Starting phenix.real_space_refine on Mon Mar 25 17:45:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/03_2024/7alw_11820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/03_2024/7alw_11820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/03_2024/7alw_11820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/03_2024/7alw_11820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/03_2024/7alw_11820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/03_2024/7alw_11820.pdb" } resolution = 3.7 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= 0.002 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 162 5.16 5 C 31968 2.51 5 N 8442 2.21 5 O 9576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 623": "NH1" <-> "NH2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 392": "OD1" <-> "OD2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C GLU 531": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C GLU 571": "OE1" <-> "OE2" Residue "C PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ARG 623": "NH1" <-> "NH2" Residue "C GLU 639": "OE1" <-> "OE2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D GLU 424": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 517": "OE1" <-> "OE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D GLU 531": "OE1" <-> "OE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D ARG 563": "NH1" <-> "NH2" Residue "D GLU 571": "OE1" <-> "OE2" Residue "D PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D ARG 623": "NH1" <-> "NH2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 392": "OD1" <-> "OD2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "E GLU 424": "OE1" <-> "OE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 480": "OE1" <-> "OE2" Residue "E PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 517": "OE1" <-> "OE2" Residue "E GLU 526": "OE1" <-> "OE2" Residue "E GLU 531": "OE1" <-> "OE2" Residue "E GLU 555": "OE1" <-> "OE2" Residue "E ARG 563": "NH1" <-> "NH2" Residue "E GLU 571": "OE1" <-> "OE2" Residue "E PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E ARG 619": "NH1" <-> "NH2" Residue "E ARG 623": "NH1" <-> "NH2" Residue "E GLU 639": "OE1" <-> "OE2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 392": "OD1" <-> "OD2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F GLU 424": "OE1" <-> "OE2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 480": "OE1" <-> "OE2" Residue "F PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 517": "OE1" <-> "OE2" Residue "F GLU 526": "OE1" <-> "OE2" Residue "F GLU 531": "OE1" <-> "OE2" Residue "F GLU 555": "OE1" <-> "OE2" Residue "F ARG 563": "NH1" <-> "NH2" Residue "F GLU 571": "OE1" <-> "OE2" Residue "F PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 613": "OE1" <-> "OE2" Residue "F ARG 619": "NH1" <-> "NH2" Residue "F ARG 623": "NH1" <-> "NH2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 392": "OD1" <-> "OD2" Residue "G ARG 399": "NH1" <-> "NH2" Residue "G GLU 424": "OE1" <-> "OE2" Residue "G GLU 438": "OE1" <-> "OE2" Residue "G PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 480": "OE1" <-> "OE2" Residue "G PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 517": "OE1" <-> "OE2" Residue "G GLU 526": "OE1" <-> "OE2" Residue "G GLU 531": "OE1" <-> "OE2" Residue "G GLU 555": "OE1" <-> "OE2" Residue "G ARG 563": "NH1" <-> "NH2" Residue "G GLU 571": "OE1" <-> "OE2" Residue "G PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 613": "OE1" <-> "OE2" Residue "G ARG 619": "NH1" <-> "NH2" Residue "G ARG 623": "NH1" <-> "NH2" Residue "G GLU 639": "OE1" <-> "OE2" Residue "G ARG 672": "NH1" <-> "NH2" Residue "G TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 392": "OD1" <-> "OD2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "H GLU 424": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 480": "OE1" <-> "OE2" Residue "H PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 517": "OE1" <-> "OE2" Residue "H GLU 526": "OE1" <-> "OE2" Residue "H GLU 531": "OE1" <-> "OE2" Residue "H GLU 555": "OE1" <-> "OE2" Residue "H ARG 563": "NH1" <-> "NH2" Residue "H GLU 571": "OE1" <-> "OE2" Residue "H PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 613": "OE1" <-> "OE2" Residue "H ARG 619": "NH1" <-> "NH2" Residue "H ARG 623": "NH1" <-> "NH2" Residue "H GLU 639": "OE1" <-> "OE2" Residue "H ARG 672": "NH1" <-> "NH2" Residue "H TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 392": "OD1" <-> "OD2" Residue "I ARG 399": "NH1" <-> "NH2" Residue "I GLU 424": "OE1" <-> "OE2" Residue "I GLU 438": "OE1" <-> "OE2" Residue "I PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 480": "OE1" <-> "OE2" Residue "I PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 517": "OE1" <-> "OE2" Residue "I GLU 526": "OE1" <-> "OE2" Residue "I GLU 531": "OE1" <-> "OE2" Residue "I GLU 555": "OE1" <-> "OE2" Residue "I ARG 563": "NH1" <-> "NH2" Residue "I GLU 571": "OE1" <-> "OE2" Residue "I PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 613": "OE1" <-> "OE2" Residue "I ARG 619": "NH1" <-> "NH2" Residue "I ARG 623": "NH1" <-> "NH2" Residue "I GLU 639": "OE1" <-> "OE2" Residue "I ARG 672": "NH1" <-> "NH2" Residue "I TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 392": "OD1" <-> "OD2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J GLU 424": "OE1" <-> "OE2" Residue "J GLU 438": "OE1" <-> "OE2" Residue "J PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 480": "OE1" <-> "OE2" Residue "J PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 517": "OE1" <-> "OE2" Residue "J GLU 526": "OE1" <-> "OE2" Residue "J GLU 531": "OE1" <-> "OE2" Residue "J GLU 555": "OE1" <-> "OE2" Residue "J ARG 563": "NH1" <-> "NH2" Residue "J GLU 571": "OE1" <-> "OE2" Residue "J PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 613": "OE1" <-> "OE2" Residue "J ARG 619": "NH1" <-> "NH2" Residue "J ARG 623": "NH1" <-> "NH2" Residue "J GLU 639": "OE1" <-> "OE2" Residue "J ARG 672": "NH1" <-> "NH2" Residue "J TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 392": "OD1" <-> "OD2" Residue "K ARG 399": "NH1" <-> "NH2" Residue "K GLU 424": "OE1" <-> "OE2" Residue "K GLU 438": "OE1" <-> "OE2" Residue "K PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 480": "OE1" <-> "OE2" Residue "K PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 517": "OE1" <-> "OE2" Residue "K GLU 526": "OE1" <-> "OE2" Residue "K GLU 531": "OE1" <-> "OE2" Residue "K GLU 555": "OE1" <-> "OE2" Residue "K ARG 563": "NH1" <-> "NH2" Residue "K GLU 571": "OE1" <-> "OE2" Residue "K PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 613": "OE1" <-> "OE2" Residue "K ARG 619": "NH1" <-> "NH2" Residue "K ARG 623": "NH1" <-> "NH2" Residue "K GLU 639": "OE1" <-> "OE2" Residue "K ARG 672": "NH1" <-> "NH2" Residue "K TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 392": "OD1" <-> "OD2" Residue "L ARG 399": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L GLU 438": "OE1" <-> "OE2" Residue "L PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 480": "OE1" <-> "OE2" Residue "L PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 517": "OE1" <-> "OE2" Residue "L GLU 526": "OE1" <-> "OE2" Residue "L GLU 531": "OE1" <-> "OE2" Residue "L GLU 555": "OE1" <-> "OE2" Residue "L ARG 563": "NH1" <-> "NH2" Residue "L GLU 571": "OE1" <-> "OE2" Residue "L PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 613": "OE1" <-> "OE2" Residue "L ARG 619": "NH1" <-> "NH2" Residue "L ARG 623": "NH1" <-> "NH2" Residue "L GLU 639": "OE1" <-> "OE2" Residue "L ARG 672": "NH1" <-> "NH2" Residue "L TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 392": "OD1" <-> "OD2" Residue "M ARG 399": "NH1" <-> "NH2" Residue "M GLU 424": "OE1" <-> "OE2" Residue "M GLU 438": "OE1" <-> "OE2" Residue "M PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 480": "OE1" <-> "OE2" Residue "M PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 517": "OE1" <-> "OE2" Residue "M GLU 526": "OE1" <-> "OE2" Residue "M GLU 531": "OE1" <-> "OE2" Residue "M GLU 555": "OE1" <-> "OE2" Residue "M ARG 563": "NH1" <-> "NH2" Residue "M GLU 571": "OE1" <-> "OE2" Residue "M PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 613": "OE1" <-> "OE2" Residue "M ARG 619": "NH1" <-> "NH2" Residue "M ARG 623": "NH1" <-> "NH2" Residue "M GLU 639": "OE1" <-> "OE2" Residue "M ARG 672": "NH1" <-> "NH2" Residue "M TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 392": "OD1" <-> "OD2" Residue "N ARG 399": "NH1" <-> "NH2" Residue "N GLU 424": "OE1" <-> "OE2" Residue "N GLU 438": "OE1" <-> "OE2" Residue "N PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 480": "OE1" <-> "OE2" Residue "N PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 517": "OE1" <-> "OE2" Residue "N GLU 526": "OE1" <-> "OE2" Residue "N GLU 531": "OE1" <-> "OE2" Residue "N GLU 555": "OE1" <-> "OE2" Residue "N ARG 563": "NH1" <-> "NH2" Residue "N GLU 571": "OE1" <-> "OE2" Residue "N PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 613": "OE1" <-> "OE2" Residue "N ARG 619": "NH1" <-> "NH2" Residue "N ARG 623": "NH1" <-> "NH2" Residue "N GLU 639": "OE1" <-> "OE2" Residue "N ARG 672": "NH1" <-> "NH2" Residue "N TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 392": "OD1" <-> "OD2" Residue "O ARG 399": "NH1" <-> "NH2" Residue "O GLU 424": "OE1" <-> "OE2" Residue "O GLU 438": "OE1" <-> "OE2" Residue "O PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 480": "OE1" <-> "OE2" Residue "O PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 517": "OE1" <-> "OE2" Residue "O GLU 526": "OE1" <-> "OE2" Residue "O GLU 531": "OE1" <-> "OE2" Residue "O GLU 555": "OE1" <-> "OE2" Residue "O ARG 563": "NH1" <-> "NH2" Residue "O GLU 571": "OE1" <-> "OE2" Residue "O PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 613": "OE1" <-> "OE2" Residue "O ARG 619": "NH1" <-> "NH2" Residue "O ARG 623": "NH1" <-> "NH2" Residue "O GLU 639": "OE1" <-> "OE2" Residue "O ARG 672": "NH1" <-> "NH2" Residue "O TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 392": "OD1" <-> "OD2" Residue "P ARG 399": "NH1" <-> "NH2" Residue "P GLU 424": "OE1" <-> "OE2" Residue "P GLU 438": "OE1" <-> "OE2" Residue "P PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 480": "OE1" <-> "OE2" Residue "P PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 517": "OE1" <-> "OE2" Residue "P GLU 526": "OE1" <-> "OE2" Residue "P GLU 531": "OE1" <-> "OE2" Residue "P GLU 555": "OE1" <-> "OE2" Residue "P ARG 563": "NH1" <-> "NH2" Residue "P GLU 571": "OE1" <-> "OE2" Residue "P PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 613": "OE1" <-> "OE2" Residue "P ARG 619": "NH1" <-> "NH2" Residue "P ARG 623": "NH1" <-> "NH2" Residue "P GLU 639": "OE1" <-> "OE2" Residue "P ARG 672": "NH1" <-> "NH2" Residue "P TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 392": "OD1" <-> "OD2" Residue "Q ARG 399": "NH1" <-> "NH2" Residue "Q GLU 424": "OE1" <-> "OE2" Residue "Q GLU 438": "OE1" <-> "OE2" Residue "Q PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 480": "OE1" <-> "OE2" Residue "Q PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 517": "OE1" <-> "OE2" Residue "Q GLU 526": "OE1" <-> "OE2" Residue "Q GLU 531": "OE1" <-> "OE2" Residue "Q GLU 555": "OE1" <-> "OE2" Residue "Q ARG 563": "NH1" <-> "NH2" Residue "Q GLU 571": "OE1" <-> "OE2" Residue "Q PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 613": "OE1" <-> "OE2" Residue "Q ARG 619": "NH1" <-> "NH2" Residue "Q ARG 623": "NH1" <-> "NH2" Residue "Q GLU 639": "OE1" <-> "OE2" Residue "Q ARG 672": "NH1" <-> "NH2" Residue "Q TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 392": "OD1" <-> "OD2" Residue "R ARG 399": "NH1" <-> "NH2" Residue "R GLU 424": "OE1" <-> "OE2" Residue "R GLU 438": "OE1" <-> "OE2" Residue "R PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 480": "OE1" <-> "OE2" Residue "R PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 517": "OE1" <-> "OE2" Residue "R GLU 526": "OE1" <-> "OE2" Residue "R GLU 531": "OE1" <-> "OE2" Residue "R GLU 555": "OE1" <-> "OE2" Residue "R ARG 563": "NH1" <-> "NH2" Residue "R GLU 571": "OE1" <-> "OE2" Residue "R PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 613": "OE1" <-> "OE2" Residue "R ARG 619": "NH1" <-> "NH2" Residue "R ARG 623": "NH1" <-> "NH2" Residue "R GLU 639": "OE1" <-> "OE2" Residue "R ARG 672": "NH1" <-> "NH2" Residue "R TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50148 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 25.05, per 1000 atoms: 0.50 Number of scatterers: 50148 At special positions: 0 Unit cell: (188.238, 189.882, 132.342, 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 162 16.00 O 9576 8.00 N 8442 7.00 C 31968 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: 18.17 Conformation dependent library (CDL) restraints added in 8.9 seconds 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11592 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 72 sheets defined 45.