "I TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 534": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I GLU 554": "OE1" <-> "OE2" Residue "I PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 578": "OE1" <-> "OE2" Residue "I ARG 599": "NH1" <-> "NH2" Residue "I PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 649": "OD1" <-> "OD2" Residue "I GLU 650": "OE1" <-> "OE2" Residue "I PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 701": "OE1" <-> "OE2" Residue "I GLU 706": "OE1" <-> "OE2" Residue "I ARG 708": "NH1" <-> "NH2" Residue "I GLU 712": "OE1" <-> "OE2" Residue "I ASP 734": "OD1" <-> "OD2" Residue "I PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 737": "OE1" <-> "OE2" Residue "I ARG 741": "NH1" <-> "NH2" Residue "I ASP 749": "OD1" <-> "OD2" Residue "I ARG 753": "NH1" <-> "NH2" Residue "I GLU 756": "OE1" <-> "OE2" Residue "I PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 772": "NH1" <-> "NH2" Residue "J ARG 239": "NH1" <-> "NH2" Residue "J PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 281": "OE1" <-> "OE2" Residue "J PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 294": "OE1" <-> "OE2" Residue "J ASP 354": "OD1" <-> "OD2" Residue "J ARG 358": "NH1" <-> "NH2" Residue "J GLU 366": "OE1" <-> "OE2" Residue "J GLU 440": "OE1" <-> "OE2" Residue "J GLU 466": "OE1" <-> "OE2" Residue "J GLU 488": "OE1" <-> "OE2" Residue "J ASP 501": "OD1" <-> "OD2" Residue "J PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 546": "OE1" <-> "OE2" Residue "J PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 599": "NH1" <-> "NH2" Residue "J GLU 607": "OE1" <-> "OE2" Residue "J PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 649": "OD1" <-> "OD2" Residue "J GLU 650": "OE1" <-> "OE2" Residue "J ASP 669": "OD1" <-> "OD2" Residue "J GLU 673": "OE1" <-> "OE2" Residue "J PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 701": "OE1" <-> "OE2" Residue "J GLU 706": "OE1" <-> "OE2" Residue "J ARG 708": "NH1" <-> "NH2" Residue "J GLU 730": "OE1" <-> "OE2" Residue "J GLU 737": "OE1" <-> "OE2" Residue "J ARG 741": "NH1" <-> "NH2" Residue "J ARG 753": "NH1" <-> "NH2" Residue "J GLU 756": "OE1" <-> "OE2" Residue "J PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 772": "NH1" <-> "NH2" Residue "J PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 239": "NH1" <-> "NH2" Residue "K TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 281": "OE1" <-> "OE2" Residue "K PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 354": "OD1" <-> "OD2" Residue "K ARG 358": "NH1" <-> "NH2" Residue "K GLU 417": "OE1" <-> "OE2" Residue "K GLU 440": "OE1" <-> "OE2" Residue "K GLU 466": "OE1" <-> "OE2" Residue "K GLU 488": "OE1" <-> "OE2" Residue "K ASP 501": "OD1" <-> "OD2" Residue "K TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 534": "OE1" <-> "OE2" Residue "K GLU 546": "OE1" <-> "OE2" Residue "K PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 599": "NH1" <-> "NH2" Residue "K PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 650": "OE1" <-> "OE2" Residue "K ASP 669": "OD1" <-> "OD2" Residue "K GLU 706": "OE1" <-> "OE2" Residue "K ARG 708": "NH1" <-> "NH2" Residue "K ASP 734": "OD1" <-> "OD2" Residue "K ARG 741": "NH1" <-> "NH2" Residue "K ARG 753": "NH1" <-> "NH2" Residue "K GLU 756": "OE1" <-> "OE2" Residue "K ARG 772": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "L TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 354": "OD1" <-> "OD2" Residue "L ARG 358": "NH1" <-> "NH2" Residue "L ASP 368": "OD1" <-> "OD2" Residue "L GLU 402": "OE1" <-> "OE2" Residue "L GLU 417": "OE1" <-> "OE2" Residue "L GLU 440": "OE1" <-> "OE2" Residue "L GLU 466": "OE1" <-> "OE2" Residue "L GLU 488": "OE1" <-> "OE2" Residue "L GLU 491": "OE1" <-> "OE2" Residue "L GLU 498": "OE1" <-> "OE2" Residue "L TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 534": "OE1" <-> "OE2" Residue "L GLU 546": "OE1" <-> "OE2" Residue "L GLU 554": "OE1" <-> "OE2" Residue "L PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 578": "OE1" <-> "OE2" Residue "L ARG 599": "NH1" <-> "NH2" Residue "L PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 650": "OE1" <-> "OE2" Residue "L ASP 669": "OD1" <-> "OD2" Residue "L PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 701": "OE1" <-> "OE2" Residue "L GLU 706": "OE1" <-> "OE2" Residue "L ARG 708": "NH1" <-> "NH2" Residue "L GLU 712": "OE1" <-> "OE2" Residue "L ASP 734": "OD1" <-> "OD2" Residue "L GLU 737": "OE1" <-> "OE2" Residue "L ARG 741": "NH1" <-> "NH2" Residue "L ASP 749": "OD1" <-> "OD2" Residue "L ARG 753": "NH1" <-> "NH2" Residue "L GLU 756": "OE1" <-> "OE2" Residue "L PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 772": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51828 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "B" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "C" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "D" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "E" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "F" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "G" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "H" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "I" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "J" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "K" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Chain: "L" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4319 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 4 Time building chain proxies: 25.93, per 1000 atoms: 0.50 Number of scatterers: 51828 At special positions: 0 Unit cell: (140.385, 156.429, 169.799, 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 264 16.00 O 9696 8.00 N 9252 7.00 C 32616 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: 20.32 Conformation dependent library (CDL) restraints added in 9.2 seconds 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12336 Finding SS restraints... Secondary structure from input PDB file: 311 helices and 36 sheets defined 54.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.509A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.966A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.549A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.865A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 4.302A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.512A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.121A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.890A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.535A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.786A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 713 removed outlier: 3.544A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 712 " --> pdb=" O ARG A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.696A pdb=" N GLU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 743 Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.576A pdb=" N HIS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.909A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.620A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.761A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.686A pdb=" N SER B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.608A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.218A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.594A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.726A pdb=" N ILE B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 611 removed outlier: 3.894A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 713 removed outlier: 3.979A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 712 " --> pdb=" O ARG B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 742 removed outlier: 4.116A pdb=" N GLU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 740 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.509A pdb=" N HIS C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.922A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.508A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.824A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 337 removed outlier: 3.736A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 407 through 427 Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.932A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.103A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.503A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.731A pdb=" N ILE C 562 " --> pdb=" O ASN C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.786A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 711 removed outlier: 3.773A pdb=" N LYS C 696 " --> pdb=" O GLN C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 742 removed outlier: 3.885A pdb=" N MET C 740 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 762 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.511A pdb=" N HIS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.947A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.586A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.871A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 337 removed outlier: 4.392A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 407 through 427 Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.526A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.112A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 536 removed outlier: 3.846A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.148A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.811A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 713 removed outlier: 3.554A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 696 " --> pdb=" O GLN D 692 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 712 " --> pdb=" O ARG D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 742 removed outlier: 3.553A pdb=" N GLU D 738 " --> pdb=" O ASP D 734 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET D 740 " --> pdb=" O PHE D 736 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'E' and resid 210 through 221 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 227 through 232 removed outlier: 4.017A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.574A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.761A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 321 No H-bonds generated for 'chain 'E' and resid 319 through 321' Processing helix chain 'E' and resid 322 through 337 removed outlier: 3.639A pdb=" N SER E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 407 through 427 Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.603A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.227A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.561A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 555 through 557 No H-bonds generated for 'chain 'E' and resid 555 through 557' Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 611 removed outlier: 3.802A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET E 611 " --> pdb=" O GLU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 713 removed outlier: 3.934A pdb=" N LYS E 696 " --> pdb=" O GLN E 692 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU E 712 " --> pdb=" O ARG E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 742 removed outlier: 4.054A pdb=" N GLU E 738 " --> pdb=" O ASP E 734 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET E 740 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 762 Processing helix chain 'F' and resid 210 through 221 Processing helix chain 'F' and resid 221 through 226 removed outlier: 