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE A 533 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG A 672 " --> pdb=" O ARG A 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU B 497 " --> pdb=" O HIS B 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE B 533 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 555 " --> pdb=" O ARG B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA B 568 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU B 615 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG B 672 " --> pdb=" O ARG B 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU C 481 " --> pdb=" O VAL C 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU C 497 " --> pdb=" O HIS C 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR C 520 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE C 533 " --> pdb=" O TYR C 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG C 538 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 555 " --> pdb=" O ARG C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA C 568 " --> pdb=" O SER C 564 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU C 615 " --> pdb=" O ASP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 621 No H-bonds generated for 'chain 'C' and resid 619 through 621' Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 664 through 666 No H-bonds generated for 'chain 'C' and resid 664 through 666' Processing helix chain 'C' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG C 672 " --> pdb=" O ARG C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU D 481 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU D 497 " --> pdb=" O HIS D 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS D 500 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE D 533 " --> pdb=" O TYR D 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU D 555 " --> pdb=" O ARG D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA D 568 " --> pdb=" O SER D 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU D 615 " --> pdb=" O ASP D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 637 through 649 Processing helix chain 'D' and resid 664 through 666 No H-bonds generated for 'chain 'D' and resid 664 through 666' Processing helix chain 'D' and resid 667 through 676 removed outlier: 3.527A pdb=" N ARG D 672 " --> pdb=" O ARG D 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP E 404 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU E 481 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG E 482 " --> pdb=" O GLU E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU E 497 " --> pdb=" O HIS E 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS E 500 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG E 506 " --> pdb=" O SER E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG E 519 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR E 520 " --> pdb=" O GLN E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE E 533 " --> pdb=" O TYR E 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG E 538 " --> pdb=" O LYS E 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 539 " --> pdb=" O GLU E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG E 551 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU E 555 " --> pdb=" O ARG E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA E 568 " --> pdb=" O SER E 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP E 572 " --> pdb=" O ALA E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR E 596 " --> pdb=" O ARG E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU E 615 " --> pdb=" O ASP E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 621 No H-bonds generated for 'chain 'E' and resid 619 through 621' Processing helix chain 'E' and resid 637 through 649 Processing helix chain 'E' and resid 664 through 666 No H-bonds generated for 'chain 'E' and resid 664 through 666' Processing helix chain 'E' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG E 672 " --> pdb=" O ARG E 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP F 404 " --> pdb=" O ALA F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU F 481 " --> pdb=" O VAL F 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU F 497 " --> pdb=" O HIS F 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS F 500 " --> pdb=" O VAL F 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG F 506 " --> pdb=" O SER F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG F 519 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR F 520 " --> pdb=" O GLN F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE F 533 " --> pdb=" O TYR F 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG F 538 " --> pdb=" O LYS F 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 555 removed outlier: 3.875A pdb=" N ARG F 551 " --> pdb=" O GLU F 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 555 " --> pdb=" O ARG F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA F 568 " --> pdb=" O SER F 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP F 572 " --> pdb=" O ALA F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR F 596 " --> pdb=" O ARG F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU F 615 " --> pdb=" O ASP F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 637 through 649 Processing helix chain 'F' and resid 664 through 666 No H-bonds generated for 'chain 'F' and resid 664 through 666' Processing helix chain 'F' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG F 672 " --> pdb=" O ARG F 668 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL G 397 " --> pdb=" O GLU G 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP G 404 " --> pdb=" O ALA G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 458 Processing helix chain 'G' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU G 481 " --> pdb=" O VAL G 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG G 482 " --> pdb=" O GLU G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU G 497 " --> pdb=" O HIS G 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS G 500 " --> pdb=" O VAL G 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 506 " --> pdb=" O SER G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG G 519 " --> pdb=" O ILE G 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR G 520 " --> pdb=" O GLN G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE G 533 " --> pdb=" O TYR G 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG G 538 " --> pdb=" O LYS G 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G 539 " --> pdb=" O GLU G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG G 551 " --> pdb=" O GLU G 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU G 555 " --> pdb=" O ARG G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA G 568 " --> pdb=" O SER G 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP G 572 " --> pdb=" O ALA G 568 " (cutoff:3.500A) Processing helix chain 'G' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR G 596 " --> pdb=" O ARG G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU G 615 " --> pdb=" O ASP G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 621 No H-bonds generated for 'chain 'G' and resid 619 through 621' Processing helix chain 'G' and resid 637 through 649 Processing helix chain 'G' and resid 664 through 666 No H-bonds generated for 'chain 'G' and resid 664 through 666' Processing helix chain 'G' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG G 672 " --> pdb=" O ARG G 668 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL H 397 " --> pdb=" O GLU H 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP H 404 " --> pdb=" O ALA H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 458 Processing helix chain 'H' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU H 481 " --> pdb=" O VAL H 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG H 482 " --> pdb=" O GLU H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU H 497 " --> pdb=" O HIS H 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS H 500 " --> pdb=" O VAL H 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG H 506 " --> pdb=" O SER H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG H 519 " --> pdb=" O ILE H 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR H 520 " --> pdb=" O GLN H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE H 533 " --> pdb=" O TYR H 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG H 538 " --> pdb=" O LYS H 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE H 539 " --> pdb=" O GLU H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG H 551 " --> pdb=" O GLU H 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU H 555 " --> pdb=" O ARG H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA H 568 " --> pdb=" O SER H 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP H 572 " --> pdb=" O ALA H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR H 596 " --> pdb=" O ARG H 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU H 615 " --> pdb=" O ASP H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 621 No H-bonds generated for 'chain 'H' and resid 619 through 621' Processing helix chain 'H' and resid 637 through 649 Processing helix chain 'H' and resid 664 through 666 No H-bonds generated for 'chain 'H' and resid 664 through 666' Processing helix chain 'H' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG H 672 " --> pdb=" O ARG H 668 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL I 397 " --> pdb=" O GLU I 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP I 404 " --> pdb=" O ALA I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 458 Processing helix chain 'I' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU I 481 " --> pdb=" O VAL I 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG I 482 " --> pdb=" O GLU I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU I 497 " --> pdb=" O HIS I 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS I 500 " --> pdb=" O VAL I 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG I 506 " --> pdb=" O SER I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG I 519 " --> pdb=" O ILE I 515 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR I 520 " --> pdb=" O GLN I 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE I 533 " --> pdb=" O TYR I 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG I 538 " --> pdb=" O LYS I 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 539 " --> pdb=" O GLU I 535 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG I 551 " --> pdb=" O GLU I 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU I 555 " --> pdb=" O ARG I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA I 568 " --> pdb=" O SER I 564 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP I 572 " --> pdb=" O ALA I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR I 596 " --> pdb=" O ARG I 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU I 615 " --> pdb=" O ASP I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 621 No H-bonds generated for 'chain 'I' and resid 619 through 621' Processing helix chain 'I' and resid 637 through 649 Processing helix chain 'I' and resid 664 through 666 No H-bonds generated for 'chain 'I' and resid 664 through 666' Processing helix chain 'I' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG I 672 " --> pdb=" O ARG I 668 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL J 397 " --> pdb=" O GLU J 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP J 404 " --> pdb=" O ALA J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU J 481 " --> pdb=" O VAL J 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG J 482 " --> pdb=" O GLU J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU J 497 " --> pdb=" O HIS J 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS J 500 " --> pdb=" O VAL J 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG J 506 " --> pdb=" O SER J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG J 519 " --> pdb=" O ILE J 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR J 520 " --> pdb=" O GLN J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE J 533 " --> pdb=" O TYR J 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG J 538 " --> pdb=" O LYS J 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG J 551 " --> pdb=" O GLU J 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU J 555 " --> pdb=" O ARG J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA J 568 " --> pdb=" O SER J 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP J 572 " --> pdb=" O ALA J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR J 596 " --> pdb=" O ARG J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU J 615 " --> pdb=" O ASP J 611 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 621 No H-bonds generated for 'chain 'J' and resid 619 through 621' Processing helix chain 'J' and resid 637 through 649 Processing helix chain 'J' and resid 664 through 666 No H-bonds generated for 'chain 'J' and resid 664 through 666' Processing helix chain 'J' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG J 672 " --> pdb=" O ARG J 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL K 397 " --> pdb=" O GLU K 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP K 404 " --> pdb=" O ALA K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 458 Processing helix chain 'K' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU K 481 " --> pdb=" O VAL K 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG K 482 " --> pdb=" O GLU K 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU K 497 " --> pdb=" O HIS K 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS K 500 " --> pdb=" O VAL K 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG K 506 " --> pdb=" O SER K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG K 519 " --> pdb=" O ILE K 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR K 520 " --> pdb=" O GLN K 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE K 533 " --> pdb=" O TYR K 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG K 538 " --> pdb=" O LYS K 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE K 539 " --> pdb=" O GLU K 535 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 555 removed outlier: 3.875A pdb=" N ARG K 551 " --> pdb=" O GLU K 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU K 555 " --> pdb=" O ARG K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA K 568 " --> pdb=" O SER K 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP K 572 " --> pdb=" O ALA K 568 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR K 596 " --> pdb=" O ARG K 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU K 615 " --> pdb=" O ASP K 611 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 621 No H-bonds generated for 'chain 'K' and resid 619 through 621' Processing helix chain 'K' and resid 637 through 649 Processing helix chain 'K' and resid 664 through 666 No H-bonds generated for 'chain 'K' and resid 664 through 666' Processing helix chain 'K' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG K 672 " --> pdb=" O ARG K 668 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL L 397 " --> pdb=" O GLU L 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP L 404 " --> pdb=" O ALA L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 458 Processing helix chain 'L' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU L 481 " --> pdb=" O VAL L 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG L 482 " --> pdb=" O GLU L 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU L 497 " --> pdb=" O HIS L 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS L 500 " --> pdb=" O VAL L 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG L 506 " --> pdb=" O SER L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG L 519 " --> pdb=" O ILE L 515 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR L 520 " --> pdb=" O GLN L 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE L 533 " --> pdb=" O TYR L 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG L 538 " --> pdb=" O LYS L 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG L 551 " --> pdb=" O GLU L 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU L 555 " --> pdb=" O ARG L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA L 568 " --> pdb=" O SER L 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP L 572 " --> pdb=" O ALA L 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR L 596 " --> pdb=" O ARG L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU L 615 " --> pdb=" O ASP L 611 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 621 No H-bonds generated for 'chain 'L' and resid 619 through 621' Processing helix chain 'L' and resid 637 through 649 Processing helix chain 'L' and resid 664 through 666 No H-bonds generated for 'chain 'L' and resid 664 through 666' Processing helix chain 'L' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG L 672 " --> pdb=" O ARG L 668 " (cutoff:3.500A) Processing helix chain 'M' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL M 397 " --> pdb=" O GLU M 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP M 404 " --> pdb=" O ALA M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 458 Processing helix chain 'M' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU M 481 " --> pdb=" O VAL M 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG M 482 " --> pdb=" O GLU M 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU M 497 " --> pdb=" O HIS M 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS M 500 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG M 506 " --> pdb=" O SER M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG M 519 " --> pdb=" O ILE M 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR M 520 " --> pdb=" O GLN M 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE M 533 " --> pdb=" O TYR M 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG M 538 " --> pdb=" O LYS M 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG M 551 " --> pdb=" O GLU M 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU M 555 " --> pdb=" O ARG M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA M 568 " --> pdb=" O SER M 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP M 572 " --> pdb=" O ALA M 568 " (cutoff:3.500A) Processing helix chain 'M' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER M 588 " --> pdb=" O GLU M 584 " (cutoff:3.500A) Processing helix chain 'M' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR M 596 " --> pdb=" O ARG M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 611 through 618 removed outlier: 3.732A pdb=" N GLU M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 621 No H-bonds generated for 'chain 'M' and resid 619 through 621' Processing helix chain 'M' and resid 637 through 649 Processing helix chain 'M' and resid 664 through 666 No H-bonds generated for 'chain 'M' and resid 664 through 666' Processing helix chain 'M' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG M 672 " --> pdb=" O ARG M 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 393 through 406 removed outlier: 3.622A pdb=" N VAL N 397 " --> pdb=" O GLU N 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP N 404 " --> pdb=" O ALA N 400 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 458 Processing helix chain 'N' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU N 481 " --> pdb=" O VAL N 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG N 482 " --> pdb=" O GLU N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU N 497 " --> pdb=" O HIS N 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS N 500 " --> pdb=" O VAL N 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG N 506 " --> pdb=" O SER N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG N 519 " --> pdb=" O ILE N 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR N 520 " --> pdb=" O GLN N 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE N 533 " --> pdb=" O TYR N 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG N 538 " --> pdb=" O LYS N 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE N 539 " --> pdb=" O GLU N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG N 551 " --> pdb=" O GLU N 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU N 555 " --> pdb=" O ARG N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA N 568 " --> pdb=" O SER N 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP N 572 " --> pdb=" O ALA N 568 " (cutoff:3.500A) Processing helix chain 'N' and resid 578 through 588 removed outlier: 3.531A pdb=" N SER N 588 " --> pdb=" O GLU N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR N 596 " --> pdb=" O ARG N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU N 615 " --> pdb=" O ASP N 611 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 621 No H-bonds generated for 'chain 'N' and resid 619 through 621' Processing helix chain 'N' and resid 637 through 649 Processing helix chain 'N' and resid 664 through 666 No H-bonds generated for 'chain 'N' and resid 664 through 666' Processing helix chain 'N' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG N 672 " --> pdb=" O ARG N 668 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL O 397 " --> pdb=" O GLU O 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP O 404 " --> pdb=" O ALA O 400 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 458 Processing helix chain 'O' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU O 481 " --> pdb=" O VAL O 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG O 482 " --> pdb=" O GLU O 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU O 497 " --> pdb=" O HIS O 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS O 500 " --> pdb=" O VAL O 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG O 506 " --> pdb=" O SER O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG O 519 " --> pdb=" O ILE O 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR O 520 " --> pdb=" O GLN O 516 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE O 533 " --> pdb=" O TYR O 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG O 538 " --> pdb=" O LYS O 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE O 539 " --> pdb=" O GLU O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG O 551 " --> pdb=" O GLU O 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU O 555 " --> pdb=" O ARG O 551 " (cutoff:3.500A) Processing helix chain 'O' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA O 568 " --> pdb=" O SER O 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP O 572 " --> pdb=" O ALA O 568 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER O 588 " --> pdb=" O GLU O 584 " (cutoff:3.500A) Processing helix chain 'O' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR O 596 " --> pdb=" O ARG O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU O 615 " --> pdb=" O ASP O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 621 No H-bonds generated for 'chain 'O' and resid 619 through 621' Processing helix chain 'O' and resid 637 through 649 Processing helix chain 'O' and resid 664 through 666 No H-bonds generated for 'chain 'O' and resid 664 through 666' Processing helix chain 'O' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG O 672 " --> pdb=" O ARG O 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL P 397 " --> pdb=" O GLU P 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP P 404 " --> pdb=" O ALA P 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 458 Processing helix chain 'P' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU P 481 " --> pdb=" O VAL P 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG P 482 " --> pdb=" O GLU P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU P 497 " --> pdb=" O HIS P 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS P 500 " --> pdb=" O VAL P 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG P 506 " --> pdb=" O SER P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG P 519 " --> pdb=" O ILE P 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR P 520 " --> pdb=" O GLN P 516 " (cutoff:3.500A) Processing helix chain 'P' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE P 533 " --> pdb=" O TYR P 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG P 538 " --> pdb=" O LYS P 534 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE P 539 " --> pdb=" O GLU P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG P 551 " --> pdb=" O GLU P 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU P 555 " --> pdb=" O ARG P 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA P 568 " --> pdb=" O SER P 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP P 572 " --> pdb=" O ALA P 568 " (cutoff:3.500A) Processing helix chain 'P' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER P 588 " --> pdb=" O GLU P 584 " (cutoff:3.500A) Processing helix chain 'P' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR P 596 " --> pdb=" O ARG P 592 " (cutoff:3.500A) Processing helix chain 'P' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU P 615 " --> pdb=" O ASP P 611 " (cutoff:3.500A) Processing helix chain 'P' and resid 619 through 621 No H-bonds generated for 'chain 'P' and resid 619 through 621' Processing helix chain 'P' and resid 637 through 649 Processing helix chain 'P' and resid 664 through 666 No H-bonds generated for 'chain 'P' and resid 664 through 666' Processing helix chain 'P' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG P 672 " --> pdb=" O ARG P 668 " (cutoff:3.500A) Processing helix chain 'Q' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL Q 397 " --> pdb=" O GLU Q 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP Q 404 " --> pdb=" O ALA Q 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 453 through 458 Processing helix chain 'Q' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU Q 481 " --> pdb=" O VAL Q 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG Q 482 " --> pdb=" O GLU Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 508 removed outlier: 3.652A pdb=" N LEU Q 497 " --> pdb=" O HIS Q 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS Q 500 " --> pdb=" O VAL Q 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG Q 506 " --> pdb=" O SER Q 502 " (cutoff:3.500A) Processing helix chain 'Q' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG Q 519 " --> pdb=" O ILE Q 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR Q 520 " --> pdb=" O GLN Q 516 " (cutoff:3.500A) Processing helix chain 'Q' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE Q 533 " --> pdb=" O TYR Q 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG Q 538 " --> pdb=" O LYS Q 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE Q 539 " --> pdb=" O GLU Q 535 " (cutoff:3.500A) Processing helix chain 'Q' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG Q 551 " --> pdb=" O GLU Q 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU Q 555 " --> pdb=" O ARG Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA Q 568 " --> pdb=" O SER Q 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP Q 572 " --> pdb=" O ALA Q 568 " (cutoff:3.500A) Processing helix chain 'Q' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER Q 588 " --> pdb=" O GLU Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR Q 596 " --> pdb=" O ARG Q 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU Q 615 " --> pdb=" O ASP Q 611 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 621 No H-bonds generated for 'chain 'Q' and resid 619 through 621' Processing helix chain 'Q' and resid 637 through 649 Processing helix chain 'Q' and resid 664 through 666 No H-bonds generated for 'chain 'Q' and resid 664 through 666' Processing helix chain 'Q' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG Q 672 " --> pdb=" O ARG Q 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL R 397 " --> pdb=" O GLU R 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP R 404 " --> pdb=" O ALA R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 453 through 458 Processing helix chain 'R' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU R 481 " --> pdb=" O VAL R 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG R 482 " --> pdb=" O GLU R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU R 497 " --> pdb=" O HIS R 493 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS R 500 " --> pdb=" O VAL R 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG R 506 " --> pdb=" O SER R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG R 519 " --> pdb=" O ILE R 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR R 520 " --> pdb=" O GLN R 516 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE R 533 " --> pdb=" O TYR R 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG R 538 " --> pdb=" O LYS R 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE R 539 " --> pdb=" O GLU R 535 " (cutoff:3.500A) Processing helix chain 'R' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG R 551 " --> pdb=" O GLU R 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU R 555 " --> pdb=" O ARG R 551 " (cutoff:3.500A) Processing helix chain 'R' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA R 568 " --> pdb=" O SER R 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP R 572 " --> pdb=" O ALA R 568 " (cutoff:3.500A) Processing helix chain 'R' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER R 588 " --> pdb=" O GLU R 584 " (cutoff:3.500A) Processing helix chain 'R' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR R 596 " --> pdb=" O ARG R 592 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU R 615 " --> pdb=" O ASP R 611 " (cutoff:3.500A) Processing helix chain 'R' and resid 619 through 621 No H-bonds generated for 'chain 'R' and resid 619 through 621' Processing helix chain 'R' and resid 637 through 649 Processing helix chain 'R' and resid 664 through 666 No H-bonds generated for 'chain 'R' and resid 664 through 666' Processing helix chain 'R' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG R 672 " --> pdb=" O ARG R 668 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU A 373 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG A 415 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 375 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN A 417 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL A 377 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A 424 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR A 425 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG A 436 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 427 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG A 447 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 491 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 604 through 605 Processing sheet with id=AA4, first strand: chain 'A' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU A 661 " --> pdb=" O LEU A 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU B 373 " --> pdb=" O HIS B 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG B 415 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 375 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN B 417 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL B 377 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU B 424 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR B 425 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B 436 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 427 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG B 447 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 491 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 604 through 605 Processing sheet with id=AA8, first strand: chain 'B' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU B 661 " --> pdb=" O LEU B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU C 373 " --> pdb=" O HIS C 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG C 415 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE C 375 " --> pdb=" O ARG C 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN C 417 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL C 377 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU C 424 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR C 425 " --> pdb=" O ARG C 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG C 436 " --> pdb=" O TYR C 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 427 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG C 447 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 491 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 604 through 605 Processing sheet with id=AB3, first strand: chain 'C' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU C 661 " --> pdb=" O LEU C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU D 373 " --> pdb=" O HIS D 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG D 415 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 375 " --> pdb=" O ARG D 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 417 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL D 377 " --> pdb=" O ASN D 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU D 424 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR D 425 " --> pdb=" O ARG D 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG D 436 " --> pdb=" O TYR D 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 427 " --> pdb=" O VAL D 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG D 447 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE D 491 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 604 through 605 Processing sheet with id=AB7, first strand: chain 'D' and resid 661 through 662 removed outlier: 6.967A pdb=" N LEU D 661 " --> pdb=" O LEU D 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU E 373 " --> pdb=" O HIS E 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG E 415 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE E 375 " --> pdb=" O ARG E 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN E 417 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL E 377 " --> pdb=" O ASN E 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU E 424 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR E 425 " --> pdb=" O ARG E 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG E 436 " --> pdb=" O TYR E 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 427 " --> pdb=" O VAL E 434 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG E 447 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 491 " --> pdb=" O ARG E 447 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 604 through 605 Processing sheet with id=AC2, first strand: chain 'E' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU E 661 " --> pdb=" O LEU E 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU F 373 " --> pdb=" O HIS F 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG F 415 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE F 375 " --> pdb=" O ARG F 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN F 417 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL F 377 " --> pdb=" O ASN F 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU F 424 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR F 425 " --> pdb=" O ARG F 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 436 " --> pdb=" O TYR F 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE F 427 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG F 447 " --> pdb=" O PHE F 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE F 491 " --> pdb=" O ARG F 447 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 604 through 605 Processing sheet with id=AC6, first strand: chain 'F' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU F 661 " --> pdb=" O LEU F 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU G 373 " --> pdb=" O HIS G 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG G 415 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE G 375 " --> pdb=" O ARG G 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN G 417 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL G 377 " --> pdb=" O ASN G 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU G 424 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR G 425 " --> pdb=" O ARG G 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG G 436 " --> pdb=" O TYR G 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE G 427 " --> pdb=" O VAL G 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG G 447 " --> pdb=" O PHE G 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE G 491 " --> pdb=" O ARG G 447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 604 through 605 Processing sheet with id=AD1, first strand: chain 'G' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU G 661 " --> pdb=" O LEU G 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU H 373 " --> pdb=" O HIS H 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG H 415 " --> pdb=" O LEU H 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE H 375 " --> pdb=" O ARG H 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN H 417 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL H 377 " --> pdb=" O ASN H 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU H 424 " --> pdb=" O ASP H 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR H 425 " --> pdb=" O ARG H 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG H 436 " --> pdb=" O TYR H 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE H 427 " --> pdb=" O VAL H 434 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG H 447 " --> pdb=" O PHE H 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE H 491 " --> pdb=" O ARG H 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 604 through 605 Processing sheet with id=AD5, first strand: chain 'H' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU H 661 " --> pdb=" O LEU H 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU I 373 " --> pdb=" O HIS I 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG I 415 " --> pdb=" O LEU I 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE I 375 " --> pdb=" O ARG I 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN I 417 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL I 377 " --> pdb=" O ASN I 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU I 424 " --> pdb=" O ASP I 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR I 425 " --> pdb=" O ARG I 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG I 436 " --> pdb=" O TYR I 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE I 427 " --> pdb=" O VAL I 434 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG I 447 " --> pdb=" O PHE I 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE I 491 " --> pdb=" O ARG I 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 604 through 605 Processing sheet with id=AD9, first strand: chain 'I' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU I 661 " --> pdb=" O LEU I 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU J 373 " --> pdb=" O HIS J 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG J 415 " --> pdb=" O LEU J 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE J 375 " --> pdb=" O ARG J 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN J 417 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL J 377 " --> pdb=" O ASN J 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU J 424 " --> pdb=" O ASP J 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR J 425 " --> pdb=" O ARG J 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG J 436 " --> pdb=" O TYR J 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE J 427 " --> pdb=" O VAL J 434 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG J 447 " --> pdb=" O PHE J 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE J 491 " --> pdb=" O ARG J 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 604 through 605 Processing sheet with id=AE4, first strand: chain 'J' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU J 661 " --> pdb=" O LEU J 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'K' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU K 373 " --> pdb=" O HIS K 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG K 415 " --> pdb=" O LEU K 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE K 375 " --> pdb=" O ARG K 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN K 417 " --> pdb=" O ILE K 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL K 377 " --> pdb=" O ASN K 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU K 424 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR K 425 " --> pdb=" O ARG K 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG K 436 " --> pdb=" O TYR K 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE K 427 " --> pdb=" O VAL K 434 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG K 447 " --> pdb=" O PHE K 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE K 491 " --> pdb=" O ARG K 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 604 through 605 Processing sheet with id=AE8, first strand: chain 'K' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU K 661 " --> pdb=" O LEU K 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'L' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU L 373 " --> pdb=" O HIS L 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG L 415 " --> pdb=" O LEU L 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE L 375 " --> pdb=" O ARG L 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN L 417 " --> pdb=" O ILE L 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL L 377 " --> pdb=" O ASN L 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU L 424 " --> pdb=" O ASP L 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR L 425 " --> pdb=" O ARG L 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG L 436 " --> pdb=" O TYR L 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE L 427 " --> pdb=" O VAL L 434 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG L 447 " --> pdb=" O PHE L 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE L 491 " --> pdb=" O ARG L 447 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 604 through 605 Processing sheet with id=AF3, first strand: chain 'L' and resid 661 through 662 removed outlier: 6.967A pdb=" N LEU L 661 " --> pdb=" O LEU L 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU M 373 " --> pdb=" O HIS M 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG M 415 " --> pdb=" O LEU M 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE M 375 " --> pdb=" O ARG M 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN M 417 " --> pdb=" O ILE M 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL M 377 " --> pdb=" O ASN M 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU M 424 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR M 425 " --> pdb=" O ARG M 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG M 436 " --> pdb=" O TYR M 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE M 427 " --> pdb=" O VAL M 434 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG M 447 " --> pdb=" O PHE M 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE M 491 " --> pdb=" O ARG M 447 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 604 through 605 Processing sheet with id=AF7, first strand: chain 'M' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU M 661 " --> pdb=" O LEU M 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'N' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU N 373 " --> pdb=" O HIS N 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG N 415 " --> pdb=" O LEU N 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE N 375 " --> pdb=" O ARG N 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN N 417 " --> pdb=" O ILE N 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL N 377 " --> pdb=" O ASN N 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU N 424 " --> pdb=" O ASP N 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR N 425 " --> pdb=" O ARG N 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG N 436 " --> pdb=" O TYR N 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE N 427 " --> pdb=" O VAL N 434 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG N 447 " --> pdb=" O PHE N 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE N 491 " --> pdb=" O ARG N 447 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 604 through 605 Processing sheet with id=AG2, first strand: chain 'N' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU N 661 " --> pdb=" O LEU N 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'O' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU O 373 " --> pdb=" O HIS O 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG O 415 " --> pdb=" O LEU O 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE O 375 " --> pdb=" O ARG O 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN O 417 " --> pdb=" O ILE O 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL O 377 " --> pdb=" O ASN O 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU O 424 " --> pdb=" O ASP O 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR O 425 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG O 436 " --> pdb=" O TYR O 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE O 427 " --> pdb=" O VAL O 434 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG O 447 " --> pdb=" O PHE O 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE O 491 " --> pdb=" O ARG O 447 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 604 through 605 Processing sheet with id=AG6, first strand: chain 'O' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU O 661 " --> pdb=" O LEU O 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'P' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU P 373 " --> pdb=" O HIS P 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG P 415 " --> pdb=" O LEU P 373 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE P 375 " --> pdb=" O ARG P 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN P 417 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL P 377 " --> pdb=" O ASN P 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU P 424 " --> pdb=" O ASP P 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR P 425 " --> pdb=" O ARG P 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG P 436 " --> pdb=" O TYR P 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE P 427 " --> pdb=" O VAL P 434 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG P 447 " --> pdb=" O PHE P 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE P 491 " --> pdb=" O ARG P 447 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 604 through 605 Processing sheet with id=AH1, first strand: chain 'P' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU P 661 " --> pdb=" O LEU P 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'Q' and resid 412 through 417 removed outlier: 7.022A pdb=" N LEU Q 373 " --> pdb=" O HIS Q 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG Q 415 " --> pdb=" O LEU Q 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE Q 375 " --> pdb=" O ARG Q 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN Q 417 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL Q 377 " --> pdb=" O ASN Q 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU Q 424 " --> pdb=" O ASP Q 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR Q 425 " --> pdb=" O ARG Q 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG Q 436 " --> pdb=" O TYR Q 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE Q 427 " --> pdb=" O VAL Q 434 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG Q 447 " --> pdb=" O PHE Q 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE Q 491 " --> pdb=" O ARG Q 447 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 604 through 605 Processing sheet with id=AH5, first strand: chain 'Q' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU Q 661 " --> pdb=" O LEU Q 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'R' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU R 373 " --> pdb=" O HIS R 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG R 415 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE R 375 " --> pdb=" O ARG R 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN R 417 " --> pdb=" O ILE R 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL R 377 " --> pdb=" O ASN R 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU R 424 " --> pdb=" O ASP R 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR R 425 " --> pdb=" O ARG R 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG R 436 " --> pdb=" O TYR R 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE R 427 " --> pdb=" O VAL R 434 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG R 447 " --> pdb=" O PHE R 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE R 491 " --> pdb=" O ARG R 447 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 604 through 605 Processing sheet with id=AH9, first strand: chain 'R' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU R 661 " --> pdb=" O LEU R 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 1584 hydrogen bonds defined for protein. 4698 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: 19.51 Time building geometry restraints manager: 19.76 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: 16786 1.34 - 1.46: 9349 1.46 - 1.57: 24589 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 51012 Sorted by residual: bond pdb=" CB VAL Q 553 " pdb=" CG2 VAL Q 553 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" CB VAL E 553 " pdb=" CG2 VAL E 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB VAL D 553 " pdb=" CG2 VAL D 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB VAL A 553 " pdb=" CG2 VAL A 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB VAL M 553 " pdb=" CG2 VAL M 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 ... (remaining 51007 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.40: 810 105.40 - 112.54: 26379 112.54 - 119.68: 17778 119.68 - 126.82: 23542 126.82 - 133.96: 485 Bond angle restraints: 68994 Sorted by residual: angle pdb=" N ALA D 441 " pdb=" CA ALA D 441 " pdb=" C ALA D 441 " ideal model delta sigma weight residual 113.15 107.90 5.25 1.19e+00 7.06e-01 1.95e+01 angle pdb=" N ALA N 441 " pdb=" CA ALA N 441 " pdb=" C ALA N 441 " ideal model delta sigma weight residual 113.15 107.90 5.25 1.19e+00 7.06e-01 1.95e+01 angle pdb=" N ALA B 441 " pdb=" CA ALA B 441 " pdb=" C ALA B 441 " ideal model delta sigma weight residual 113.15 107.91 5.24 1.19e+00 7.06e-01 1.94e+01 angle pdb=" N ALA P 441 " pdb=" CA ALA P 441 " pdb=" C ALA P 441 " ideal model delta sigma weight residual 113.15 107.92 5.23 1.19e+00 7.06e-01 1.93e+01 angle pdb=" N ALA C 441 " pdb=" CA ALA C 441 " pdb=" C ALA C 441 " ideal model delta sigma weight residual 113.15 107.92 5.23 1.19e+00 7.06e-01 1.93e+01 ... (remaining 68989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 27073 16.90 - 33.80: 3238 33.80 - 50.69: 618 50.69 - 67.59: 139 67.59 - 84.49: 90 Dihedral angle restraints: 31158 sinusoidal: 13068 harmonic: 18090 Sorted by residual: dihedral pdb=" CA LEU J 385 " pdb=" C LEU J 385 " pdb=" N GLU J 386 " pdb=" CA GLU J 386 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU K 385 " pdb=" C LEU K 385 " pdb=" N GLU K 386 " pdb=" CA GLU K 386 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU A 385 " pdb=" C LEU A 385 " pdb=" N GLU A 386 " pdb=" CA GLU A 386 " ideal model delta harmonic sigma weight residual 180.00 137.66 42.34 0 5.00e+00 4.00e-02 7.17e+01 ... (remaining 31155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4416 0.041 - 0.083: 2567 0.083 - 0.124: 601 0.124 - 0.165: 138 0.165 - 0.207: 36 Chirality restraints: 7758 Sorted by residual: chirality pdb=" CA ILE M 458 " pdb=" N ILE M 458 " pdb=" C ILE M 458 " pdb=" CB ILE M 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE Q 458 " pdb=" N ILE Q 458 " pdb=" C ILE Q 458 " pdb=" CB ILE Q 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE D 458 " pdb=" N ILE D 458 " pdb=" C ILE D 458 " pdb=" CB ILE D 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 7755 not shown) Planarity restraints: 8928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 639 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" CD GLU D 639 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU D 639 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 639 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 639 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" CD GLU K 639 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU K 639 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU K 639 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 639 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.09e+00 pdb=" CD GLU C 639 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU C 639 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 639 " 0.009 2.00e-02 2.50e+03 ... (remaining 8925 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3031 2.70 - 3.25: 53341 3.25 - 3.80: 78002 3.80 - 4.35: 100259 4.35 - 4.90: 165771 Nonbonded interactions: 400404 Sorted by model distance: nonbonded pdb=" O LEU B 385 " pdb=" N ALA B 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU D 385 " pdb=" N ALA D 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU I 385 " pdb=" N ALA I 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU L 385 " pdb=" N ALA L 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU N 385 " pdb=" N ALA N 387 " model vdw 2.151 2.520 ... (remaining 400399 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.910 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: 0.040 Extract box with map and model: 31.160 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 125.780 Find NCS groups from input model: 3.590 Set up NCS constraints: 0.440 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: 0.020 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.010 0.056 51012 Z= 0.638 Angle : 0.960 10.433 68994 Z= 0.529 Chirality : 0.052 0.207 7758 Planarity : 0.004 0.036 8928 Dihedral : 15.639 84.488 19566 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 17.33 % Favored : 82.37 % Rotamer: Outliers : 0.98 % Allowed : 7.52 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 0.60 % 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: -6.45 (0.07), residues: 6156 helix: -4.69 (0.05), residues: 2736 sheet: -3.48 (0.17), residues: 558 loop : -3.96 (0.09), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 474 HIS 0.006 0.002 HIS P 493 PHE 0.014 0.003 PHE N 490 TYR 0.013 0.002 TYR D 529 ARG 0.007 0.001 ARG H 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 831 time to evaluate : 6.045 Fit side-chains REVERT: A 474 TRP cc_start: 0.7414 (m100) cc_final: 0.7184 (m100) REVERT: A 480 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7785 (pt0) REVERT: A 503 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.8150 (t-90) REVERT: B 393 GLU cc_start: 0.7794 (tp30) cc_final: 0.7092 (tp30) REVERT: B 474 TRP cc_start: 0.7385 (m100) cc_final: 0.7140 (m100) REVERT: B 480 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: B 503 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8132 (t-90) REVERT: C 474 TRP cc_start: 0.7348 (m100) cc_final: 0.7035 (m100) REVERT: C 480 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: D 480 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: D 503 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8176 (t-90) REVERT: E 480 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: E 503 