3.510A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.937A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.524A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.990A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 337 removed outlier: 3.767A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 407 through 427 Processing helix chain 'F' and resid 440 through 444 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.737A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 4.099A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 536 removed outlier: 3.571A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 558 through 569 removed outlier: 3.742A pdb=" N ILE F 562 " --> pdb=" O ASN F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.728A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 711 removed outlier: 3.580A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS F 696 " --> pdb=" O GLN F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 742 removed outlier: 3.848A pdb=" N MET F 740 " --> pdb=" O PHE F 736 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 762 Processing helix chain 'G' and resid 210 through 221 removed outlier: 3.506A pdb=" N GLU G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 226 removed outlier: 3.551A pdb=" N HIS G 226 " --> pdb=" O LEU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.955A pdb=" N ALA G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 263 Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 280 through 296 removed outlier: 3.510A pdb=" N SER G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN G 296 " --> pdb=" O GLU G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.881A pdb=" N ILE G 309 " --> pdb=" O GLU G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 337 removed outlier: 3.515A pdb=" N ILE G 324 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 385 Processing helix chain 'G' and resid 397 through 403 Processing helix chain 'G' and resid 407 through 427 Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'G' and resid 448 through 458 Processing helix chain 'G' and resid 482 through 499 removed outlier: 4.517A pdb=" N TYR G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Proline residue: G 496 - end of helix Processing helix chain 'G' and resid 499 through 507 removed outlier: 4.127A pdb=" N PHE G 503 " --> pdb=" O HIS G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 536 removed outlier: 3.887A pdb=" N ALA G 530 " --> pdb=" O LEU G 526 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE G 531 " --> pdb=" O LEU G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 553 Processing helix chain 'G' and resid 558 through 569 Processing helix chain 'G' and resid 580 through 586 Processing helix chain 'G' and resid 598 through 611 removed outlier: 3.820A pdb=" N GLN G 603 " --> pdb=" O ARG G 599 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET G 611 " --> pdb=" O GLU G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 661 Processing helix chain 'G' and resid 671 through 679 Processing helix chain 'G' and resid 683 through 713 removed outlier: 3.541A pdb=" N CYS G 691 " --> pdb=" O LEU G 687 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS G 696 " --> pdb=" O GLN G 692 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 712 " --> pdb=" O ARG G 708 " (cutoff:3.500A) Processing helix chain 'G' and resid 734 through 739 removed outlier: 3.661A pdb=" N GLU G 738 " --> pdb=" O ASP G 734 " (cutoff:3.500A) Processing helix chain 'G' and resid 740 through 743 Processing helix chain 'G' and resid 750 through 760 Processing helix chain 'H' and resid 210 through 221 Processing helix chain 'H' and resid 221 through 226 removed outlier: 3.543A pdb=" N HIS H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.927A pdb=" N ALA H 232 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 261 Processing helix chain 'H' and resid 271 through 277 Processing helix chain 'H' and resid 280 through 296 removed outlier: 3.512A pdb=" N SER H 284 " --> pdb=" O GLY H 280 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 310 removed outlier: 3.764A pdb=" N ILE H 309 " --> pdb=" O GLU H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 337 removed outlier: 4.058A pdb=" N VAL H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER H 326 " --> pdb=" O ARG H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 385 Processing helix chain 'H' and resid 397 through 403 Processing helix chain 'H' and resid 407 through 427 Processing helix chain 'H' and resid 440 through 444 Processing helix chain 'H' and resid 448 through 458 Processing helix chain 'H' and resid 482 through 499 removed outlier: 4.554A pdb=" N TYR H 495 " --> pdb=" O GLU H 491 " (cutoff:3.500A) Proline residue: H 496 - end of helix Processing helix chain 'H' and resid 499 through 506 removed outlier: 4.212A pdb=" N PHE H 503 " --> pdb=" O HIS H 499 " (cutoff:3.500A) Processing helix chain 'H' and resid 524 through 535 removed outlier: 3.584A pdb=" N ALA H 530 " --> pdb=" O LEU H 526 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE H 531 " --> pdb=" O LEU H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 553 Processing helix chain 'H' and resid 558 through 569 Processing helix chain 'H' and resid 580 through 586 Processing helix chain 'H' and resid 598 through 611 removed outlier: 3.878A pdb=" N GLN H 603 " --> pdb=" O ARG H 599 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET H 611 " --> pdb=" O GLU H 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 649 through 661 Processing helix chain 'H' and resid 671 through 679 Processing helix chain 'H' and resid 683 through 713 removed outlier: 3.944A pdb=" N LYS H 696 " --> pdb=" O GLN H 692 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU H 712 " --> pdb=" O ARG H 708 " (cutoff:3.500A) Processing helix chain 'H' and resid 734 through 742 removed outlier: 4.096A pdb=" N GLU H 738 " --> pdb=" O ASP H 734 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET H 740 " --> pdb=" O PHE H 736 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE H 742 " --> pdb=" O GLU H 738 " (cutoff:3.500A) Processing helix chain 'H' and resid 750 through 762 Processing helix chain 'I' and resid 210 through 221 Processing helix chain 'I' and resid 221 through 226 Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.940A pdb=" N ALA I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 261 Processing helix chain 'I' and resid 270 through 277 Processing helix chain 'I' and resid 280 through 296 removed outlier: 3.553A pdb=" N SER I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 310 removed outlier: 3.928A pdb=" N ILE I 309 " --> pdb=" O GLU I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 337 removed outlier: 3.756A pdb=" N VAL I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER I 326 " --> pdb=" O ARG I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 353 Processing helix chain 'I' and resid 373 through 385 Processing helix chain 'I' and resid 397 through 402 Processing helix chain 'I' and resid 407 through 427 Processing helix chain 'I' and resid 440 through 444 Processing helix chain 'I' and resid 448 through 458 Processing helix chain 'I' and resid 482 through 499 removed outlier: 4.876A pdb=" N TYR I 495 " --> pdb=" O GLU I 491 " (cutoff:3.500A) Proline residue: I 496 - end of helix Processing helix chain 'I' and resid 499 through 506 removed outlier: 4.027A pdb=" N PHE I 503 " --> pdb=" O HIS I 499 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU I 504 " --> pdb=" O PRO I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 536 removed outlier: 3.516A pdb=" N ALA I 528 " --> pdb=" O LYS I 524 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 530 " --> pdb=" O LEU I 526 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE I 531 " --> pdb=" O LEU I 527 " (cutoff:3.500A) Processing helix chain 'I' and resid 543 through 553 Processing helix chain 'I' and resid 558 through 569 removed outlier: 3.699A pdb=" N ILE I 562 " --> pdb=" O ASN I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 586 Processing helix chain 'I' and resid 598 through 610 removed outlier: 3.777A pdb=" N GLN I 603 " --> pdb=" O ARG I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 649 through 661 Processing helix chain 'I' and resid 671 through 679 removed outlier: 3.506A pdb=" N LEU I 675 " --> pdb=" O ASP I 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 683 through 711 removed outlier: 3.792A pdb=" N LYS I 696 " --> pdb=" O GLN I 692 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 742 removed outlier: 3.887A pdb=" N MET I 740 " --> pdb=" O PHE I 736 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE I 742 " --> pdb=" O GLU I 738 " (cutoff:3.500A) Processing helix chain 'I' and resid 750 through 762 Processing helix chain 'J' and resid 210 through 221 Processing helix chain 'J' and resid 221 through 226 removed outlier: 3.533A pdb=" N HIS J 226 " --> pdb=" O LEU J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.944A pdb=" N ALA J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 261 Processing helix chain 'J' and resid 271 through 277 Processing helix chain 'J' and resid 280 through 296 removed outlier: 3.505A pdb=" N SER J 284 " --> pdb=" O GLY J 280 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 310 removed outlier: 3.878A pdb=" N ILE J 309 " --> pdb=" O GLU J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 337 removed outlier: 4.306A pdb=" N VAL J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER J 326 " --> pdb=" O ARG J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 385 Processing helix chain 'J' and resid 397 through 403 Processing helix chain 'J' and resid 407 through 427 Processing helix chain 'J' and resid 440 through 444 Processing helix chain 'J' and resid 448 through 458 Processing helix chain 'J' and resid 482 through 499 removed outlier: 4.525A pdb=" N TYR J 495 " --> pdb=" O GLU J 491 " (cutoff:3.500A) Proline residue: J 496 - end of helix Processing helix chain 'J' and resid 499 through 507 removed outlier: 4.121A pdb=" N PHE J 503 " --> pdb=" O HIS J 499 " (cutoff:3.500A) Processing helix chain 'J' and resid 524 through 536 removed outlier: 3.843A pdb=" N ALA J 530 " --> pdb=" O LEU J 526 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE J 531 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 543 through 553 Processing helix chain 'J' and resid 558 through 569 removed outlier: 3.527A pdb=" N ILE J 562 " --> pdb=" O ASN J 558 " (cutoff:3.500A) Processing helix chain 'J' and resid 580 through 586 Processing helix chain 'J' and resid 598 through 611 removed outlier: 3.782A pdb=" N GLN J 603 " --> pdb=" O ARG J 599 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET J 611 " --> pdb=" O GLU J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 661 Processing helix chain 'J' and resid 671 through 679 Processing helix chain 'J' and resid 683 through 713 removed outlier: 3.554A pdb=" N CYS J 691 " --> pdb=" O LEU J 687 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS J 696 " --> pdb=" O GLN J 692 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 712 " --> pdb=" O ARG J 708 " (cutoff:3.500A) Processing helix chain 'J' and resid 734 through 739 Processing helix chain 'J' and resid 750 through 760 Processing helix chain 'K' and resid 210 through 221 Processing helix chain 'K' and resid 221 through 226 removed outlier: 3.593A pdb=" N HIS K 226 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 232 removed outlier: 4.012A pdb=" N ALA K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 261 Processing helix chain 'K' and resid 271 through 277 Processing helix chain 'K' and resid 280 through 294 removed outlier: 3.660A pdb=" N SER K 284 " --> pdb=" O GLY K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 310 removed outlier: 3.760A pdb=" N ILE K 309 " --> pdb=" O GLU K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 321 No H-bonds generated for 'chain 'K' and resid 319 through 321' Processing helix chain 'K' and resid 322 through 337 removed outlier: 3.627A pdb=" N SER K 326 " --> pdb=" O ARG K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 385 Processing helix chain 'K' and resid 397 through 402 Processing helix chain 'K' and resid 407 through 427 Processing helix chain 'K' and resid 440 through 444 Processing helix chain 'K' and resid 448 through 458 Processing helix chain 'K' and resid 482 through 499 removed outlier: 4.555A pdb=" N TYR K 495 " --> pdb=" O GLU K 491 " (cutoff:3.500A) Proline residue: K 496 - end of helix Processing helix chain 'K' and resid 499 through 506 removed outlier: 4.213A pdb=" N PHE K 503 " --> pdb=" O HIS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 535 removed outlier: 3.735A pdb=" N ILE K 531 " --> pdb=" O LEU K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 543 through 553 Processing helix chain 'K' and resid 558 through 569 removed outlier: 3.598A pdb=" N ILE K 562 " --> pdb=" O ASN K 558 " (cutoff:3.500A) Processing helix chain 'K' and resid 580 through 586 Processing helix chain 'K' and resid 598 through 611 removed outlier: 3.765A pdb=" N GLN K 603 " --> pdb=" O ARG K 599 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET K 611 " --> pdb=" O GLU K 607 " (cutoff:3.500A) Processing helix chain 'K' and resid 613 through 615 No H-bonds generated for 'chain 'K' and resid 613 through 615' Processing helix chain 'K' and resid 649 through 661 Processing helix chain 'K' and resid 671 through 679 Processing helix chain 'K' and resid 683 through 713 removed outlier: 3.987A pdb=" N LYS K 696 " --> pdb=" O GLN K 692 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU K 712 " --> pdb=" O ARG K 708 " (cutoff:3.500A) Processing helix chain 'K' and resid 734 through 742 removed outlier: 4.055A pdb=" N GLU K 738 " --> pdb=" O ASP K 734 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET K 740 " --> pdb=" O PHE K 736 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE K 742 " --> pdb=" O GLU K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 750 through 762 Processing helix chain 'L' and resid 210 through 221 Processing helix chain 'L' and resid 221 through 226 removed outlier: 3.511A pdb=" N HIS L 226 " --> pdb=" O LEU L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 removed outlier: 3.935A pdb=" N ALA L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 261 Processing helix chain 'L' and resid 270 through 277 Processing helix chain 'L' and resid 280 through 296 removed outlier: 3.533A pdb=" N SER L 284 " --> pdb=" O GLY L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 310 removed outlier: 3.929A pdb=" N ILE L 309 " --> pdb=" O GLU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 337 removed outlier: 3.750A pdb=" N VAL L 325 " --> pdb=" O GLU L 321 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER L 326 " --> pdb=" O ARG L 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 353 Processing helix chain 'L' and resid 373 through 385 Processing helix chain 'L' and resid 397 through 402 removed outlier: 3.538A pdb=" N ASN L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 407 through 427 Processing helix chain 'L' and resid 440 through 444 Processing helix chain 'L' and resid 448 through 458 Processing helix chain 'L' and resid 482 through 499 removed outlier: 4.885A pdb=" N TYR L 495 " --> pdb=" O GLU L 491 " (cutoff:3.500A) Proline residue: L 496 - end of helix Processing helix chain 'L' and resid 499 through 506 removed outlier: 4.036A pdb=" N PHE L 503 " --> pdb=" O HIS L 499 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU L 504 " --> pdb=" O PRO L 500 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 536 removed outlier: 3.659A pdb=" N ALA L 530 " --> pdb=" O LEU L 526 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE L 531 " --> pdb=" O LEU L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 553 Processing helix chain 'L' and resid 558 through 569 removed outlier: 3.691A pdb=" N ILE L 562 " --> pdb=" O ASN L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 586 Processing helix chain 'L' and resid 598 through 610 removed outlier: 3.734A pdb=" N GLN L 603 " --> pdb=" O ARG L 599 " (cutoff:3.500A) Processing helix chain 'L' and resid 649 through 661 Processing helix chain 'L' and resid 671 through 679 removed outlier: 3.530A pdb=" N LEU L 675 " --> pdb=" O ASP L 671 " (cutoff:3.500A) Processing helix chain 'L' and resid 683 through 711 removed outlier: 3.586A pdb=" N CYS L 691 " --> pdb=" O LEU L 687 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS L 696 " --> pdb=" O GLN L 692 " (cutoff:3.500A) Processing helix chain 'L' and resid 734 through 742 removed outlier: 3.830A pdb=" N MET L 740 " --> pdb=" O PHE L 736 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE L 742 " --> pdb=" O GLU L 738 " (cutoff:3.500A) Processing helix chain 'L' and resid 750 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.012A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 622 through 623 removed outlier: 7.910A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 513 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 541 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 270 removed outlier: 5.983A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 241 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 513 through 517 removed outlier: 7.016A pdb=" N GLY B 513 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.130A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 514 through 517 Processing sheet with id=AA9, first strand: chain 'C' and resid 538 through 541 Processing sheet with id=AB1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.013A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 622 through 623 removed outlier: 7.900A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY D 513 " --> pdb=" O LEU D 639 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 538 through 541 Processing sheet with id=AB4, first strand: chain 'E' and resid 265 through 270 removed outlier: 5.977A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 241 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 514 through 517 Processing sheet with id=AB6, first strand: chain 'E' and resid 538 through 541 Processing sheet with id=AB7, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.190A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 514 through 517 Processing sheet with id=AB9, first strand: chain 'F' and resid 538 through 541 Processing sheet with id=AC1, first strand: chain 'G' and resid 265 through 270 removed outlier: 6.012A pdb=" N ALA G 299 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET G 344 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE G 301 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ALA G 346 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE G 303 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE G 241 " --> pdb=" O ALA G 345 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR G 347 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU G 243 " --> pdb=" O THR G 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 622 through 623 removed outlier: 7.897A pdb=" N THR G 623 " --> pdb=" O VAL G 514 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE G 516 " --> pdb=" O THR G 623 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY G 513 " --> pdb=" O LEU G 639 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN G 641 " --> pdb=" O GLY G 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 538 through 541 Processing sheet with id=AC4, first strand: chain 'H' and resid 265 through 270 removed outlier: 5.969A pdb=" N ALA H 299 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET H 344 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE H 301 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA H 346 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE H 303 " --> pdb=" O ALA H 346 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 241 " --> pdb=" O VAL H 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 513 through 517 removed outlier: 7.012A pdb=" N GLY H 513 " --> pdb=" O LEU H 639 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN H 641 " --> pdb=" O GLY H 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 538 through 541 Processing sheet with id=AC7, first strand: chain 'I' and resid 265 through 268 removed outlier: 6.140A pdb=" N ALA I 299 " --> pdb=" O ILE I 342 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N MET I 344 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE I 301 " --> pdb=" O MET I 344 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ALA I 346 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE I 303 " --> pdb=" O ALA I 346 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE I 241 " --> pdb=" O ALA I 345 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR I 347 " --> pdb=" O ILE I 241 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU I 243 " --> pdb=" O THR I 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 514 through 517 Processing sheet with id=AC9, first strand: chain 'I' and resid 538 through 541 Processing sheet with id=AD1, first strand: chain 'J' and resid 265 through 270 removed outlier: 6.003A pdb=" N ALA J 299 " --> pdb=" O ILE J 342 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET J 344 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE J 301 " --> pdb=" O MET J 344 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA J 346 " --> pdb=" O ILE J 301 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE J 303 " --> pdb=" O ALA J 346 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE J 241 " --> pdb=" O ALA J 345 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR J 347 " --> pdb=" O ILE J 241 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU J 243 " --> pdb=" O THR J 347 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 622 through 623 removed outlier: 7.888A pdb=" N THR J 623 " --> pdb=" O VAL J 514 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE J 516 " --> pdb=" O THR J 623 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY J 513 " --> pdb=" O LEU J 639 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN J 641 " --> pdb=" O GLY J 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 538 through 541 Processing sheet with id=AD4, first strand: chain 'K' and resid 265 through 270 removed outlier: 5.992A pdb=" N ALA K 299 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N MET K 344 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE K 301 " --> pdb=" O MET K 344 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA K 346 " --> pdb=" O ILE K 301 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE K 303 " --> pdb=" O ALA K 346 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE K 241 " --> pdb=" O VAL K 343 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 513 through 517 removed outlier: 7.027A pdb=" N GLY K 513 " --> pdb=" O LEU K 639 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN K 641 " --> pdb=" O GLY K 513 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 538 through 541 Processing sheet with id=AD7, first strand: chain 'L' and resid 265 through 268 removed outlier: 6.147A pdb=" N ALA L 299 " --> pdb=" O ILE L 342 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N MET L 344 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE L 301 " --> pdb=" O MET L 344 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA L 346 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE L 241 " --> pdb=" O ALA L 345 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR L 347 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU L 243 " --> pdb=" O THR L 347 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 514 through 517 Processing sheet with id=AD9, first strand: chain 'L' and resid 538 through 541 2327 hydrogen bonds defined for protein. 