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8126 (t-90) REVERT: F 480 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: F 503 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8150 (t-90) REVERT: F 525 MET cc_start: 0.9111 (mtp) cc_final: 0.8872 (mtp) REVERT: G 480 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: H 393 GLU cc_start: 0.7769 (tp30) cc_final: 0.7216 (tp30) REVERT: H 474 TRP cc_start: 0.7396 (m100) cc_final: 0.6711 (m100) REVERT: H 480 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: H 503 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8210 (t-90) REVERT: I 474 TRP cc_start: 0.7419 (m100) cc_final: 0.6734 (m100) REVERT: I 480 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7807 (pt0) REVERT: I 503 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8172 (t-90) REVERT: J 480 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: J 503 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8151 (t-90) REVERT: K 393 GLU cc_start: 0.7768 (tp30) cc_final: 0.7212 (tp30) REVERT: K 474 TRP cc_start: 0.7399 (m100) cc_final: 0.6756 (m100) REVERT: K 480 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: K 503 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8211 (t-90) REVERT: L 474 TRP cc_start: 0.7425 (m100) cc_final: 0.6684 (m100) REVERT: L 480 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: L 503 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (t-90) REVERT: M 474 TRP cc_start: 0.7424 (m100) cc_final: 0.7188 (m100) REVERT: M 480 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: M 503 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (t-90) REVERT: N 393 GLU cc_start: 0.7788 (tp30) cc_final: 0.7079 (tp30) REVERT: N 474 TRP cc_start: 0.7388 (m100) cc_final: 0.7136 (m100) REVERT: N 480 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: N 503 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8136 (t-90) REVERT: O 474 TRP cc_start: 0.7348 (m100) cc_final: 0.7038 (m100) REVERT: O 480 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: P 503 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8134 (t-90) REVERT: Q 474 TRP cc_start: 0.7423 (m100) cc_final: 0.7209 (m100) REVERT: Q 480 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: Q 503 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8133 (t-90) REVERT: R 480 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: R 503 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8183 (t-90) REVERT: R 525 MET cc_start: 0.9061 (mtp) cc_final: 0.8838 (mtp) outliers start: 54 outliers final: 0 residues processed: 850 average time/residue: 0.5922 time to fit residues: 833.4257 Evaluate side-chains 563 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 531 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain F residue 480 GLU Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain I residue 480 GLU Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain J residue 480 GLU Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 480 GLU Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain L residue 480 GLU Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain M residue 480 GLU Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain N residue 480 GLU Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain O residue 480 GLU Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain Q residue 480 GLU Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain R residue 503 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 516 optimal weight: 0.9990 chunk 463 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 479 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 357 optimal weight: 0.9980 chunk 555 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS A 561 ASN B 465 HIS B 561 ASN C 465 HIS C 500 HIS C 561 ASN D 465 HIS D 561 ASN E 465 HIS E 561 ASN F 465 HIS F 561 ASN G 465 HIS G 561 ASN G 600 ASN H 465 HIS H 561 ASN I 465 HIS I 561 ASN J 465 HIS J 561 ASN J 600 ASN K 465 HIS K 561 ASN L 465 HIS L 561 ASN M 465 HIS M 561 ASN N 465 HIS N 561 ASN O 465 HIS O 561 ASN P 465 HIS P 561 ASN Q 465 HIS Q 561 ASN R 465 HIS R 561 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 51012 Z= 0.189 Angle : 0.708 11.925 68994 Z= 0.355 Chirality : 0.046 0.214 7758 Planarity : 0.004 0.027 8928 Dihedral : 7.399 44.745 6993 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.56 % Favored : 89.15 % Rotamer: Outliers : 2.27 % Allowed : 12.60 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.26 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.09), residues: 6156 helix: -2.99 (0.08), residues: 2862 sheet: -2.78 (0.17), residues: 468 loop : -3.40 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 499 HIS 0.002 0.001 HIS C 503 PHE 0.010 0.001 PHE R 610 TYR 0.013 0.001 TYR F 460 ARG 0.003 0.000 ARG P 544 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 696 time to evaluate : 5.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.7755 (m-80) cc_final: 0.7436 (m-80) REVERT: B 393 GLU cc_start: 0.7804 (tp30) cc_final: 0.7172 (tp30) REVERT: B 473 PHE cc_start: 0.7787 (m-80) cc_final: 0.7276 (m-80) REVERT: C 473 PHE cc_start: 0.7747 (m-80) cc_final: 0.7056 (m-80) REVERT: C 480 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7427 (tm-30) REVERT: C 507 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6638 (mt-10) REVERT: D 473 PHE cc_start: 0.7804 (m-80) cc_final: 0.7470 (m-80) REVERT: E 473 PHE cc_start: 0.7880 (m-80) cc_final: 0.7678 (m-80) REVERT: E 480 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 473 PHE cc_start: 0.7782 (m-80) cc_final: 0.7205 (m-80) REVERT: F 480 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7421 (tm-30) REVERT: F 503 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7813 (t-90) REVERT: G 474 TRP cc_start: 0.6795 (m100) cc_final: 0.6493 (m100) REVERT: G 586 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9217 (mp) REVERT: H 393 GLU cc_start: 0.7789 (tp30) cc_final: 0.7379 (tp30) REVERT: H 473 PHE cc_start: 0.7865 (m-80) cc_final: 0.7431 (m-80) REVERT: I 473 PHE cc_start: 0.7759 (m-80) cc_final: 0.7243 (m-80) REVERT: I 474 TRP cc_start: 0.6878 (m100) cc_final: 0.6335 (m100) REVERT: J 473 PHE cc_start: 0.7903 (m-80) cc_final: 0.7332 (m-80) REVERT: K 393 GLU cc_start: 0.7771 (tp30) cc_final: 0.7367 (tp30) REVERT: K 473 PHE cc_start: 0.7877 (m-80) cc_final: 0.7439 (m-80) REVERT: L 473 PHE cc_start: 0.7771 (m-80) cc_final: 0.7251 (m-80) REVERT: L 474 TRP cc_start: 0.6847 (m100) cc_final: 0.6311 (m100) REVERT: M 473 PHE cc_start: 0.7759 (m-80) cc_final: 0.7443 (m-80) REVERT: N 393 GLU cc_start: 0.7787 (tp30) cc_final: 0.7158 (tp30) REVERT: N 473 PHE cc_start: 0.7772 (m-80) cc_final: 0.7259 (m-80) REVERT: O 473 PHE cc_start: 0.7762 (m-80) cc_final: 0.7053 (m-80) REVERT: O 480 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7420 (tm-30) REVERT: O 507 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6645 (mt-10) REVERT: P 473 PHE cc_start: 0.7841 (m-80) cc_final: 0.7634 (m-80) REVERT: Q 480 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7452 (tm-30) REVERT: R 473 PHE cc_start: 0.7762 (m-80) cc_final: 0.7304 (m-80) REVERT: R 480 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7774 (pt0) outliers start: 125 outliers final: 77 residues processed: 796 average time/residue: 0.5220 time to fit residues: 721.8370 Evaluate side-chains 591 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 512 time to evaluate : 6.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 586 ILE Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 666 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 308 optimal weight: 0.3980 chunk 172 optimal weight: 0.3980 chunk 462 optimal weight: 2.9990 chunk 378 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 556 optimal weight: 7.9990 chunk 601 optimal weight: 1.9990 chunk 495 optimal weight: 1.9990 chunk 552 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 446 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 452 GLN G 452 GLN I 500 HIS J 500 HIS L 500 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 51012 Z= 0.206 Angle : 0.653 11.207 68994 Z= 0.327 Chirality : 0.046 0.185 7758 Planarity : 0.003 0.043 8928 Dihedral : 6.315 40.077 6922 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.75 % Favored : 88.95 % Rotamer: Outliers : 2.83 % Allowed : 15.23 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.09), residues: 6156 helix: -2.33 (0.09), residues: 2880 sheet: -2.48 (0.17), residues: 486 loop : -3.11 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 474 HIS 0.003 0.001 HIS L 500 PHE 0.009 0.001 PHE G 473 TYR 0.009 0.001 TYR F 460 ARG 0.003 0.000 ARG H 544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 685 time to evaluate : 5.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.7795 (m-80) cc_final: 0.7466 (m-80) REVERT: A 507 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 693 GLN cc_start: 0.8264 (mp10) cc_final: 0.8037 (pm20) REVERT: B 393 GLU cc_start: 0.7727 (tp30) cc_final: 0.7166 (tp30) REVERT: B 473 PHE cc_start: 0.7696 (m-80) cc_final: 0.7164 (m-80) REVERT: C 473 PHE cc_start: 0.7854 (m-80) cc_final: 0.6978 (m-80) REVERT: D 473 PHE cc_start: 0.7844 (m-80) cc_final: 0.7564 (m-80) REVERT: D 693 GLN cc_start: 0.8225 (mp10) cc_final: 0.8011 (pm20) REVERT: F 473 PHE cc_start: 0.7735 (m-80) cc_final: 0.7128 (m-80) REVERT: F 480 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7669 (pt0) REVERT: H 393 GLU cc_start: 0.7698 (tp30) cc_final: 0.7258 (tp30) REVERT: H 473 PHE cc_start: 0.7706 (m-80) cc_final: 0.7268 (m-80) REVERT: H 639 GLU cc_start: 0.7949 (tp30) cc_final: 0.7656 (tp30) REVERT: I 473 PHE cc_start: 0.7780 (m-80) cc_final: 0.7279 (m-80) REVERT: I 639 GLU cc_start: 0.7948 (tp30) cc_final: 0.7714 (tp30) REVERT: J 473 PHE cc_start: 0.7937 (m-80) cc_final: 0.7329 (m-80) REVERT: K 393 GLU cc_start: 0.7727 (tp30) cc_final: 0.7252 (tp30) REVERT: K 473 PHE cc_start: 0.7737 (m-80) cc_final: 0.7297 (m-80) REVERT: K 639 GLU cc_start: 0.7957 (tp30) cc_final: 0.7662 (tp30) REVERT: L 473 PHE cc_start: 0.7780 (m-80) cc_final: 0.7283 (m-80) REVERT: L 639 GLU cc_start: 0.7968 (tp30) cc_final: 0.7735 (tp30) REVERT: M 473 PHE cc_start: 0.7807 (m-80) cc_final: 0.7474 (m-80) REVERT: M 507 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6925 (mt-10) REVERT: M 693 GLN cc_start: 0.8257 (mp10) cc_final: 0.8030 (pm20) REVERT: N 393 GLU cc_start: 0.7702 (tp30) cc_final: 0.7138 (tp30) REVERT: N 473 PHE cc_start: 0.7687 (m-80) cc_final: 0.7162 (m-80) REVERT: O 473 PHE cc_start: 0.7866 (m-80) cc_final: 0.6972 (m-80) REVERT: P 473 PHE cc_start: 0.7909 (m-80) cc_final: 0.7685 (m-80) REVERT: P 480 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: P 693 GLN cc_start: 0.8168 (mp10) cc_final: 0.7966 (pm20) REVERT: Q 480 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7354 (tm-30) REVERT: R 473 PHE cc_start: 0.7681 (m-80) cc_final: 0.7070 (m-80) REVERT: R 480 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7734 (pt0) REVERT: R 693 GLN cc_start: 0.8200 (mp10) cc_final: 0.7986 (pm20) outliers start: 156 outliers final: 112 residues processed: 811 average time/residue: 0.5516 time to fit residues: 772.6407 Evaluate side-chains 640 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 527 time to evaluate : 6.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 503 HIS Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 525 MET Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 503 HIS Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 666 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 288 optimal weight: 0.0870 chunk 61 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 558 optimal weight: 0.8980 chunk 591 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 529 optimal weight: 0.7980 chunk 159 optimal weight: 0.0970 overall best weight: 0.