6930 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: 19.02 Time building geometry restraints manager: 22.04 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: 17683 1.34 - 1.46: 7354 1.46 - 1.58: 27179 1.58 - 1.70: 8 1.70 - 1.81: 444 Bond restraints: 52668 Sorted by residual: bond pdb=" CB PRO J 350 " pdb=" CG PRO J 350 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.90e+00 bond pdb=" CB PRO G 350 " pdb=" CG PRO G 350 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.85e+00 bond pdb=" CB PRO A 350 " pdb=" CG PRO A 350 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.82e+00 bond pdb=" CB PRO D 350 " pdb=" CG PRO D 350 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.71e+00 bond pdb=" CB PRO E 350 " pdb=" CG PRO E 350 " ideal model delta sigma weight residual 1.492 1.623 -0.131 5.00e-02 4.00e+02 6.91e+00 ... (remaining 52663 not shown) Histogram of bond angle deviations from ideal: 96.15 - 103.99: 1092 103.99 - 111.83: 23457 111.83 - 119.66: 21038 119.66 - 127.50: 24915 127.50 - 135.34: 430 Bond angle restraints: 70932 Sorted by residual: angle pdb=" CA PRO E 350 " pdb=" N PRO E 350 " pdb=" CD PRO E 350 " ideal model delta sigma weight residual 112.00 99.04 12.96 1.40e+00 5.10e-01 8.57e+01 angle pdb=" CA PRO B 350 " pdb=" N PRO B 350 " pdb=" CD PRO B 350 " ideal model delta sigma weight residual 112.00 99.18 12.82 1.40e+00 5.10e-01 8.38e+01 angle pdb=" CA PRO H 350 " pdb=" N PRO H 350 " pdb=" CD PRO H 350 " ideal model delta sigma weight residual 112.00 99.19 12.81 1.40e+00 5.10e-01 8.38e+01 angle pdb=" CA PRO K 350 " pdb=" N PRO K 350 " pdb=" CD PRO K 350 " ideal model delta sigma weight residual 112.00 99.19 12.81 1.40e+00 5.10e-01 8.37e+01 angle pdb=" CA PRO J 350 " pdb=" N PRO J 350 " pdb=" CD PRO J 350 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.34e+01 ... (remaining 70927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 29063 17.99 - 35.97: 2931 35.97 - 53.96: 504 53.96 - 71.95: 86 71.95 - 89.93: 32 Dihedral angle restraints: 32616 sinusoidal: 13632 harmonic: 18984 Sorted by residual: dihedral pdb=" CA GLN G 760 " pdb=" C GLN G 760 " pdb=" N THR G 761 " pdb=" CA THR G 761 " ideal model delta harmonic sigma weight residual 180.00 145.88 34.12 0 5.00e+00 4.00e-02 4.66e+01 dihedral pdb=" CA GLN J 760 " pdb=" C GLN J 760 " pdb=" N THR J 761 " pdb=" CA THR J 761 " ideal model delta harmonic sigma weight residual 180.00 146.02 33.98 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA GLU J 261 " pdb=" C GLU J 261 " pdb=" N THR J 262 " pdb=" CA THR J 262 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 32613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 7383 0.107 - 0.213: 443 0.213 - 0.320: 58 0.320 - 0.426: 4 0.426 - 0.533: 8 Chirality restraints: 7896 Sorted by residual: chirality pdb=" CB ILE B 479 " pdb=" CA ILE B 479 " pdb=" CG1 ILE B 479 " pdb=" CG2 ILE B 479 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CB ILE E 479 " pdb=" CA ILE E 479 " pdb=" CG1 ILE E 479 " pdb=" CG2 ILE E 479 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CB ILE K 479 " pdb=" CA ILE K 479 " pdb=" CG1 ILE K 479 " pdb=" CG2 ILE K 479 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.59e+00 ... (remaining 7893 not shown) Planarity restraints: 9384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 349 " 0.067 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO K 350 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO K 350 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 350 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 349 " -0.067 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO H 350 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 350 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 350 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 349 " -0.066 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO E 350 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO E 350 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 350 " -0.052 5.00e-02 4.00e+02 ... (remaining 9381 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2675 2.72 - 3.26: 54908 3.26 - 3.81: 85670 3.81 - 4.35: 109906 4.35 - 4.90: 182026 Nonbonded interactions: 435185 Sorted by model distance: nonbonded pdb=" O LEU L 381 " pdb=" OG1 THR L 385 " model vdw 2.172 2.440 nonbonded pdb=" O LEU C 381 " pdb=" OG1 THR C 385 " model vdw 2.178 2.440 nonbonded pdb=" OG SER A 326 " pdb=" O PRO F 272 " model vdw 2.180 2.440 nonbonded pdb=" O LEU I 381 " pdb=" OG1 THR I 385 " model vdw 2.182 2.440 nonbonded pdb=" O PRO A 272 " pdb=" OG SER B 326 " model vdw 2.188 2.440 ... (remaining 435180 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 No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.050 Extract box with map and model: 8.160 Check model and map are aligned: 0.770 Set scattering table: 0.490 Process input model: 127.210 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 0.141 52668 Z= 0.380 Angle : 1.006 12.964 70932 Z= 0.580 Chirality : 0.058 0.533 7896 Planarity : 0.006 0.093 9384 Dihedral : 14.602 89.933 20280 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.74 (0.09), residues: 6516 helix: -1.52 (0.08), residues: 3696 sheet: -2.50 (0.25), residues: 408 loop : -1.91 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 476 HIS 0.014 0.002 HIS A 317 PHE 0.036 0.003 PHE I 674 TYR 0.035 0.002 TYR L 244 ARG 0.019 0.001 ARG H 772 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1194 time to evaluate : 6.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.7684 (tptp) cc_final: 0.7420 (tppt) REVERT: A 508 MET cc_start: 0.7758 (ttt) cc_final: 0.7496 (ttt) REVERT: A 640 ASP cc_start: 0.8002 (p0) cc_final: 0.7638 (p0) REVERT: B 221 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6890 (tp30) REVERT: B 560 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7371 (ttt-90) REVERT: B 669 ASP cc_start: 0.6890 (p0) cc_final: 0.6542 (p0) REVERT: C 261 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6796 (mm-30) REVERT: C 315 LYS cc_start: 0.7874 (tptt) cc_final: 0.6992 (mmmt) REVERT: C 327 GLN cc_start: 0.8121 (tp40) cc_final: 0.7678 (tp-100) REVERT: C 525 THR cc_start: 0.8628 (m) cc_final: 0.8382 (t) REVERT: C 620 ILE cc_start: 0.8950 (mt) cc_final: 0.8744 (mt) REVERT: D 315 LYS cc_start: 0.7595 (tptp) cc_final: 0.7379 (tppt) REVERT: D 327 GLN cc_start: 0.7764 (tp40) cc_final: 0.7314 (tp-100) REVERT: D 508 MET cc_start: 0.7782 (ttt) cc_final: 0.7500 (ttt) REVERT: D 640 ASP cc_start: 0.7877 (p0) cc_final: 0.7662 (p0) REVERT: E 560 ARG cc_start: 0.7534 (ttt90) cc_final: 0.7254 (ttt-90) REVERT: E 647 LEU cc_start: 0.8290 (mt) cc_final: 0.8048 (mt) REVERT: E 689 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6565 (mp0) REVERT: F 315 LYS cc_start: 0.7679 (tptt) cc_final: 0.6978 (mmmt) REVERT: F 327 GLN cc_start: 0.8022 (tp40) cc_final: 0.7514 (tp-100) REVERT: F 378 LEU cc_start: 0.8362 (tt) cc_final: 0.7897 (tt) REVERT: F 402 GLU cc_start: 0.7073 (pt0) cc_final: 0.6727 (pt0) REVERT: F 620 ILE cc_start: 0.8955 (mt) cc_final: 0.8741 (mt) REVERT: G 225 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7337 (ttp80) REVERT: G 315 LYS cc_start: 0.7668 (mppt) cc_final: 0.7361 (mtmt) REVERT: G 327 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7286 (tp-100) REVERT: G 508 MET cc_start: 0.7794 (ttt) cc_final: 0.7515 (ttt) REVERT: G 640 ASP cc_start: 0.7979 (p0) cc_final: 0.7620 (p0) REVERT: H 226 HIS cc_start: 0.7926 (p90) cc_final: 0.7701 (p-80) REVERT: H 560 ARG cc_start: 0.7527 (ttt90) cc_final: 0.7258 (ttt-90) REVERT: H 689 GLU cc_start: 0.6824 (mp0) cc_final: 0.6398 (mp0) REVERT: I 261 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6836 (mm-30) REVERT: I 327 GLN cc_start: 0.8012 (tp40) cc_final: 0.7547 (tp-100) REVERT: I 525 THR cc_start: 0.8696 (m) cc_final: 0.8423 (t) REVERT: I 613 THR cc_start: 0.7047 (p) cc_final: 0.6711 (p) REVERT: I 620 ILE cc_start: 0.8918 (mt) cc_final: 0.8715 (mt) REVERT: J 315 LYS cc_start: 0.7729 (tptp) cc_final: 0.7442 (tppt) REVERT: J 317 HIS cc_start: 0.6584 (t70) cc_final: 0.6184 (t-90) REVERT: J 327 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7269 (tp-100) REVERT: J 442 MET cc_start: 0.6168 (ttp) cc_final: 0.5959 (mpp) REVERT: J 508 MET cc_start: 0.7764 (ttt) cc_final: 0.7503 (ttt) REVERT: J 607 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7254 (mp0) REVERT: J 640 ASP cc_start: 0.7936 (p0) cc_final: 0.7682 (p0) REVERT: K 560 ARG cc_start: 0.7643 (ttt90) cc_final: 0.7426 (ttt-90) REVERT: K 669 ASP cc_start: 0.6393 (p0) cc_final: 0.6186 (p0) REVERT: L 327 GLN cc_start: 0.8056 (tp40) cc_final: 0.7519 (tp-100) REVERT: L 378 LEU cc_start: 0.8139 (tt) cc_final: 0.7937 (tt) REVERT: L 525 THR cc_start: 0.8625 (m) cc_final: 0.8397 (t) REVERT: L 613 THR cc_start: 0.6986 (p) cc_final: 0.6611 (p) REVERT: L 620 ILE cc_start: 0.8853 (mt) cc_final: 0.8631 (mt) outliers start: 0 outliers final: 0 residues processed: 1194 average time/residue: 0.7041 time to fit residues: 1327.4795 Evaluate side-chains 937 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 937 time to evaluate : 5.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 0.9990 chunk 500 optimal weight: 0.0020 chunk 277 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 337 optimal weight: 0.6980 chunk 267 optimal weight: 0.9980 chunk 517 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 chunk 314 optimal weight: 0.6980 chunk 385 optimal weight: 10.0000 chunk 599 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 458 GLN ** C 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 624 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 558 ASN ** E 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN F 401 ASN F 533 ASN F 568 GLN G 558 ASN G 624 ASN ** H 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 HIS I 327 GLN ** I 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 317 HIS J 401 ASN J 558 ASN J 624 ASN L 327 GLN L 401 ASN L 458 GLN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 52668 Z= 0.191 Angle : 0.621 7.492 70932 Z= 0.324 Chirality : 0.046 0.263 7896 Planarity : 0.005 0.071 9384 Dihedral : 5.566 27.735 7152 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.40 % Allowed : 8.97 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.10), residues: 6516 helix: -0.77 (0.08), residues: 3744 sheet: -1.98 (0.26), residues: 408 loop : -1.64 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 454 HIS 0.007 0.001 HIS B 317 PHE 0.024 0.002 PHE K 265 TYR 0.020 0.001 TYR L 244 ARG 0.007 0.001 ARG F 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1053 time to evaluate : 6.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 351 ASN cc_start: 0.7677 (p0) cc_final: 0.7354 (p0) REVERT: B 560 ARG cc_start: 0.7607 (ttt90) cc_final: 0.7310 (ttt-90) REVERT: B 620 ILE cc_start: 0.8861 (mt) cc_final: 0.8642 (mt) REVERT: B 669 ASP cc_start: 0.6938 (p0) cc_final: 0.6607 (p0) REVERT: B 740 MET cc_start: 0.7979 (tpt) cc_final: 0.7718 (tpt) REVERT: B 756 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 225 ARG cc_start: 0.7433 (mtp-110) cc_final: 0.6919 (mtp-110) REVERT: C 315 LYS cc_start: 0.7879 (tptt) cc_final: 0.7009 (mmmt) REVERT: C 327 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7678 (tp-100) REVERT: C 402 GLU cc_start: 0.6293 (pm20) cc_final: 0.6054 (pm20) REVERT: C 620 ILE cc_start: 0.8801 (mt) cc_final: 0.8578 (mt) REVERT: C 689 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: D 620 ILE cc_start: 0.8835 (mt) cc_final: 0.8634 (mt) REVERT: E 351 ASN cc_start: 0.7650 (p0) cc_final: 0.7381 (p0) REVERT: E 647 LEU cc_start: 0.8116 (mt) cc_final: 0.7873 (mt) REVERT: E 686 ASP cc_start: 0.6314 (t0) cc_final: 0.6079 (t0) REVERT: E 689 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6443 (mp0) REVERT: E 744 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7050 (mtp85) REVERT: F 315 LYS cc_start: 0.7940 (tptt) cc_final: 0.7038 (mmmt) REVERT: F 327 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7627 (tp-100) REVERT: F 402 GLU cc_start: 0.6701 (pt0) cc_final: 0.6349 (pt0) REVERT: F 417 GLU cc_start: 0.7581 (tp30) cc_final: 0.7324 (tp30) REVERT: F 458 GLN cc_start: 0.8373 (mp10) cc_final: 0.8132 (mp10) REVERT: F 620 ILE cc_start: 0.8786 (mt) cc_final: 0.8562 (mt) REVERT: G 221 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7538 (tm-30) REVERT: G 327 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7423 (tp-100) REVERT: G 442 MET cc_start: 0.6211 (ttp) cc_final: 0.5882 (ttp) REVERT: G 620 ILE cc_start: 0.8855 (mt) cc_final: 0.8653 (mt) REVERT: G 740 MET cc_start: 0.7807 (tpt) cc_final: 0.7498 (tpt) REVERT: G 760 GLN cc_start: 0.6118 (mt0) cc_final: 0.5753 (mt0) REVERT: H 221 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7513 (tm-30) REVERT: H 351 ASN cc_start: 0.7693 (p0) cc_final: 0.7359 (p0) REVERT: H 560 ARG cc_start: 0.7528 (ttt90) cc_final: 0.7253 (ttt-90) REVERT: H 689 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: I 225 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7304 (mtp-110) REVERT: I 402 GLU cc_start: 0.6864 (pm20) cc_final: 0.6370 (pm20) REVERT: I 613 THR cc_start: 0.7065 (p) cc_final: 0.6685 (p) REVERT: I 689 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: J 221 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7390 (tm-30) REVERT: J 327 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7469 (tp-100) REVERT: J 740 MET cc_start: 0.8128 (tpt) cc_final: 0.7759 (tpt) REVERT: K 351 ASN cc_start: 0.7689 (p0) cc_final: 0.7438 (p0) REVERT: K 560 ARG cc_start: 0.7602 (ttt90) cc_final: 0.7387 (ttt-90) REVERT: K 620 ILE cc_start: 0.8838 (mt) cc_final: 0.8637 (mt) REVERT: K 669 ASP cc_start: 0.6442 (p0) cc_final: 0.6119 (p0) REVERT: K 679 THR cc_start: 0.8237 (p) cc_final: 0.8017 (p) REVERT: L 327 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7625 (tp-100) REVERT: L 378 LEU cc_start: 0.8038 (tt) cc_final: 0.7562 (tt) REVERT: L 613 THR cc_start: 0.7015 (p) cc_final: 0.6646 (p) REVERT: L 620 ILE cc_start: 0.8653 (mt) cc_final: 0.8413 (mt) REVERT: L 740 MET cc_start: 0.8182 (tpt) cc_final: 0.7903 (tpt) outliers start: 77 outliers final: 39 residues processed: 1095 average time/residue: 0.7173 time to fit residues: 1247.1095 Evaluate side-chains 931 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 889 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 478 ASP Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 604 ILE Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 498 optimal weight: 9.9990 chunk 408 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 600 optimal weight: 0.5980 chunk 648 optimal weight: 1.9990 chunk 534 optimal weight: 2.9990 chunk 595 optimal weight: 0.0470 chunk 204 optimal weight: 3.9990 chunk 481 optimal weight: 0.6980 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 533 ASN C 558 ASN ** C 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 GLN I 558 ASN ** I 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 401 ASN J 760 GLN L 226 HIS L 317 HIS L 401 ASN L 558 ASN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 52668 Z= 0.231 Angle : 0.592 8.546 70932 Z= 0.307 Chirality : 0.046 0.266 7896 Planarity : 0.004 0.067 9384 Dihedral : 5.225 25.784 7152 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.20 % Allowed : 12.55 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 6516 helix: -0.39 (0.09), residues: 3720 sheet: -1.73 (0.26), residues: 408 loop : -1.46 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 454 HIS 0.004 0.001 HIS C 226 PHE 0.017 0.002 PHE K 265 TYR 0.025 0.002 TYR L 244 ARG 0.008 0.000 ARG E 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 962 time to evaluate : 5.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7275 (mtp) cc_final: 0.6992 (mtp) REVERT: A 737 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6899 (mt-10) REVERT: B 254 ILE cc_start: 0.7708 (mt) cc_final: 0.7395 (mt) REVERT: B 442 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.4963 (ptm) REVERT: B 620 ILE cc_start: 0.8899 (mt) cc_final: 0.8646 (mt) REVERT: B 647 LEU cc_start: 0.8212 (mt) cc_final: 0.8000 (mt) REVERT: B 669 ASP cc_start: 0.6966 (p0) cc_final: 0.6655 (p0) REVERT: C 225 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.6819 (mtp85) REVERT: C 315 LYS cc_start: 0.7814 (tptt) cc_final: 0.6904 (mmmt) REVERT: C 327 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7714 (tp-100) REVERT: C 402 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6219 (pm20) REVERT: C 442 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5035 (ptm) REVERT: C 689 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: D 315 LYS cc_start: 0.7771 (tptt) cc_final: 0.7538 (tppt) REVERT: D 332 MET cc_start: 0.7246 (mtp) cc_final: 0.6968 (mtp) REVERT: E 254 ILE cc_start: 0.7735 (mt) cc_final: 0.7415 (mt) REVERT: E 261 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6726 (mp0) REVERT: E 442 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.4948 (ptm) REVERT: E 560 ARG cc_start: 0.7598 (ttt-90) cc_final: 0.7362 (ttt-90) REVERT: E 620 ILE cc_start: 0.8987 (mt) cc_final: 0.8763 (mt) REVERT: E 686 ASP cc_start: 0.6186 (t0) cc_final: 0.5976 (t0) REVERT: F 315 LYS cc_start: 0.7921 (tptt) cc_final: 0.6986 (mmmt) REVERT: F 327 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7522 (tp-100) REVERT: F 401 ASN cc_start: 0.8334 (m-40) cc_final: 0.8032 (m-40) REVERT: F 402 GLU cc_start: 0.6710 (pt0) cc_final: 0.6427 (pt0) REVERT: F 417 GLU cc_start: 0.7737 (tp30) cc_final: 0.7430 (tp30) REVERT: F 442 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5403 (ptm) REVERT: F 620 ILE cc_start: 0.8879 (mt) cc_final: 0.8654 (mt) REVERT: F 689 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6231 (mp0) REVERT: G 327 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7318 (tp-100) REVERT: G 332 MET cc_start: 0.7324 (mtp) cc_final: 0.6951 (mtp) REVERT: G 760 GLN cc_start: 0.6048 (mt0) cc_final: 0.5781 (mt0) REVERT: H 351 ASN cc_start: 0.7624 (p0) cc_final: 0.7403 (p0) REVERT: H 442 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.4911 (ptm) REVERT: H 560 ARG cc_start: 0.7557 (ttt90) cc_final: 0.7248 (ttt-90) REVERT: H 620 ILE cc_start: 0.8979 (mt) cc_final: 0.8763 (mt) REVERT: H 689 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: I 402 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6112 (pm20) REVERT: I 442 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5372 (ptm) REVERT: I 613 THR cc_start: 0.7034 (p) cc_final: 0.6703 (p) REVERT: I 620 ILE cc_start: 0.8874 (mt) cc_final: 0.8663 (mt) REVERT: J 327 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7383 (tp-100) REVERT: J 332 MET cc_start: 0.7310 (mtp) cc_final: 0.6938 (mtp) REVERT: K 254 ILE cc_start: 0.7656 (mt) cc_final: 0.7371 (mt) REVERT: K 442 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.4942 (ptm) REVERT: K 560 ARG cc_start: 0.7608 (ttt90) cc_final: 0.7398 (ttt-90) REVERT: K 620 ILE cc_start: 0.8888 (mt) cc_final: 0.8652 (mt) REVERT: K 669 ASP cc_start: 0.6465 (p0) cc_final: 0.6209 (p0) REVERT: L 327 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7538 (tp-100) REVERT: L 442 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5001 (ptm) REVERT: L 613 THR cc_start: 0.7012 (p) cc_final: 0.6706 (p) REVERT: L 620 ILE cc_start: 0.8715 (mt) cc_final: 0.8496 (mt) REVERT: L 689 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: L 740 MET cc_start: 0.8053 (tpt) cc_final: 0.7767 (tpt) outliers start: 121 outliers final: 74 residues processed: 1019 average time/residue: 0.7015 time to fit residues: 1138.4392 Evaluate side-chains 959 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 871 time to evaluate : 6.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 624 ASN Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 442 MET Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 402 GLU Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain J residue 478 ASP Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 624 ASN Chi-restraints excluded: chain J residue 633 ILE Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain J residue 749 ASP Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain K residue 556 GLU Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain L residue 442 MET Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 683 SER Chi-restraints excluded: chain L residue 689 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 0.2980 chunk 451 optimal weight: 5.9990 chunk 311 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 403 optimal weight: 0.9980 chunk 602 optimal weight: 7.9990 chunk 637 optimal weight: 0.5980 chunk 314 optimal weight: 0.9980 chunk 571 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** C 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN ** E 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN ** I 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 401 ASN K 458 GLN L 401 ASN L 533 ASN L 536 GLN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 52668 Z= 0.176 Angle : 0.553 9.434 70932 Z= 0.286 Chirality : 0.045 0.283 7896 Planarity : 0.004 0.068 9384 Dihedral : 4.967 24.372 7152 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.43 % Allowed : 14.02 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.11), residues: 6516 helix: -0.15 (0.09), residues: 3708 sheet: -1.44 (0.26), residues: 408 loop : -1.31 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 454 HIS 0.003 0.000 HIS B 226 PHE 0.017 0.001 PHE K 674 TYR 0.027 0.001 TYR L 244 ARG 0.019 0.000 ARG J 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 949 time to evaluate : 5.