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS B 452 GLN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 HIS G 452 GLN H 500 HIS I 452 GLN J 452 GLN K 500 HIS L 452 GLN M 500 HIS O 500 HIS P 500 HIS Q 500 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 51012 Z= 0.187 Angle : 0.649 11.339 68994 Z= 0.323 Chirality : 0.045 0.178 7758 Planarity : 0.003 0.049 8928 Dihedral : 5.904 37.342 6916 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.36 % Favored : 89.34 % Rotamer: Outliers : 3.50 % Allowed : 15.20 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.10), residues: 6156 helix: -1.97 (0.09), residues: 2934 sheet: -2.35 (0.18), residues: 486 loop : -3.05 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 474 HIS 0.002 0.001 HIS I 465 PHE 0.007 0.001 PHE G 473 TYR 0.026 0.001 TYR E 460 ARG 0.008 0.000 ARG J 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 637 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.7468 (m-80) cc_final: 0.7076 (m-80) REVERT: B 393 GLU cc_start: 0.7695 (tp30) cc_final: 0.7250 (tp30) REVERT: B 473 PHE cc_start: 0.7742 (m-80) cc_final: 0.7309 (m-80) REVERT: C 473 PHE cc_start: 0.7858 (m-80) cc_final: 0.6990 (m-80) REVERT: C 480 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7301 (tm-30) REVERT: D 473 PHE cc_start: 0.7813 (m-80) cc_final: 0.7362 (m-80) REVERT: F 473 PHE cc_start: 0.7818 (m-80) cc_final: 0.7223 (m-80) REVERT: F 480 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7366 (tm-30) REVERT: H 393 GLU cc_start: 0.7646 (tp30) cc_final: 0.7331 (tp30) REVERT: H 473 PHE cc_start: 0.7814 (m-80) cc_final: 0.7460 (m-10) REVERT: H 639 GLU cc_start: 0.8002 (tp30) cc_final: 0.7767 (tp30) REVERT: I 473 PHE cc_start: 0.7802 (m-80) cc_final: 0.7269 (m-80) REVERT: J 473 PHE cc_start: 0.7604 (m-80) cc_final: 0.7070 (m-80) REVERT: K 393 GLU cc_start: 0.7623 (tp30) cc_final: 0.7331 (tp30) REVERT: K 473 PHE cc_start: 0.7802 (m-80) cc_final: 0.7420 (m-80) REVERT: K 639 GLU cc_start: 0.8000 (tp30) cc_final: 0.7773 (tp30) REVERT: L 473 PHE cc_start: 0.7811 (m-80) cc_final: 0.7274 (m-80) REVERT: M 473 PHE cc_start: 0.7491 (m-80) cc_final: 0.7095 (m-80) REVERT: M 474 TRP cc_start: 0.6790 (m100) cc_final: 0.6585 (m100) REVERT: N 393 GLU cc_start: 0.7683 (tp30) cc_final: 0.7233 (tp30) REVERT: N 473 PHE cc_start: 0.7729 (m-80) cc_final: 0.7298 (m-80) REVERT: O 473 PHE cc_start: 0.7857 (m-80) cc_final: 0.6961 (m-80) REVERT: O 480 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7301 (tm-30) REVERT: P 480 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7374 (pt0) REVERT: R 473 PHE cc_start: 0.7825 (m-80) cc_final: 0.7407 (m-80) REVERT: R 480 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7696 (pt0) outliers start: 193 outliers final: 123 residues processed: 796 average time/residue: 0.5446 time to fit residues: 749.0167 Evaluate side-chains 653 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 529 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 540 VAL Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 540 VAL Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 666 ASP Chi-restraints excluded: chain R residue 690 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 492 optimal weight: 3.9990 chunk 335 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 440 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 504 optimal weight: 5.9990 chunk 408 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 530 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS C 465 HIS D 452 GLN D 465 HIS E 465 HIS F 465 HIS G 465 HIS H 465 HIS ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 465 HIS ** J 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 HIS ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 465 HIS ** M 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 HIS Q 465 HIS R 465 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 51012 Z= 0.255 Angle : 0.684 10.941 68994 Z= 0.338 Chirality : 0.047 0.239 7758 Planarity : 0.003 0.055 8928 Dihedral : 5.874 36.869 6912 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.72 % Favored : 88.99 % Rotamer: Outliers : 3.99 % Allowed : 16.32 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.10), residues: 6156 helix: -1.68 (0.09), residues: 2952 sheet: -2.14 (0.19), residues: 486 loop : -3.07 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 474 HIS 0.004 0.001 HIS E 465 PHE 0.009 0.001 PHE H 473 TYR 0.018 0.001 TYR E 460 ARG 0.012 0.000 ARG D 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 580 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.7732 (m-80) cc_final: 0.7363 (m-80) REVERT: B 393 GLU cc_start: 0.7766 (tp30) cc_final: 0.7163 (tp30) REVERT: B 473 PHE cc_start: 0.7837 (m-80) cc_final: 0.7289 (m-80) REVERT: C 473 PHE cc_start: 0.7927 (m-80) cc_final: 0.7102 (m-80) REVERT: C 480 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7301 (tm-30) REVERT: F 473 PHE cc_start: 0.7856 (m-80) cc_final: 0.7393 (m-80) REVERT: F 480 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7285 (tm-30) REVERT: H 393 GLU cc_start: 0.7743 (tp30) cc_final: 0.7281 (tp30) REVERT: H 473 PHE cc_start: 0.7696 (m-80) cc_final: 0.7311 (m-80) REVERT: H 639 GLU cc_start: 0.8064 (tp30) cc_final: 0.7832 (tp30) REVERT: I 473 PHE cc_start: 0.7943 (m-80) cc_final: 0.7396 (m-80) REVERT: I 480 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7321 (tm-30) REVERT: J 473 PHE cc_start: 0.7743 (m-80) cc_final: 0.7231 (m-80) REVERT: K 393 GLU cc_start: 0.7738 (tp30) cc_final: 0.7287 (tp30) REVERT: K 473 PHE cc_start: 0.7887 (m-80) cc_final: 0.7486 (m-10) REVERT: K 639 GLU cc_start: 0.8062 (tp30) cc_final: 0.7838 (tp30) REVERT: L 473 PHE cc_start: 0.7947 (m-80) cc_final: 0.7408 (m-80) REVERT: L 480 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7321 (tm-30) REVERT: M 473 PHE cc_start: 0.7716 (m-80) cc_final: 0.7392 (m-80) REVERT: N 393 GLU cc_start: 0.7750 (tp30) cc_final: 0.7149 (tp30) REVERT: N 473 PHE cc_start: 0.7844 (m-80) cc_final: 0.7328 (m-80) REVERT: O 386 GLU cc_start: 0.5018 (tp30) cc_final: 0.4781 (tp30) REVERT: O 473 PHE cc_start: 0.7919 (m-80) cc_final: 0.7093 (m-80) REVERT: O 480 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7307 (tm-30) REVERT: P 473 PHE cc_start: 0.7918 (m-80) cc_final: 0.7582 (m-80) REVERT: P 480 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: Q 480 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7705 (pt0) REVERT: R 473 PHE cc_start: 0.7842 (m-80) cc_final: 0.7363 (m-80) REVERT: R 480 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7624 (pt0) outliers start: 220 outliers final: 155 residues processed: 746 average time/residue: 0.5875 time to fit residues: 768.6818 Evaluate side-chains 655 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 499 time to evaluate : 5.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain H residue 690 LEU Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain K residue 690 LEU Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 559 ILE Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Chi-restraints excluded: chain R residue 666 ASP Chi-restraints excluded: chain R residue 690 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 6.9990 chunk 532 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 592 optimal weight: 0.9980 chunk 491 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 310 optimal weight: 0.7980 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 465 HIS B 452 GLN D 452 GLN G 452 GLN G 500 HIS I 452 GLN J 452 GLN L 452 GLN M 465 HIS O 465 HIS P 465 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 51012 Z= 0.181 Angle : 0.641 11.262 68994 Z= 0.318 Chirality : 0.046 0.248 7758 Planarity : 0.003 0.032 8928 Dihedral : 5.580 35.663 6912 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.93 % Favored : 89.78 % Rotamer: Outliers : 3.69 % Allowed : 16.99 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.10), residues: 6156 helix: -1.21 (0.09), residues: 2916 sheet: -1.13 (0.22), residues: 486 loop : -3.25 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 474 HIS 0.004 0.001 HIS M 465 PHE 0.011 0.001 PHE M 473 TYR 0.012 0.001 TYR E 460 ARG 0.009 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 598 time to evaluate : 6.222 Fit side-chains REVERT: A 507 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6801 (mt-10) REVERT: B 393 GLU cc_start: 0.7758 (tp30) cc_final: 0.7162 (tp30) REVERT: B 473 PHE cc_start: 0.7939 (m-80) cc_final: 0.7428 (m-80) REVERT: B 562 MET cc_start: 0.8673 (tpt) cc_final: 0.8316 (tpt) REVERT: C 473 PHE cc_start: 0.7872 (m-80) cc_final: 0.7077 (m-80) REVERT: C 480 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7284 (tm-30) REVERT: E 417 ASN cc_start: 0.8069 (m-40) cc_final: 0.7768 (m-40) REVERT: F 473 PHE cc_start: 0.7845 (m-80) cc_final: 0.7422 (m-80) REVERT: F 480 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7273 (tm-30) REVERT: H 393 GLU cc_start: 0.7643 (tp30) cc_final: 0.7173 (tp30) REVERT: I 473 PHE cc_start: 0.7937 (m-80) cc_final: 0.7424 (m-80) REVERT: J 473 PHE cc_start: 0.7771 (m-80) cc_final: 0.7374 (m-80) REVERT: J 480 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7307 (tm-30) REVERT: K 393 GLU cc_start: 0.7629 (tp30) cc_final: 0.7171 (tp30) REVERT: K 473 PHE cc_start: 0.7801 (m-80) cc_final: 0.7443 (m-10) REVERT: L 473 PHE cc_start: 0.7945 (m-80) cc_final: 0.7435 (m-80) REVERT: M 473 PHE cc_start: 0.7271 (m-80) cc_final: 0.7069 (m-10) REVERT: M 507 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6820 (mt-10) REVERT: N 393 GLU cc_start: 0.7742 (tp30) cc_final: 0.7149 (tp30) REVERT: N 473 PHE cc_start: 0.7922 (m-80) cc_final: 0.7395 (m-80) REVERT: N 562 MET cc_start: 0.8656 (tpt) cc_final: 0.8315 (tpt) REVERT: O 473 PHE cc_start: 0.7863 (m-80) cc_final: 0.7032 (m-80) REVERT: O 480 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7288 (tm-30) REVERT: P 473 PHE cc_start: 0.7774 (m-80) cc_final: 0.7439 (m-80) REVERT: P 480 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: Q 417 ASN cc_start: 0.8055 (m-40) cc_final: 0.7763 (m-40) REVERT: Q 480 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7715 (pt0) REVERT: R 473 PHE cc_start: 0.7796 (m-80) cc_final: 0.7374 (m-80) REVERT: R 480 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7593 (pt0) outliers start: 203 outliers final: 138 residues processed: 751 average time/residue: 0.5397 time to fit residues: 701.9832 Evaluate side-chains 633 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 494 time to evaluate : 6.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain H residue 690 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain K residue 690 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 490 PHE Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain N residue 610 PHE Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Chi-restraints excluded: chain R residue 666 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 337 optimal weight: 0.8980 chunk 432 optimal weight: 0.0060 chunk 335 optimal weight: 7.9990 chunk 498 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 chunk 589 optimal weight: 9.9990 chunk 369 optimal weight: 7.9990 chunk 359 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 465 HIS M 381 GLN ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51012 Z= 0.216 Angle : 0.661 10.878 68994 Z= 0.328 Chirality : 0.046 0.252 7758 Planarity : 0.003 0.060 8928 Dihedral : 5.597 35.666 6912 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.38 % Favored : 89.33 % Rotamer: Outliers : 3.76 % Allowed : 17.72 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.55 % 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: -2.86 (0.10), residues: 6156 helix: -0.95 (0.09), residues: 2916 sheet: -0.97 (0.23), residues: 486 loop : -3.19 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 474 HIS 0.003 0.001 HIS O 503 PHE 0.018 0.001 PHE H 473 TYR 0.016 0.001 TYR Q 460 ARG 0.018 0.000 ARG P 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 541 time to evaluate : 5.840 Fit side-chains revert: symmetry clash REVERT: A 417 ASN cc_start: 0.7844 (m-40) cc_final: 0.7501 (m-40) REVERT: B 417 ASN cc_start: 0.8140 (m-40) cc_final: 0.7894 (m-40) REVERT: B 473 PHE cc_start: 0.7998 (m-80) cc_final: 0.7434 (m-80) REVERT: C 473 PHE cc_start: 0.7593 (m-80) cc_final: 0.7070 (m-80) REVERT: C 480 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7268 (tm-30) REVERT: E 480 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7426 (tm-30) REVERT: F 480 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7277 (tm-30) REVERT: H 393 GLU cc_start: 0.7620 (tp30) cc_final: 0.7149 (tp30) REVERT: H 480 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7302 (tm-30) REVERT: I 473 PHE cc_start: 0.7712 (m-80) cc_final: 0.7280 (m-80) REVERT: I 545 MET cc_start: 0.8374 (ttp) cc_final: 0.8173 (ttm) REVERT: J 473 PHE cc_start: 0.7781 (m-80) cc_final: 0.7376 (m-80) REVERT: J 480 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7305 (tm-30) REVERT: K 393 GLU cc_start: 0.7621 (tp30) cc_final: 0.7146 (tp30) REVERT: K 447 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7058 (ptm-80) REVERT: K 473 PHE cc_start: 0.7838 (m-80) cc_final: 0.7545 (m-80) REVERT: L 473 PHE cc_start: 0.7714 (m-80) cc_final: 0.7286 (m-80) REVERT: L 480 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7366 (tm-30) REVERT: L 545 MET cc_start: 0.8380 (ttp) cc_final: 0.8146 (ttm) REVERT: M 417 ASN cc_start: 0.7839 (m-40) cc_final: 0.7503 (m-40) REVERT: M 473 PHE cc_start: 0.7543 (m-80) cc_final: 0.7309 (m-80) REVERT: N 417 ASN cc_start: 0.8141 (m-40) cc_final: 0.7887 (m-40) REVERT: N 473 PHE cc_start: 0.7992 (m-80) cc_final: 0.7420 (m-80) REVERT: O 473 PHE cc_start: 0.7575 (m-80) cc_final: 0.7068 (m-80) REVERT: O 480 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7271 (tm-30) REVERT: P 480 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: Q 491 PHE cc_start: 0.7292 (m-80) cc_final: 0.7037 (m-80) REVERT: R 480 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7598 (pt0) outliers start: 207 outliers final: 158 residues processed: 692 average time/residue: 0.5284 time to fit residues: 635.9401 Evaluate side-chains 625 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 465 time to evaluate : 5.