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7351 (mtp) cc_final: 0.6980 (mtp) REVERT: A 737 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6944 (mt-10) REVERT: B 254 ILE cc_start: 0.7640 (mt) cc_final: 0.7306 (mt) REVERT: B 442 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.4930 (ptm) REVERT: C 315 LYS cc_start: 0.7824 (tptt) cc_final: 0.6941 (mmmt) REVERT: C 327 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7723 (tp-100) REVERT: C 442 MET cc_start: 0.6043 (mpp) cc_final: 0.4876 (ptm) REVERT: D 332 MET cc_start: 0.7335 (mtp) cc_final: 0.6959 (mtp) REVERT: E 254 ILE cc_start: 0.7672 (mt) cc_final: 0.7326 (mt) REVERT: E 442 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.4909 (ptm) REVERT: E 560 ARG cc_start: 0.7532 (ttt-90) cc_final: 0.7291 (ttt-90) REVERT: E 620 ILE cc_start: 0.8902 (mt) cc_final: 0.8690 (mt) REVERT: E 669 ASP cc_start: 0.6411 (p0) cc_final: 0.6091 (p0) REVERT: E 686 ASP cc_start: 0.6440 (t0) cc_final: 0.6210 (t0) REVERT: E 689 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: E 744 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7250 (mtp-110) REVERT: F 315 LYS cc_start: 0.7929 (tptt) cc_final: 0.6922 (mmmt) REVERT: F 327 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7537 (tp-100) REVERT: F 401 ASN cc_start: 0.8233 (m-40) cc_final: 0.7991 (m-40) REVERT: F 417 GLU cc_start: 0.7580 (tp30) cc_final: 0.7289 (tp30) REVERT: F 442 MET cc_start: 0.6050 (mpp) cc_final: 0.4836 (ptm) REVERT: F 620 ILE cc_start: 0.8825 (mt) cc_final: 0.8598 (mt) REVERT: F 689 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: G 327 GLN cc_start: 0.7723 (tp-100) cc_final: 0.7481 (tp-100) REVERT: G 760 GLN cc_start: 0.6151 (mt0) cc_final: 0.5903 (mt0) REVERT: H 442 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5013 (ptm) REVERT: H 560 ARG cc_start: 0.7522 (ttt90) cc_final: 0.7248 (ttt-90) REVERT: I 402 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5967 (pm20) REVERT: I 442 MET cc_start: 0.6025 (mpp) cc_final: 0.4786 (ptm) REVERT: I 613 THR cc_start: 0.6989 (p) cc_final: 0.6770 (p) REVERT: I 620 ILE cc_start: 0.8774 (mt) cc_final: 0.8562 (mt) REVERT: J 327 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7447 (tp-100) REVERT: J 401 ASN cc_start: 0.8348 (m-40) cc_final: 0.8010 (m110) REVERT: K 254 ILE cc_start: 0.7711 (mt) cc_final: 0.7397 (mt) REVERT: K 442 MET cc_start: 0.5960 (OUTLIER) cc_final: 0.5128 (ptm) REVERT: K 560 ARG cc_start: 0.7575 (ttt90) cc_final: 0.7350 (ttt-90) REVERT: K 620 ILE cc_start: 0.8867 (mt) cc_final: 0.8635 (mt) REVERT: K 669 ASP cc_start: 0.6290 (p0) cc_final: 0.6078 (p0) REVERT: L 327 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7549 (tp-100) REVERT: L 380 ILE cc_start: 0.8788 (mm) cc_final: 0.8473 (mt) REVERT: L 401 ASN cc_start: 0.7950 (m-40) cc_final: 0.7581 (m-40) REVERT: L 442 MET cc_start: 0.6013 (mpp) cc_final: 0.4843 (ptm) REVERT: L 613 THR cc_start: 0.6973 (p) cc_final: 0.6690 (p) REVERT: L 620 ILE cc_start: 0.8670 (mt) cc_final: 0.8455 (mt) outliers start: 134 outliers final: 70 residues processed: 1024 average time/residue: 0.6859 time to fit residues: 1121.0324 Evaluate side-chains 945 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 868 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 442 MET Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 402 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 478 ASP Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 509 THR Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain J residue 749 ASP Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 629 ILE Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 4.9990 chunk 362 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 475 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 544 optimal weight: 1.9990 chunk 440 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 325 optimal weight: 0.0020 chunk 572 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN ** E 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 750 ASN J 558 ASN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 52668 Z= 0.254 Angle : 0.584 9.857 70932 Z= 0.300 Chirality : 0.046 0.285 7896 Planarity : 0.004 0.065 9384 Dihedral : 4.934 25.020 7152 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.21 % Allowed : 15.49 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.11), residues: 6516 helix: 0.01 (0.09), residues: 3636 sheet: -1.42 (0.26), residues: 408 loop : -1.23 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 454 HIS 0.002 0.001 HIS A 317 PHE 0.016 0.002 PHE D 618 TYR 0.027 0.002 TYR L 244 ARG 0.011 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 920 time to evaluate : 6.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6979 (mt-10) REVERT: B 254 ILE cc_start: 0.7749 (mt) cc_final: 0.7420 (mt) REVERT: B 442 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.4890 (ptm) REVERT: C 315 LYS cc_start: 0.7860 (tptt) cc_final: 0.6886 (mmmt) REVERT: C 327 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7783 (tp-100) REVERT: C 442 MET cc_start: 0.6304 (mpp) cc_final: 0.5547 (ptm) REVERT: D 678 MET cc_start: 0.7757 (mmp) cc_final: 0.7556 (mmp) REVERT: E 254 ILE cc_start: 0.7768 (mt) cc_final: 0.7412 (mt) REVERT: E 261 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6870 (mp0) REVERT: E 442 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.4871 (ptm) REVERT: E 560 ARG cc_start: 0.7539 (ttt-90) cc_final: 0.7311 (ttt-90) REVERT: E 669 ASP cc_start: 0.6433 (p0) cc_final: 0.6109 (p0) REVERT: E 686 ASP cc_start: 0.6617 (t0) cc_final: 0.6399 (t0) REVERT: E 689 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: E 744 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7247 (mtp85) REVERT: F 315 LYS cc_start: 0.7942 (tptt) cc_final: 0.6910 (mmmt) REVERT: F 327 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7593 (tp-100) REVERT: F 401 ASN cc_start: 0.8339 (m-40) cc_final: 0.7954 (m-40) REVERT: F 402 GLU cc_start: 0.6653 (pt0) cc_final: 0.6453 (pt0) REVERT: F 417 GLU cc_start: 0.7706 (tp30) cc_final: 0.7392 (tp30) REVERT: F 442 MET cc_start: 0.6414 (mpp) cc_final: 0.5657 (ptm) REVERT: F 620 ILE cc_start: 0.8924 (mt) cc_final: 0.8706 (mt) REVERT: F 689 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: G 327 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7659 (tp-100) REVERT: G 704 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6899 (mp0) REVERT: G 740 MET cc_start: 0.7723 (tpt) cc_final: 0.7463 (tpt) REVERT: G 760 GLN cc_start: 0.6358 (mt0) cc_final: 0.6104 (mt0) REVERT: H 442 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.4635 (ptm) REVERT: H 560 ARG cc_start: 0.7521 (ttt90) cc_final: 0.7237 (ttt-90) REVERT: I 442 MET cc_start: 0.6108 (mpp) cc_final: 0.5410 (ptm) REVERT: I 456 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8233 (mt) REVERT: I 613 THR cc_start: 0.7123 (p) cc_final: 0.6753 (p) REVERT: J 327 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7646 (tp-100) REVERT: K 254 ILE cc_start: 0.7824 (mt) cc_final: 0.7500 (mt) REVERT: K 442 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.4857 (ptm) REVERT: L 327 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7620 (tp-100) REVERT: L 401 ASN cc_start: 0.8256 (m-40) cc_final: 0.7923 (m-40) REVERT: L 402 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: L 442 MET cc_start: 0.6331 (mpp) cc_final: 0.5654 (ptm) REVERT: L 613 THR cc_start: 0.7049 (p) cc_final: 0.6761 (p) outliers start: 122 outliers final: 89 residues processed: 975 average time/residue: 0.6818 time to fit residues: 1059.7511 Evaluate side-chains 944 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 847 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 624 ASN Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain G residue 749 ASP Chi-restraints excluded: chain H residue 442 MET Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 478 ASP Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 509 THR Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 624 ASN Chi-restraints excluded: chain J residue 633 ILE Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain J residue 749 ASP Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 556 GLU Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 629 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 5.9990 chunk 574 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 374 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 638 optimal weight: 0.7980 chunk 530 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 335 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN ** E 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 HIS I 558 ASN L 558 ASN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 52668 Z= 0.193 Angle : 0.577 13.289 70932 Z= 0.292 Chirality : 0.045 0.299 7896 Planarity : 0.004 0.064 9384 Dihedral : 4.823 24.255 7152 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.14 % Allowed : 16.65 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 6516 helix: 0.16 (0.09), residues: 3624 sheet: -1.27 (0.27), residues: 408 loop : -1.12 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 454 HIS 0.002 0.000 HIS F 317 PHE 0.017 0.001 PHE J 618 TYR 0.027 0.001 TYR L 244 ARG 0.009 0.000 ARG E 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 915 time to evaluate : 6.129 Fit side-chains revert: symmetry clash REVERT: A 315 LYS cc_start: 0.7272 (tppt) cc_final: 0.7059 (tptt) REVERT: B 254 ILE cc_start: 0.7701 (mt) cc_final: 0.7373 (mt) REVERT: B 442 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.5216 (ptm) REVERT: B 641 GLN cc_start: 0.6806 (mp10) cc_final: 0.6273 (mp10) REVERT: C 315 LYS cc_start: 0.7876 (tptt) cc_final: 0.6890 (mmmt) REVERT: C 327 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7774 (tp-100) REVERT: C 442 MET cc_start: 0.6501 (mpp) cc_final: 0.5560 (ptm) REVERT: D 315 LYS cc_start: 0.7162 (tppt) cc_final: 0.6945 (tptt) REVERT: D 401 ASN cc_start: 0.8424 (m110) cc_final: 0.8110 (m-40) REVERT: D 483 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6544 (mt-10) REVERT: D 678 MET cc_start: 0.7743 (mmp) cc_final: 0.7533 (mmp) REVERT: E 254 ILE cc_start: 0.7716 (mt) cc_final: 0.7373 (mt) REVERT: E 261 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6828 (mp0) REVERT: E 442 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.5189 (ptm) REVERT: E 669 ASP cc_start: 0.6119 (p0) cc_final: 0.5825 (p0) REVERT: E 686 ASP cc_start: 0.6582 (t0) cc_final: 0.6369 (t0) REVERT: E 744 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7196 (mtp-110) REVERT: F 315 LYS cc_start: 0.7933 (tptt) cc_final: 0.6856 (mmmt) REVERT: F 327 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7610 (tp-100) REVERT: F 401 ASN cc_start: 0.8327 (m-40) cc_final: 0.7952 (m-40) REVERT: F 402 GLU cc_start: 0.6771 (pt0) cc_final: 0.6529 (pt0) REVERT: F 442 MET cc_start: 0.6434 (mpp) cc_final: 0.5265 (ptm) REVERT: F 620 ILE cc_start: 0.8852 (mt) cc_final: 0.8633 (mt) REVERT: F 689 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: G 327 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7343 (tp-100) REVERT: G 401 ASN cc_start: 0.8405 (m110) cc_final: 0.8110 (m-40) REVERT: G 760 GLN cc_start: 0.6439 (mt0) cc_final: 0.6230 (mt0) REVERT: H 442 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.5021 (ptm) REVERT: H 560 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7193 (ttt-90) REVERT: I 402 GLU cc_start: 0.6957 (pt0) cc_final: 0.6321 (pm20) REVERT: I 442 MET cc_start: 0.6444 (mpp) cc_final: 0.5799 (ptm) REVERT: I 456 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8235 (mt) REVERT: I 613 THR cc_start: 0.7070 (p) cc_final: 0.6771 (p) REVERT: J 327 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7346 (tp-100) REVERT: K 254 ILE cc_start: 0.7777 (mt) cc_final: 0.7450 (mt) REVERT: K 442 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5192 (ptm) REVERT: K 560 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7359 (ttt-90) REVERT: K 641 GLN cc_start: 0.6807 (mp10) cc_final: 0.6276 (mp10) REVERT: L 327 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7606 (tp-100) REVERT: L 442 MET cc_start: 0.6478 (mpp) cc_final: 0.5444 (ptm) REVERT: L 613 THR cc_start: 0.7040 (p) cc_final: 0.6710 (p) outliers start: 118 outliers final: 81 residues processed: 978 average time/residue: 0.6851 time to fit residues: 1070.4125 Evaluate side-chains 936 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 849 time to evaluate : 6.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 442 MET Chi-restraints excluded: chain H residue 504 LEU Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 478 ASP Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 509 THR Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 633 ILE Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain J residue 749 ASP Chi-restraints excluded: chain K residue 320 VAL Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain K residue 556 GLU Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 629 ILE Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 363 optimal weight: 4.9990 chunk 466 optimal weight: 0.9980 chunk 361 optimal weight: 0.7980 chunk 537 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 636 optimal weight: 0.0050 chunk 398 optimal weight: 0.7980 chunk 387 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 52668 Z= 0.162 Angle : 0.558 10.193 70932 Z= 0.285 Chirality : 0.045 0.328 7896 Planarity : 0.004 0.062 9384 Dihedral : 4.681 21.540 7152 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.98 % Allowed : 17.67 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.11), residues: 6516 helix: 0.32 (0.09), residues: 3636 sheet: -1.14 (0.27), residues: 408 loop : -1.12 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 454 HIS 0.002 0.000 HIS A 317 PHE 0.018 0.001 PHE E 618 TYR 0.026 0.001 TYR L 244 ARG 0.007 0.000 ARG H 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 923 time to evaluate : 5.605 Fit side-chains revert: symmetry clash REVERT: A 315 LYS cc_start: 0.7425 (tppt) cc_final: 0.7222 (tptt) REVERT: A 401 ASN cc_start: 0.8396 (m110) cc_final: 0.8113 (m-40) REVERT: A 449 MET cc_start: 0.7622 (mmm) cc_final: 0.7368 (tpp) REVERT: B 254 ILE cc_start: 0.7636 (mt) cc_final: 0.7307 (mt) REVERT: B 762 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6973 (mp) REVERT: C 225 ARG cc_start: 0.6655 (mtp-110) cc_final: 0.6381 (ttp-110) REVERT: C 315 LYS cc_start: 0.7878 (tptt) cc_final: 0.6897 (mmmt) REVERT: C 327 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7766 (tp-100) REVERT: C 442 MET cc_start: 0.6468 (mpp) cc_final: 0.5567 (ptm) REVERT: D 401 ASN cc_start: 0.8421 (m110) cc_final: 0.8123 (m-40) REVERT: D 449 MET cc_start: 0.7608 (mmm) cc_final: 0.7398 (tpp) REVERT: D 560 ARG cc_start: 0.7807 (ttt-90) cc_final: 0.7403 (ttt-90) REVERT: D 678 MET cc_start: 0.7769 (mmp) cc_final: 0.7537 (mmp) REVERT: E 221 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6959 (tp30) REVERT: E 254 ILE cc_start: 0.7656 (mt) cc_final: 0.7313 (mt) REVERT: E 669 ASP cc_start: 0.6134 (p0) cc_final: 0.5853 (p0) REVERT: E 686 ASP cc_start: 0.6568 (t0) cc_final: 0.6354 (t0) REVERT: E 744 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7159 (mtp-110) REVERT: F 315 LYS cc_start: 0.7936 (tptt) cc_final: 0.6846 (mmmt) REVERT: F 327 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7581 (tp-100) REVERT: F 401 ASN cc_start: 0.8299 (m-40) cc_final: 0.7975 (m-40) REVERT: F 442 MET cc_start: 0.6468 (mpp) cc_final: 0.5538 (ptm) REVERT: F 582 ILE cc_start: 0.8474 (mt) cc_final: 0.8245 (mt) REVERT: F 620 ILE cc_start: 0.8796 (mt) cc_final: 0.8572 (mt) REVERT: F 733 ARG cc_start: 0.6821 (ptt90) cc_final: 0.5794 (tpp-160) REVERT: G 327 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7320 (tp-100) REVERT: G 401 ASN cc_start: 0.8404 (m110) cc_final: 0.8111 (m-40) REVERT: G 449 MET cc_start: 0.7593 (mmm) cc_final: 0.7372 (tpp) REVERT: G 502 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7926 (mmtt) REVERT: H 560 ARG cc_start: 0.7456 (ttt90) cc_final: 0.7164 (ttt-90) REVERT: H 766 ARG cc_start: 0.5694 (mmt90) cc_final: 0.5440 (mmt-90) REVERT: I 442 MET cc_start: 0.6284 (mpp) cc_final: 0.5440 (ptm) REVERT: I 582 ILE cc_start: 0.8508 (mt) cc_final: 0.8296 (mt) REVERT: I 613 THR cc_start: 0.7044 (p) cc_final: 0.6722 (p) REVERT: I 689 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: J 327 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7319 (tp-100) REVERT: J 449 MET cc_start: 0.7627 (mmm) cc_final: 0.7392 (tpp) REVERT: J 740 MET cc_start: 0.8006 (tpt) cc_final: 0.7750 (tpt) REVERT: K 254 ILE cc_start: 0.7680 (mt) cc_final: 0.7390 (mt) REVERT: K 560 ARG cc_start: 0.7548 (ttt-90) cc_final: 0.7303 (ttt-90) REVERT: L 327 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7589 (tp-100) REVERT: L 442 MET cc_start: 0.6441 (mpp) cc_final: 0.5528 (ptm) REVERT: L 582 ILE cc_start: 0.8499 (mt) cc_final: 0.8258 (mt) REVERT: L 613 THR cc_start: 0.6992 (p) cc_final: 0.6681 (p) REVERT: L 733 ARG cc_start: 0.6870 (ptt90) cc_final: 0.5814 (tpp-160) outliers start: 109 outliers final: 75 residues processed: 977 average time/residue: 0.6929 time to fit residues: 1081.9778 Evaluate side-chains 940 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 863 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 509 THR Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain J residue 749 ASP Chi-restraints excluded: chain K residue 320 VAL Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain L residue 320 VAL Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 629 ILE Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 8.9990 chunk 254 optimal weight: 0.8980 chunk 379 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 404 optimal weight: 10.0000 chunk 433 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 500 optimal weight: 0.0270 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 602 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 52668 Z= 0.176 Angle : 0.554 9.730 70932 Z= 0.283 Chirality : 0.045 0.294 7896 Planarity : 0.004 0.062 9384 Dihedral : 4.608 21.519 7152 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.03 % Allowed : 18.01 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 6516 helix: 0.41 (0.09), residues: 3636 sheet: -1.06 (0.27), residues: 408 loop : -1.08 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 454 HIS 0.002 0.000 HIS A 317 PHE 0.019 0.001 PHE D 618 TYR 0.024 0.001 TYR L 244 ARG 0.009 0.000 ARG E 635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 900 time to evaluate : 5.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7736 (mmm) cc_final: 0.7436 (tpp) REVERT: A 740 MET cc_start: 0.7398 (tpt) cc_final: 0.7028 (tpt) REVERT: B 254 ILE cc_start: 0.7637 (mt) cc_final: 0.7306 (mt) REVERT: B 504 LEU cc_start: 0.8317 (pp) cc_final: 0.8110 (pp) REVERT: C 225 ARG cc_start: 0.6644 (mtp-110) cc_final: 0.6371 (ttp-110) REVERT: C 315 LYS cc_start: 0.7877 (tptt) cc_final: 0.6893 (mmmt) REVERT: C 327 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7776 (tp-100) REVERT: C 442 MET cc_start: 0.6468 (mpp) cc_final: 0.5559 (ptm) REVERT: D 401 ASN cc_start: 0.8435 (m110) cc_final: 0.8114 (m-40) REVERT: D 449 MET cc_start: 0.7737 (mmm) cc_final: 0.7465 (tpp) REVERT: D 560 ARG cc_start: 0.7791 (ttt-90) cc_final: 0.7578 (ttt-90) REVERT: D 678 MET cc_start: 0.7802 (mmp) cc_final: 0.7578 (mmp) REVERT: E 221 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6950 (tp30) REVERT: E 254 ILE cc_start: 0.7645 (mt) cc_final: 0.7307 (mt) REVERT: E 401 ASN cc_start: 0.8305 (m-40) cc_final: 0.8026 (m-40) REVERT: E 504 LEU cc_start: 0.8290 (pp) cc_final: 0.8084 (pp) REVERT: E 669 ASP cc_start: 0.6135 (p0) cc_final: 0.5858 (p0) REVERT: E 686 ASP cc_start: 0.6580 (t0) cc_final: 0.6344 (t0) REVERT: E 689 GLU cc_start: 0.6683 (mp0) cc_final: 0.6363 (mp0) REVERT: E 744 ARG cc_start: 0.7413 (mtp85) cc_final: 0.6932 (mtp-110) REVERT: F 315 LYS cc_start: 0.7944 (tptt) cc_final: 0.6851 (mmmt) REVERT: F 327 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7617 (tp-100) REVERT: F 401 ASN cc_start: 0.8317 (m-40) cc_final: 0.7955 (m-40) REVERT: F 442 MET cc_start: 0.6427 (mpp) cc_final: 0.5405 (ptm) REVERT: F 620 ILE cc_start: 0.8801 (mt) cc_final: 0.8572 (mt) REVERT: F 671 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6402 (p0) REVERT: F 733 ARG cc_start: 0.6812 (ptt90) cc_final: 0.5768 (tpp-160) REVERT: G 327 GLN cc_start: 0.7748 (tp-100) cc_final: 0.7299 (tp-100) REVERT: G 401 ASN cc_start: 0.8415 (m110) cc_final: 0.8108 (m-40) REVERT: G 449 MET cc_start: 0.7712 (mmm) cc_final: 0.7438 (tpp) REVERT: H 560 ARG cc_start: 0.7463 (ttt90) cc_final: 0.7169 (ttt-90) REVERT: H 766 ARG cc_start: 0.5776 (mmt90) cc_final: 0.5551 (mmt-90) REVERT: I 442 MET cc_start: 0.6304 (mpp) cc_final: 0.5448 (ptm) REVERT: I 613 THR cc_start: 0.7087 (p) cc_final: 0.6753 (p) REVERT: I 689 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: I 733 ARG cc_start: 0.6836 (ptt90) cc_final: 0.5798 (tpp-160) REVERT: J 221 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7386 (tp30) REVERT: J 327 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7302 (tp-100) REVERT: J 365 ARG cc_start: 0.7329 (mmm160) cc_final: 0.7032 (mmt90) REVERT: J 449 MET cc_start: 0.7724 (mmm) cc_final: 0.7464 (tpp) REVERT: J 491 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7235 (tp30) REVERT: J 679 THR cc_start: 0.7701 (p) cc_final: 0.7462 (p) REVERT: K 254 ILE cc_start: 0.7682 (mt) cc_final: 0.7375 (mt) REVERT: K 560 ARG cc_start: 0.7518 (ttt-90) cc_final: 0.7280 (ttt-90) REVERT: L 327 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7631 (tp-100) REVERT: L 397 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5935 (mm-30) REVERT: L 442 MET cc_start: 0.6447 (mpp) cc_final: 0.5525 (ptm) REVERT: L 613 THR cc_start: 0.7054 (p) cc_final: 0.6730 (p) REVERT: L 733 ARG cc_start: 0.6851 (ptt90) cc_final: 0.5793 (tpp-160) outliers start: 112 outliers final: 90 residues processed: 965 average time/residue: 0.6841 time to fit residues: 1049.1153 Evaluate side-chains 952 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 860 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 671 ASP Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 526 LEU Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain G residue 699 ILE Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 509 THR Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain J residue 749 ASP Chi-restraints excluded: chain K residue 320 VAL Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 556 GLU Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 320 VAL Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 629 ILE Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 8.9990 chunk 609 optimal weight: 0.0870 chunk 556 optimal weight: 4.9990 chunk 592 optimal weight: 8.9990 chunk 356 optimal weight: 0.9990 chunk 258 optimal weight: 0.0270 chunk 465 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 535 optimal weight: 2.9990 chunk 560 optimal weight: 2.9990 chunk 590 optimal weight: 0.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN J 602 ASN L 401 ASN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 52668 Z= 0.183 Angle : 0.560 9.645 70932 Z= 0.286 Chirality : 0.045 0.285 7896 Planarity : 0.004 0.061 9384 Dihedral : 4.563 20.931 7152 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.98 % Allowed : 18.54 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6516 helix: 0.44 (0.09), residues: 3636 sheet: -0.98 (0.27), residues: 408 loop : -1.05 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 454 HIS 0.002 0.000 HIS A 317 PHE 0.020 0.001 PHE J 618 TYR 0.025 0.001 TYR L 244 ARG 0.012 0.000 ARG H 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 908 time to evaluate : 5.