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain H residue 690 LEU Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 447 ARG Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain K residue 690 LEU Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 490 PHE Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain N residue 610 PHE Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 559 ILE Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 540 VAL Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Chi-restraints excluded: chain R residue 666 ASP Chi-restraints excluded: chain R residue 690 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 chunk 352 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 375 optimal weight: 5.9990 chunk 401 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 463 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 51012 Z= 0.257 Angle : 0.680 10.908 68994 Z= 0.336 Chirality : 0.046 0.233 7758 Planarity : 0.003 0.069 8928 Dihedral : 5.644 35.144 6912 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.12 % Favored : 89.59 % Rotamer: Outliers : 3.85 % Allowed : 18.14 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.31 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 6156 helix: -0.93 (0.09), residues: 2970 sheet: -0.90 (0.23), residues: 486 loop : -3.10 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 474 HIS 0.005 0.001 HIS C 503 PHE 0.009 0.001 PHE F 367 TYR 0.006 0.001 TYR E 460 ARG 0.017 0.000 ARG Q 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 506 time to evaluate : 5.998 Fit side-chains revert: symmetry clash REVERT: A 386 GLU cc_start: 0.4814 (tp30) cc_final: 0.4508 (tp30) REVERT: A 417 ASN cc_start: 0.7916 (m-40) cc_final: 0.7591 (m-40) REVERT: C 473 PHE cc_start: 0.7678 (m-80) cc_final: 0.7009 (m-80) REVERT: C 480 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7289 (tm-30) REVERT: E 365 GLU cc_start: 0.8344 (tp30) cc_final: 0.8063 (tp30) REVERT: E 417 ASN cc_start: 0.8096 (m-40) cc_final: 0.7840 (m-40) REVERT: E 473 PHE cc_start: 0.8001 (m-80) cc_final: 0.7326 (m-80) REVERT: E 480 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7384 (tm-30) REVERT: F 480 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7265 (tm-30) REVERT: H 480 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7454 (tm-30) REVERT: I 473 PHE cc_start: 0.7862 (m-80) cc_final: 0.7462 (m-80) REVERT: I 480 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7430 (tm-30) REVERT: J 473 PHE cc_start: 0.7896 (m-80) cc_final: 0.7480 (m-80) REVERT: J 480 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7586 (tm-30) REVERT: K 473 PHE cc_start: 0.7847 (m-80) cc_final: 0.7576 (m-80) REVERT: K 480 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7313 (tm-30) REVERT: L 473 PHE cc_start: 0.7872 (m-80) cc_final: 0.7470 (m-80) REVERT: L 480 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7436 (tm-30) REVERT: M 386 GLU cc_start: 0.4839 (tp30) cc_final: 0.4525 (tp30) REVERT: M 417 ASN cc_start: 0.7911 (m-40) cc_final: 0.7590 (m-40) REVERT: M 447 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7425 (mmm160) REVERT: M 473 PHE cc_start: 0.7796 (m-80) cc_final: 0.7584 (m-80) REVERT: N 365 GLU cc_start: 0.8385 (tp30) cc_final: 0.8132 (tp30) REVERT: O 473 PHE cc_start: 0.7751 (m-80) cc_final: 0.7011 (m-80) REVERT: O 480 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7290 (tm-30) REVERT: P 480 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7205 (pt0) REVERT: Q 365 GLU cc_start: 0.8351 (tp30) cc_final: 0.8059 (tp30) REVERT: Q 417 ASN cc_start: 0.8084 (m-40) cc_final: 0.7818 (m-40) REVERT: Q 473 PHE cc_start: 0.7927 (m-80) cc_final: 0.7286 (m-80) REVERT: Q 480 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7370 (tm-30) REVERT: R 480 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7610 (pt0) outliers start: 212 outliers final: 167 residues processed: 663 average time/residue: 0.5360 time to fit residues: 617.7190 Evaluate side-chains 658 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 490 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 559 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain H residue 690 LEU Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 447 ARG Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain K residue 690 LEU Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 490 PHE Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 571 GLU Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain O residue 690 LEU Chi-restraints excluded: chain P residue 390 LEU Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 559 ILE Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 498 THR Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Chi-restraints excluded: chain R residue 666 ASP Chi-restraints excluded: chain R residue 690 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 0.9980 chunk 565 optimal weight: 0.9990 chunk 515 optimal weight: 0.0670 chunk 549 optimal weight: 0.9980 chunk 564 optimal weight: 0.8980 chunk 330 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 431 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 496 optimal weight: 1.9990 chunk 519 optimal weight: 8.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 ASN ** G 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 51012 Z= 0.170 Angle : 0.663 12.501 68994 Z= 0.326 Chirality : 0.044 0.239 7758 Planarity : 0.003 0.047 8928 Dihedral : 5.380 33.869 6912 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.86 % Favored : 89.85 % Rotamer: Outliers : 3.05 % Allowed : 19.32 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.34 % 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: -2.45 (0.10), residues: 6156 helix: -0.37 (0.10), residues: 2844 sheet: -0.69 (0.23), residues: 486 loop : -3.24 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 474 HIS 0.005 0.001 HIS K 503 PHE 0.013 0.001 PHE G 473 TYR 0.010 0.001 TYR D 460 ARG 0.016 0.000 ARG P 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 591 time to evaluate : 6.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASN cc_start: 0.7812 (m-40) cc_final: 0.7491 (m-40) REVERT: A 507 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6869 (mt-10) REVERT: B 562 MET cc_start: 0.8646 (tpt) cc_final: 0.8326 (tpt) REVERT: C 473 PHE cc_start: 0.7608 (m-80) cc_final: 0.7049 (m-80) REVERT: C 480 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7257 (tm-30) REVERT: E 417 ASN cc_start: 0.8070 (m-40) cc_final: 0.7817 (m-40) REVERT: E 480 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7379 (tm-30) REVERT: F 473 PHE cc_start: 0.7893 (m-80) cc_final: 0.7401 (m-80) REVERT: F 480 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7305 (tm-30) REVERT: H 466 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5476 (pp) REVERT: H 473 PHE cc_start: 0.8053 (m-80) cc_final: 0.7804 (m-80) REVERT: H 480 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7716 (pt0) REVERT: H 562 MET cc_start: 0.8477 (tpt) cc_final: 0.8095 (tpt) REVERT: I 390 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5949 (mm) REVERT: I 473 PHE cc_start: 0.7858 (m-80) cc_final: 0.7475 (m-80) REVERT: I 480 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7535 (tm-30) REVERT: J 473 PHE cc_start: 0.7846 (m-80) cc_final: 0.7492 (m-80) REVERT: J 480 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7309 (tm-30) REVERT: K 473 PHE cc_start: 0.7731 (m-80) cc_final: 0.7455 (m-80) REVERT: K 480 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7351 (tm-30) REVERT: L 473 PHE cc_start: 0.7868 (m-80) cc_final: 0.7483 (m-80) REVERT: L 480 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7538 (tm-30) REVERT: M 417 ASN cc_start: 0.7801 (m-40) cc_final: 0.7486 (m-40) REVERT: M 447 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7535 (mmm160) REVERT: M 507 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6869 (mt-10) REVERT: O 390 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5907 (mm) REVERT: O 473 PHE cc_start: 0.7379 (m-80) cc_final: 0.6990 (m-80) REVERT: O 480 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7291 (tm-30) REVERT: P 480 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: R 390 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5885 (mm) REVERT: R 473 PHE cc_start: 0.7796 (m-80) cc_final: 0.7302 (m-80) REVERT: R 480 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7627 (pt0) outliers start: 168 outliers final: 137 residues processed: 711 average time/residue: 0.5553 time to fit residues: 682.1043 Evaluate side-chains 666 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 524 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 503 HIS Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 610 PHE Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain H residue 690 LEU Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 447 ARG Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 610 PHE Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain K residue 690 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 610 PHE Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 447 ARG Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Chi-restraints excluded: chain R residue 666 ASP Chi-restraints excluded: chain R residue 690 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 0.0980 chunk 360 optimal weight: 5.9990 chunk 581 optimal weight: 0.0470 chunk 354 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 404 optimal weight: 2.9990 chunk 609 optimal weight: 1.9990 chunk 561 optimal weight: 5.9990 chunk 485 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 375 optimal weight: 7.9990 overall best weight: 1.8284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 51012 Z= 0.271 Angle : 0.729 15.724 68994 Z= 0.350 Chirality : 0.047 0.237 7758 Planarity : 0.003 0.066 8928 Dihedral : 5.574 35.658 6912 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.23 % Favored : 89.47 % Rotamer: Outliers : 2.85 % Allowed : 19.95 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.45 % 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: -2.49 (0.10), residues: 6156 helix: -0.52 (0.10), residues: 2862 sheet: -0.61 (0.24), residues: 486 loop : -3.16 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 474 HIS 0.005 0.001 HIS H 503 PHE 0.016 0.001 PHE M 473 TYR 0.009 0.001 TYR B 460 ARG 0.017 0.000 ARG E 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 521 time to evaluate : 6.081 Fit side-chains revert: symmetry clash REVERT: A 417 ASN cc_start: 0.7867 (m-40) cc_final: 0.7575 (m-40) REVERT: C 473 PHE cc_start: 0.7585 (m-80) cc_final: 0.7100 (m-80) REVERT: C 480 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7236 (tm-30) REVERT: E 480 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7351 (tm-30) REVERT: F 480 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7261 (tm-30) REVERT: H 466 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5504 (pp) REVERT: H 480 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7696 (pt0) REVERT: H 562 MET cc_start: 0.8653 (tpt) cc_final: 0.8225 (tpt) REVERT: I 473 PHE cc_start: 0.7898 (m-80) cc_final: 0.7499 (m-80) REVERT: I 480 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7417 (tm-30) REVERT: J 365 GLU cc_start: 0.8277 (tp30) cc_final: 0.8019 (tp30) REVERT: J 473 PHE cc_start: 0.7891 (m-80) cc_final: 0.7527 (m-80) REVERT: J 480 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7578 (tm-30) REVERT: K 473 PHE cc_start: 0.7880 (m-80) cc_final: 0.7597 (m-80) REVERT: K 480 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7297 (tm-30) REVERT: L 473 PHE cc_start: 0.7885 (m-80) cc_final: 0.7497 (m-80) REVERT: L 480 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7423 (tm-30) REVERT: M 417 ASN cc_start: 0.7845 (m-40) cc_final: 0.7552 (m-40) REVERT: M 447 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7529 (mmm160) REVERT: M 480 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7263 (tm-30) REVERT: N 365 GLU cc_start: 0.8285 (tp30) cc_final: 0.8084 (tp30) REVERT: O 473 PHE cc_start: 0.7599 (m-80) cc_final: 0.6958 (m-80) REVERT: O 480 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7293 (tm-30) REVERT: P 480 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: P 562 MET cc_start: 0.8655 (tpt) cc_final: 0.8298 (tpt) REVERT: R 480 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7625 (pt0) outliers start: 157 outliers final: 134 residues processed: 628 average time/residue: 0.5439 time to fit residues: 594.1331 Evaluate side-chains 642 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 506 time to evaluate : 5.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 666 ASP Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 666 ASP Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 ASP Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 610 PHE Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 666 ASP Chi-restraints excluded: chain H residue 690 LEU Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain I residue 666 ASP Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 666 ASP Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 447 ARG Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 610 PHE Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 666 ASP Chi-restraints excluded: chain K residue 690 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain L residue 666 ASP Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 666 ASP Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 666 ASP Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 666 ASP Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 666 ASP Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Chi-restraints excluded: chain R residue 666 ASP Chi-restraints excluded: chain R residue 690 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 1.9990 chunk 385 optimal weight: 9.9990 chunk 517 optimal weight: 0.0370 chunk 148 optimal weight: 8.9990 chunk 447 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 486 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 499 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 GLN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103798 restraints weight = 82698.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106403 restraints weight = 52567.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108166 restraints weight = 38408.860| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 51012 Z= 0.281 Angle : 0.733 14.904 68994 Z= 0.354 Chirality : 0.047 0.233 7758 Planarity : 0.003 0.060 8928 Dihedral : 5.597 34.067 6912 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.94 % Favored : 89.77 % Rotamer: Outliers : 3.01 % Allowed : 20.10 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.58 (0.10), residues: 6156 helix: -0.56 (0.10), residues: 2844 sheet: -0.60 (0.24), residues: 486 loop : -3.24 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 474 HIS 0.006 0.001 HIS Q 503 PHE 0.026 0.001 PHE H 473 TYR 0.014 0.001 TYR P 479 ARG 0.018 0.000 ARG E 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11973.85 seconds wall clock time: 215 minutes 36.77 seconds (12936.77 seconds total)