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7759 (mmm) cc_final: 0.7479 (tpp) REVERT: A 740 MET cc_start: 0.7387 (tpt) cc_final: 0.7028 (tpt) REVERT: B 254 ILE cc_start: 0.7639 (mt) cc_final: 0.7301 (mt) REVERT: B 504 LEU cc_start: 0.8297 (pp) cc_final: 0.8089 (pp) REVERT: B 762 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7047 (mp) REVERT: C 315 LYS cc_start: 0.7894 (tptt) cc_final: 0.6886 (mmmt) REVERT: C 327 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7783 (tp-100) REVERT: C 442 MET cc_start: 0.6469 (mpp) cc_final: 0.5564 (ptm) REVERT: D 332 MET cc_start: 0.7345 (mtp) cc_final: 0.7133 (mtp) REVERT: D 401 ASN cc_start: 0.8441 (m110) cc_final: 0.8094 (m-40) REVERT: D 449 MET cc_start: 0.7771 (mmm) cc_final: 0.7500 (tpp) REVERT: D 483 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6273 (mt-10) REVERT: D 560 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7571 (ttt-90) REVERT: D 678 MET cc_start: 0.7808 (mmp) cc_final: 0.7584 (mmp) REVERT: E 221 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7041 (tp30) REVERT: E 254 ILE cc_start: 0.7650 (mt) cc_final: 0.7301 (mt) REVERT: E 261 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6827 (mp0) REVERT: E 281 GLU cc_start: 0.6734 (pm20) cc_final: 0.6316 (pm20) REVERT: E 401 ASN cc_start: 0.8351 (m-40) cc_final: 0.7941 (m-40) REVERT: E 402 GLU cc_start: 0.6512 (pt0) cc_final: 0.6284 (pt0) REVERT: E 504 LEU cc_start: 0.8284 (pp) cc_final: 0.8061 (pp) REVERT: E 669 ASP cc_start: 0.6143 (p0) cc_final: 0.5871 (p0) REVERT: E 686 ASP cc_start: 0.6587 (t0) cc_final: 0.6205 (t0) REVERT: E 744 ARG cc_start: 0.7402 (mtp85) cc_final: 0.6834 (mtp-110) REVERT: F 315 LYS cc_start: 0.7954 (tptt) cc_final: 0.6845 (mmmt) REVERT: F 327 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7638 (tp-100) REVERT: F 401 ASN cc_start: 0.8308 (m-40) cc_final: 0.7941 (m-40) REVERT: F 620 ILE cc_start: 0.8805 (mt) cc_final: 0.8579 (mt) REVERT: F 671 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6347 (p0) REVERT: F 733 ARG cc_start: 0.6807 (ptt90) cc_final: 0.5779 (tpp-160) REVERT: G 327 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7348 (tp-100) REVERT: G 401 ASN cc_start: 0.8419 (m110) cc_final: 0.8091 (m-40) REVERT: G 449 MET cc_start: 0.7705 (mmm) cc_final: 0.7430 (tpp) REVERT: G 502 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7996 (mmtt) REVERT: H 402 GLU cc_start: 0.6740 (pt0) cc_final: 0.6400 (pt0) REVERT: H 669 ASP cc_start: 0.6395 (p0) cc_final: 0.6121 (p0) REVERT: I 442 MET cc_start: 0.6297 (mpp) cc_final: 0.5053 (ppp) REVERT: I 613 THR cc_start: 0.7091 (p) cc_final: 0.6741 (p) REVERT: I 689 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5881 (mp0) REVERT: I 733 ARG cc_start: 0.6802 (ptt90) cc_final: 0.5787 (tpp-160) REVERT: J 221 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7339 (tp30) REVERT: J 315 LYS cc_start: 0.7328 (tppt) cc_final: 0.6855 (mmmt) REVERT: J 327 GLN cc_start: 0.7732 (tp-100) cc_final: 0.7320 (tp-100) REVERT: J 365 ARG cc_start: 0.7334 (mmm160) cc_final: 0.7030 (mmt90) REVERT: J 449 MET cc_start: 0.7798 (mmm) cc_final: 0.7505 (tpp) REVERT: J 491 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7131 (tp30) REVERT: J 679 THR cc_start: 0.7867 (p) cc_final: 0.7606 (p) REVERT: K 254 ILE cc_start: 0.7668 (mt) cc_final: 0.7364 (mt) REVERT: K 766 ARG cc_start: 0.6149 (mmt-90) cc_final: 0.5806 (mmt90) REVERT: L 327 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7630 (tp-100) REVERT: L 402 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: L 442 MET cc_start: 0.6450 (mpp) cc_final: 0.5453 (ptm) REVERT: L 613 THR cc_start: 0.7064 (p) cc_final: 0.6728 (p) REVERT: L 733 ARG cc_start: 0.6838 (ptt90) cc_final: 0.5789 (tpp-160) outliers start: 109 outliers final: 95 residues processed: 967 average time/residue: 0.6850 time to fit residues: 1061.6769 Evaluate side-chains 973 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 874 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 556 GLU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 671 ASP Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 526 LEU Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 478 ASP Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 509 THR Chi-restraints excluded: chain J residue 526 LEU Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 633 ILE Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain K residue 320 VAL Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 556 GLU Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 320 VAL Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 629 ILE Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 0.0980 chunk 626 optimal weight: 1.9990 chunk 382 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 435 optimal weight: 3.9990 chunk 657 optimal weight: 0.7980 chunk 605 optimal weight: 10.0000 chunk 523 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 404 optimal weight: 8.9990 chunk 321 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN D 296 ASN E 750 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 ASN L 558 ASN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 52668 Z= 0.206 Angle : 0.573 9.462 70932 Z= 0.292 Chirality : 0.045 0.266 7896 Planarity : 0.004 0.061 9384 Dihedral : 4.575 21.081 7152 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.94 % Allowed : 18.97 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 6516 helix: 0.44 (0.09), residues: 3624 sheet: -0.95 (0.27), residues: 408 loop : -1.05 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 454 HIS 0.002 0.000 HIS I 226 PHE 0.018 0.001 PHE J 618 TYR 0.025 0.001 TYR L 244 ARG 0.010 0.000 ARG H 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13032 Ramachandran restraints generated. 6516 Oldfield, 0 Emsley, 6516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 895 time to evaluate : 5.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.7531 (tppt) cc_final: 0.7201 (tptt) REVERT: A 449 MET cc_start: 0.7796 (mmm) cc_final: 0.7459 (tpp) REVERT: A 740 MET cc_start: 0.7411 (tpt) cc_final: 0.7043 (tpt) REVERT: B 254 ILE cc_start: 0.7674 (mt) cc_final: 0.7348 (mt) REVERT: B 504 LEU cc_start: 0.8319 (pp) cc_final: 0.8100 (pp) REVERT: B 762 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7032 (mp) REVERT: C 315 LYS cc_start: 0.7960 (tptt) cc_final: 0.6910 (mmmt) REVERT: C 327 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7802 (tp-100) REVERT: C 550 MET cc_start: 0.7753 (mtm) cc_final: 0.7543 (mtp) REVERT: D 315 LYS cc_start: 0.7392 (tppt) cc_final: 0.7011 (tptt) REVERT: D 401 ASN cc_start: 0.8453 (m110) cc_final: 0.8101 (m-40) REVERT: D 449 MET cc_start: 0.7850 (mmm) cc_final: 0.7520 (tpp) REVERT: D 483 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6345 (mt-10) REVERT: D 560 ARG cc_start: 0.7784 (ttt-90) cc_final: 0.7559 (ttt-90) REVERT: D 678 MET cc_start: 0.7787 (mmp) cc_final: 0.7580 (mmp) REVERT: E 221 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7082 (tp30) REVERT: E 254 ILE cc_start: 0.7691 (mt) cc_final: 0.7343 (mt) REVERT: E 261 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6853 (mp0) REVERT: E 281 GLU cc_start: 0.6746 (pm20) cc_final: 0.6315 (pm20) REVERT: E 401 ASN cc_start: 0.8399 (m-40) cc_final: 0.8014 (m-40) REVERT: E 504 LEU cc_start: 0.8222 (pp) cc_final: 0.8006 (pp) REVERT: E 669 ASP cc_start: 0.6154 (p0) cc_final: 0.5887 (p0) REVERT: E 686 ASP cc_start: 0.6498 (t0) cc_final: 0.6293 (t0) REVERT: E 756 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7239 (mt-10) REVERT: F 315 LYS cc_start: 0.7971 (tptt) cc_final: 0.6874 (mmmt) REVERT: F 327 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7643 (tp-100) REVERT: F 401 ASN cc_start: 0.8331 (m-40) cc_final: 0.7939 (m-40) REVERT: F 442 MET cc_start: 0.6228 (mpp) cc_final: 0.5409 (ptm) REVERT: F 620 ILE cc_start: 0.8892 (mt) cc_final: 0.8685 (mt) REVERT: F 671 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6370 (p0) REVERT: F 733 ARG cc_start: 0.6801 (ptt90) cc_final: 0.5767 (tpp-160) REVERT: G 327 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7351 (tp-100) REVERT: G 401 ASN cc_start: 0.8430 (m110) cc_final: 0.8098 (m-40) REVERT: G 449 MET cc_start: 0.7732 (mmm) cc_final: 0.7421 (tpp) REVERT: H 669 ASP cc_start: 0.6413 (p0) cc_final: 0.6158 (p0) REVERT: I 220 VAL cc_start: 0.8896 (p) cc_final: 0.8677 (p) REVERT: I 613 THR cc_start: 0.7090 (p) cc_final: 0.6769 (p) REVERT: I 689 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5885 (mp0) REVERT: I 733 ARG cc_start: 0.6817 (ptt90) cc_final: 0.5785 (tpp-160) REVERT: J 315 LYS cc_start: 0.7512 (tppt) cc_final: 0.6964 (mmmt) REVERT: J 327 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7355 (tp-100) REVERT: J 449 MET cc_start: 0.7754 (mmm) cc_final: 0.7404 (tpp) REVERT: J 491 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7200 (tp30) REVERT: K 254 ILE cc_start: 0.7713 (mt) cc_final: 0.7415 (mt) REVERT: K 756 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7294 (mt-10) REVERT: L 220 VAL cc_start: 0.8865 (p) cc_final: 0.8648 (p) REVERT: L 327 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7659 (tp-100) REVERT: L 401 ASN cc_start: 0.8452 (m-40) cc_final: 0.8041 (m-40) REVERT: L 402 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: L 613 THR cc_start: 0.7082 (p) cc_final: 0.6725 (p) REVERT: L 733 ARG cc_start: 0.6834 (ptt90) cc_final: 0.5798 (tpp-160) outliers start: 107 outliers final: 92 residues processed: 955 average time/residue: 0.6177 time to fit residues: 937.4507 Evaluate side-chains 965 residues out of total 5508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 869 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 556 GLU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 671 ASP Chi-restraints excluded: chain F residue 683 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 600 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 683 SER Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain I residue 572 CYS Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 683 SER Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 478 ASP Chi-restraints excluded: chain J residue 504 LEU Chi-restraints excluded: chain J residue 509 THR Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 633 ILE Chi-restraints excluded: chain J residue 683 SER Chi-restraints excluded: chain K residue 320 VAL Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 556 GLU Chi-restraints excluded: chain K residue 623 THR Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 320 VAL Chi-restraints excluded: chain L residue 394 VAL Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 492 LEU Chi-restraints excluded: chain L residue 572 CYS Chi-restraints excluded: chain L residue 623 THR Chi-restraints excluded: chain L residue 629 ILE Chi-restraints excluded: chain L residue 683 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 6.9990 chunk 557 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 482 optimal weight: 0.0770 chunk 77 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 524 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 538 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN E 384 HIS E 760 GLN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN G 533 ASN J 533 ASN ** L 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.195361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167463 restraints weight = 55323.604| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.96 r_work: 0.3771 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 52668 Z= 0.178 Angle : 0.559 9.233 70932 Z= 0.285 Chirality : 0.044 0.263 7896 Planarity : 0.004 0.060 9384 Dihedral : 4.510 20.702 7152 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.89 % Allowed : 19.19 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 6516 helix: 0.50 (0.09), residues: 3624 sheet: -0.89 (0.27), residues: 408 loop : -1.00 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 454 HIS 0.002 0.000 HIS J 317 PHE 0.024 0.001 PHE H 768 TYR 0.025 0.001 TYR L 244 ARG 0.011 0.000 ARG J 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15826.74 seconds wall clock time: 281 minutes 16.91 seconds (16876.91 seconds total)